Cytogenetic features of rRNA genes across land plants: analysis of the Plant rDNA database.

PubMed

Garcia, Sònia; Kovařík, Ales; Leitch, Andrew R; Garnatje, Teresa

2017-03-01

The online resource http://www.plantrdnadatabase.com/ stores information on the number, chromosomal locations and structure of the 5S and 18S-5.8S-26S (35S) ribosomal DNAs (rDNA) in plants. This resource was exploited to study relationships between rDNA locus number, distribution, the occurrence of linked (L-type) and separated (S-type) 5S and 35S rDNA units, chromosome number, genome size and ploidy level. The analyses presented summarise current knowledge on rDNA locus numbers and distribution in plants. We analysed 2949 karyotypes, from 1791 species and 86 plant families, and performed ancestral character state reconstructions. The ancestral karyotype (2n = 16) has two terminal 35S sites and two interstitial 5S sites, while the median (2n = 24) presents four terminal 35S sites and three interstitial 5S sites. Whilst 86.57% of karyotypes show S-type organisation (ancestral condition), the L-type arrangement has arisen independently several times during plant evolution. A non-terminal position of 35S rDNA was found in about 25% of single-locus karyotypes, suggesting that terminal locations are not essential for functionality and expression. Single-locus karyotypes are very common, even in polyploids. In this regard, polyploidy is followed by subsequent locus loss. This results in a decrease in locus number per monoploid genome, forming part of the diploidisation process returning polyploids to a diploid-like state over time. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Analysis of multilocus zygotic associations.

PubMed

Yang, Rong-Cai

2002-05-01

While nonrandom associations between zygotes at different loci (zygotic associations) frequently occur in Hardy-Weinberg disequilibrium populations, statistical analysis of such associations has received little attention. In this article, we describe the joint distributions of zygotes at multiple loci, which are completely characterized by heterozygosities at individual loci and various multilocus zygotic associations. These zygotic associations are defined in the same fashion as the usual multilocus linkage (gametic) disequilibria on the basis of gametic and allelic frequencies. The estimation and test procedures are described with details being given for three loci. The sampling properties of the estimates are examined through Monte Carlo simulation. The estimates of three-locus associations are not free of bias due to the presence of two-locus associations and vice versa. The power of detecting the zygotic associations is small unless different loci are strongly associated and/or sample sizes are large (>100). The analysis of zygotic associations not only offers an effective means of packaging numerous genic disequilibria required for a complete characterization of multilocus structure, but also provides opportunities for making inference about evolutionary and demographic processes through a comparative assessment of zygotic association vs. gametic disequilibrium for the same set of loci in nonequilibrium populations.

Natural variation for a hybrid incompatibility between two species of Mimulus.

PubMed

Sweigart, Andrea L; Mason, Amanda R; Willis, John H

2007-01-01

Understanding the process by which hybrid incompatibility alleles become established in natural populations remains a major challenge to evolutionary biology. Previously, we discovered a two-locus Dobzhansky-Muller incompatibility that causes severe hybrid male sterility between two inbred lines of the incompletely isolated wildflower species, Mimulus guttatus and M. nasutus. An interspecific cross between these two inbred lines revealed that the M. guttatus (IM62) allele at hybrid male sterility 1 (hms1) acts dominantly in combination with recessive M. nasutus (SF5) alleles at hybrid male sterility 2 (hms2) to cause nearly complete hybrid male sterility. In this report, we extend these genetic analyses to investigate intraspecific variation for the hms1-hms2 incompatibility in natural populations of M. nasutus and M. guttatus, performing a series of interspecific crosses between individuals collected from a variety of geographic locales. Our results suggest that hms2 incompatibility alleles are common and geographically widespread within M. nasutus, but absent or rare in M. guttatus. In contrast, the hms1 locus is polymorphic within M. guttatus and the incompatibility allele appears to be extremely geographically restricted. We found evidence for the presence of the hms1 incompatibility allele in only two M. guttatus populations that exist within a few kilometers of each other. The restricted distribution of the hms1 incompatibility allele might currently limit the potential for the hms1-hms2 incompatibility to act as a species barrier between sympatric populations of M. guttatus and M. nasutus. Extensive sampling within a single M. guttatus population revealed that the hms1 locus is polymorphic and that the incompatibility allele appears to segregate at intermediate frequency, a pattern that is consistent with either genetic drift or natural selection.

[The assessment of the level of coping style and health locus of control in patients with coronary heart disease and hypertension].

PubMed

Opuchlik, Katarzyna; Wrzesińska, Magdalena; Kocur, Józef

2009-01-01

The assessment of the level of coping style and health locus of control in patients with coronary heart disease and hypertension. The sample studied consisted of 112 patients (81 M, 31 F) at the age of 35-65 years. Two groups participated in the study; first with coronary heart disease and hypertension and second with hypertension without other diseases. The Coping Inventory for Stressful Situation and Multidimensional Health Locus of Control Scale were used in the study. Two groups of patients used the most frequent task-oriented coping style. The significant differences were seen between groups in the external health locus of control (t = 2.113; p < 0.05); patients with coronary heart disease and hypertension revealed the strongest conviction that their health depended on other people. Patients with coronary heart disease and hypertension choose the task-oriented coping style. Patients with hypertension declare for internal health locus of control. Patients with coronary heart disease and hypertension declare for external locus of control.

Quantitative trait locus mapping of human blood pressure to a genetic region at or near the lipoprotein lipase gene locus on chromosome 8p22.

PubMed Central

Wu, D A; Bu, X; Warden, C H; Shen, D D; Jeng, C Y; Sheu, W H; Fuh, M M; Katsuya, T; Dzau, V J; Reaven, G M; Lusis, A J; Rotter, J I; Chen, Y D

1996-01-01

Resistance to insulin-mediated glucose disposal is a common finding in patients with non-insulin-dependent diabetes mellitus (NIDDM), as well as in nondiabetic individuals with hypertension. In an effort to identify the generic loci responsible for variations in blood pressure in individuals at increased risk of insulin resistance, we studied the distribution of blood pressure in 48 Taiwanese families with NIDDM and conducted quantitative sib-pair linkage analysis with candidate loci for insulin resistance, lipid metabolism, and blood pressure control. We found no evidence for linkage of the angiotensin converting enzyme locus on chromosome 17, nor the angiotensinogen and renin loci on chromosome 1, with either systolic or diastolic blood pressures. In contrast, we obtained significant evidence for linkage or systolic blood pressure, but not diastolic blood pressure, to a genetic region at or near the lipoprotein lipase (LPL) locus on the short arm of chromosome 8 (P = 0.002, n = 125 sib-pairs, for the haplotype generated from two simple sequence repeat markers within the LPL gene). Further strengthening this linkage observation, two flanking marker loci for LPL locus, D8S261 (9 cM telomeric to LPL locus) and D8S282 (3 cM centromeric to LPL locus), also showed evidence for linkage with systolic blood pressure (P = 0.02 and 0.0002 for D8S261 and D8S282, respectively). Two additional centromeric markers (D8S133, 5 cM from LPL locus, and NEFL, 11 cM from LPL locus) yielded significant P values of 0.01 and 0.001, respectively. Allelic variation around the LPL gene locus accounted for as much as 52-73% of the total interindividual variation in systolic blood pressure levels in this data set. Thus, we have identified a genetic locus at or near the LPL gene locus which contributes to the variation of systolic blood pressure levels in nondiabetic family members at high risk for insulin resistance and NIDDM. PMID:8621801

Effect of Ethnomathematics Teaching Approach on Senior Secondary Students' Achievement and Retention in Locus

ERIC Educational Resources Information Center

Achor, Emmanuel E.; Imoko, Benjamin I.; Uloko, Emmanuel S.

2009-01-01

This study determined the effectiveness of ethnomathematics teaching approach, ETA on students' achievement and retention in Locus. The study was carried out in education zone B of Benue State of Nigeria using a sample size of 253 Senior Secondary 2 (SS 2) students. It was a non equivalent quasi-experimental study which was guided by two research…

Fixation probability in a two-locus intersexual selection model.

PubMed

Durand, Guillermo; Lessard, Sabin

2016-06-01

We study a two-locus model of intersexual selection in a finite haploid population reproducing according to a discrete-time Moran model with a trait locus expressed in males and a preference locus expressed in females. We show that the probability of ultimate fixation of a single mutant allele for a male ornament introduced at random at the trait locus given any initial frequency state at the preference locus is increased by weak intersexual selection and recombination, weak or strong. Moreover, this probability exceeds the initial frequency of the mutant allele even in the case of a costly male ornament if intersexual selection is not too weak. On the other hand, the probability of ultimate fixation of a single mutant allele for a female preference towards a male ornament introduced at random at the preference locus is increased by weak intersexual selection and weak recombination if the female preference is not costly, and is strong enough in the case of a costly male ornament. The analysis relies on an extension of the ancestral recombination-selection graph for samples of haplotypes to take into account events of intersexual selection, while the symbolic calculation of the fixation probabilities is made possible in a reasonable time by an optimizing algorithm. Copyright © 2016 Elsevier Inc. All rights reserved.

Fecundity of Paternal and Maternal Non-Parental Female Relatives of Homosexual and Heterosexual Men

PubMed Central

Camperio Ciani, Andrea; Pellizzari, Elena

2012-01-01

A variety of social, developmental, biological and genetic factors influence sexual orientation in males. Thus, several hypotheses have attempted to explain the sustenance of genetic factors that influence male homosexuality, despite decreased fecundity within the homosexuals. Kin selection, the existence of maternal effects and two forms of balancing selection, sexually antagonistic selection and overdominance, have been proposed as compensatory mechanisms for reduced homosexual fecundity. Here, we suggest that the empirical support for kin selection and maternal effects cannot account for the low universal frequency and stability of the distribution of homosexuals. To identify the responsible compensatory mechanism, we analyzed fecundity in 2,100 European female relatives, i.e., aunts and grandmothers, of either homosexual or heterosexual probands who were matched in terms of age, culture and sampling strategy. Female relatives were chosen to avoid the sampling bias of the fraternal birth order effect, which occurs when indirectly sampling mothers though their homosexual sons. We observed that the maternal aunts and grandmothers of homosexual probands were significantly more fecund compared with the maternal aunts and maternal grandmothers of the heterosexual probands. No difference in fecundity was observed in the paternal female lines (grandmothers or aunts) from either of the two proband groups. Moreover, due to the selective increase in maternal female fecundity, the total female fecundity was significantly higher in homosexual than heterosexual probands, thus compensating for the reduced fecundity of homosexuals. Altogether, these data support an X-linked multi-locus sexually antagonistic hypothesis rather than an autosomal multi-locus overdominance hypothesis. PMID:23227237

Dissecting maize diversity in lowland South America: genetic structure and geographic distribution models.

PubMed

Bracco, Mariana; Cascales, Jimena; Hernández, Julián Cámara; Poggio, Lidia; Gottlieb, Alexandra M; Lia, Verónica V

2016-08-26

Maize landraces from South America have traditionally been assigned to two main categories: Andean and Tropical Lowland germplasm. However, the genetic structure and affiliations of the lowland gene pools have been difficult to assess due to limited sampling and the lack of comparative analysis. Here, we examined SSR and Adh2 sequence variation in a diverse sample of maize landraces from lowland middle South America, and performed a comprehensive integrative analysis of population structure and diversity including already published data of archaeological and extant specimens from the Americas. Geographic distribution models were used to explore the relationship between environmental factors and the observed genetic structure. Bayesian and multivariate analyses of population structure showed the existence of two previously overlooked lowland gene pools associated with Guaraní indigenous communities of middle South America. The singularity of this germplasm was also evidenced by the frequency distribution of microsatellite repeat motifs of the Adh2 locus and the distinct spatial pattern inferred from geographic distribution models. Our results challenge the prevailing view that lowland middle South America is just a contact zone between Andean and Tropical Lowland germplasm and highlight the occurrence of a unique, locally adapted gene pool. This information is relevant for the conservation and utilization of maize genetic resources, as well as for a better understanding of environment-genotype associations.

Extreme Conservation and Non-Neutral Evolution of the cpmA Circadian Locus in a Globally Distributed Chroococcidiopsis sp. from Naturally Stressful Habitats

PubMed Central

Dvornyk, Volodymyr; Jahan, Akhee Sabiha

2012-01-01

Cyanobacteria are among the most ancient organisms known to have circadian rhythms. The cpmA gene is involved in controlling the circadian output signal. We studied polymorphism and divergence of this gene in six populations of a stress-tolerant cyanobacterium, Chroococcidiopsis sp., sampled in extreme habitats across the globe. Despite high haplotype diversity (0.774), nucleotide diversity of cpmA is very low (π = 0.0034): the gene appears to be even more conserved than housekeeping genes. Even though the populations were sampled thousands kilometers apart, they manifested virtually no genetic differentiation at this locus (FST = 0.0228). Using various tests for neutrality, we determined that evolution of cpmA significantly departures from the neutral model and is governed by episodic positive selection. PMID:22844070

PHIP - a novel candidate breast cancer susceptibility locus on 6q14.1

PubMed Central

Jiao, Xiang; Aravidis, Christos; Marikkannu, Rajeshwari; Rantala, Johanna; Picelli, Simone; Adamovic, Tatjana; Liu, Tao; Maguire, Paula; Kremeyer, Barbara; Luo, Liping; von Holst, Susanna; Kontham, Vinaykumar; Thutkawkorapin, Jessada; Margolin, Sara; Du, Quan; Lundin, Johanna; Michailidou, Kyriaki; Bolla, Manjeet K.; Wang, Qin; Dennis, Joe; Lush, Michael; Ambrosone, Christine B.; Andrulis, Irene L.; Anton-Culver, Hoda; Antonenkova, Natalia N.; Arndt, Volker; Beckmann, Matthias W.; Blomqvist, Carl; Blot, William; Boeckx, Bram; Bojesen, Stig E.; Bonanni, Bernardo; Brand, Judith S.; Brauch, Hiltrud; Brenner, Hermann; Broeks, Annegien; Brüning, Thomas; Burwinkel, Barbara; Cai, Qiuyin; Chang-Claude, Jenny; Couch, Fergus J.; Cox, Angela; Cross, Simon S.; Deming-Halverson, Sandra L.; Devilee, Peter; dos-Santos-Silva, Isabel; Dörk, Thilo; Eriksson, Mikael; Fasching, Peter A.; Figueroa, Jonine; Flesch-Janys, Dieter; Flyger, Henrik; Gabrielson, Marike; García-Closas, Montserrat; Giles, Graham G.; González-Neira, Anna; Guénel, Pascal; Guo, Qi; Gündert, Melanie; Haiman, Christopher A.; Hallberg, Emily; Hamann, Ute; Harrington, Patricia; Hooning, Maartje J.; Hopper, John L.; Huang, Guanmengqian; Jakubowska, Anna; Jones, Michael E.; Kerin, Michael J.; Kosma, Veli-Matti; Kristensen, Vessela N.; Lambrechts, Diether; Le Marchand, Loic; Lubinski, Jan; Mannermaa, Arto; Martens, John W.M.; Meindl, Alfons; Milne, Roger L.; Mulligan, Anna Marie; Neuhausen, Susan L.; Nevanlinna, Heli; Peto, Julian; Pylkäs, Katri; Radice, Paolo; Rhenius, Valerie; Sawyer, Elinor J.; Schmidt, Marjanka K.; Schmutzler, Rita K.; Seynaeve, Caroline; Shah, Mitul; Simard, Jacques; Southey, Melissa C.; Swerdlow, Anthony J.; Truong, Thérèse; Wendt, Camilla; Winqvist, Robert; Zheng, Wei; Benitez, Javier; Dunning, Alison M.; Pharoah, Paul D.P.; Easton, Douglas F.; Czene, Kamila; Hall, Per; Lindblom, Annika

2017-01-01

Most non-BRCA1/2 breast cancer families have no identified genetic cause. We used linkage and haplotype analyses in familial and sporadic breast cancer cases to identify a susceptibility locus on chromosome 6q. Two independent genome-wide linkage analysis studies suggested a 3 Mb locus on chromosome 6q and two unrelated Swedish families with a LOD >2 together seemed to share a haplotype in 6q14.1. We hypothesized that this region harbored a rare high-risk founder allele contributing to breast cancer in these two families. Sequencing of DNA and RNA from the two families did not detect any pathogenic mutations. Finally, 29 SNPs in the region were analyzed in 44,214 cases and 43,532 controls from BCAC, and the original haplotypes in the two families were suggested as low-risk alleles for European and Swedish women specifically. There was also some support for one additional independent moderate-risk allele in Swedish familial samples. The results were consistent with our previous findings in familial breast cancer and supported a breast cancer susceptibility locus at 6q14.1 around the PHIP gene. PMID:29262523

Molecular characterization of Shiga-toxigenic Escherichia coli isolated from diverse sources from India by multi-locus variable number tandem repeat analysis (MLVA).

PubMed

Kumar, A; Taneja, N; Sharma, R K; Sharma, H; Ramamurthy, T; Sharma, M

2014-12-01

In a first study from India, a diverse collection of 140 environmental and clinical non-O157 Shiga-toxigenic Escherichia coli strains from a large geographical area in north India was typed by multi-locus variable number tandem repeat analysis (MLVA). The distribution of major virulence genes stx1, stx2 and eae was found to be 78%, 70% and 10%, respectively; 15 isolates were enterohaemorrhagic E. coli (stx1 +/stx2 + and eae +). By MLVA analysis, 44 different alleles were obtained. Dendrogram analysis revealed 104 different genotypes and 19 MLVA-type complexes divided into two main lineages, i.e. mutton and animal stool. Human isolates presented a statistically significant greater odds ratio for clustering with mutton samples compared to animal stool isolates. Five human isolates clustered with animal stool strains suggesting that some of the human infections may be from cattle, perhaps through milk, contact or the environment. Further epidemiological studies are required to explore these sources in context with occurrence of human cases.

Characterization of microsatellite loci isolated in Mountain Plover (Charadrius montanus)

USGS Publications Warehouse

John, J. St; Kysela, R.F.; Oyler-McCance, S.J.

2007-01-01

Primers for 15 microsatellite loci were developed for Mountain Plover, a species whose distribution and abundance have been reduced drastically in the past 30 years. In a screen of 126 individuals collected from four breeding locales across the species' range, levels of polymorphism ranged from two to 13 alleles per locus. No two loci were found to be linked, although one locus revealed significant departures from Hardy-Weinberg equilibrium. These microsatellite loci can be used in population genetic studies, ultimately aiding in management efforts for Mountain Plover. Additionally, these markers can potentially be used in studies investigating the mating system of Mountain Plover. ?? 2007 Blackwell Publishing Ltd.

The renal urate transporter SLC17A1 locus: confirmation of association with gout.

PubMed

Hollis-Moffatt, Jade E; Phipps-Green, Amanda J; Chapman, Brett; Jones, Gregory T; van Rij, Andre; Gow, Peter J; Harrison, Andrew A; Highton, John; Jones, Peter B; Montgomery, Grant W; Stamp, Lisa K; Dalbeth, Nicola; Merriman, Tony R

2012-04-27

Two major gout-causing genes have been identified, the urate transport genes SLC2A9 and ABCG2. Variation within the SLC17A1 locus, which encodes sodium-dependent phosphate transporter 1, a renal transporter of uric acid, has also been associated with serum urate concentration. However, evidence for association with gout is equivocal. We investigated the association of the SLC17A1 locus with gout in New Zealand sample sets. Five variants (rs1165196, rs1183201, rs9358890, rs3799344, rs12664474) were genotyped across a New Zealand sample set totaling 971 cases and 1,742 controls. Cases were ascertained according to American Rheumatism Association criteria. Two population groups were studied: Caucasian and Polynesian. At rs1183201 (SLC17A1), evidence for association with gout was observed in both the Caucasian (odds ratio (OR) = 0.67, P = 3.0 × 10-6) and Polynesian (OR = 0.74, P = 3.0 × 10-3) groups. Meta-analysis confirmed association of rs1183201 with gout at a genome-wide level of significance (OR = 0.70, P = 3.0 × 10-8). Haplotype analysis suggested the presence of a common protective haplotype. We confirm the SLC17A1 locus as the third associated with gout at a genome-wide level of significance.

Maxwell Strata and Cut Locus in the Sub-Riemannian Problem on the Engel Group

NASA Astrophysics Data System (ADS)

Ardentov, Andrei A.; Sachkov, Yuri L.

2017-12-01

We consider the nilpotent left-invariant sub-Riemannian structure on the Engel group. This structure gives a fundamental local approximation of a generic rank 2 sub-Riemannian structure on a 4-manifold near a generic point (in particular, of the kinematic models of a car with a trailer). On the other hand, this is the simplest sub-Riemannian structure of step three. We describe the global structure of the cut locus (the set of points where geodesics lose their global optimality), the Maxwell set (the set of points that admit more than one minimizer), and the intersection of the cut locus with the caustic (the set of conjugate points along all geodesics). The group of symmetries of the cut locus is described: it is generated by a one-parameter group of dilations R+ and a discrete group of reflections Z2 × Z2 × Z2. The cut locus admits a stratification with 6 three-dimensional strata, 12 two-dimensional strata, and 2 one-dimensional strata. Three-dimensional strata of the cut locus are Maxwell strata of multiplicity 2 (for each point there are 2 minimizers). Two-dimensional strata of the cut locus consist of conjugate points. Finally, one-dimensional strata are Maxwell strata of infinite multiplicity, they consist of conjugate points as well. Projections of sub-Riemannian geodesics to the 2-dimensional plane of the distribution are Euler elasticae. For each point of the cut locus, we describe the Euler elasticae corresponding to minimizers coming to this point. Finally, we describe the structure of the optimal synthesis, i. e., the set of minimizers for each terminal point in the Engel group.

Genome-wide association analysis identifies a meningioma risk locus at 11p15.5.

PubMed

Claus, Elizabeth B; Cornish, Alex J; Broderick, Peter; Schildkraut, Joellen M; Dobbins, Sara E; Holroyd, Amy; Calvocoressi, Lisa; Lu, Lingeng; Hansen, Helen M; Smirnov, Ivan; Walsh, Kyle M; Schramm, Johannes; Hoffmann, Per; Nöthen, Markus M; Jöckel, Karl-Heinz; Swerdlow, Anthony; Larsen, Signe Benzon; Johansen, Christoffer; Simon, Matthias; Bondy, Melissa; Wrensch, Margaret; Houlston, Richard; Wiemels, Joseph L

2018-05-12

Meningioma are adult brain tumors originating in the meningeal coverings of the brain and spinal cord, with significant heritable basis. Genome-wide association studies (GWAS) have previously identified only a single risk locus for meningioma, at 10p12.31. To identify a susceptibility locus for meningioma, we conducted a meta-analysis of two GWAS, imputed using a merged reference panel of 1,000 Genomes and UK10K data, with validation in two independent sample series totaling 2,138 cases and 12,081 controls. We identified a new susceptibility locus for meningioma at 11p15.5 (rs2686876, odds ratio = 1.44, P = 9.86 × 10-9). A number of genes localize to the region of linkage disequilibrium encompassing rs2686876, including RIC8A, which plays a central role in the development of neural crest-derived structures, such as the meninges. This finding advances our understanding of the genetic basis of meningioma development and provides additional support for a polygenic model of meningioma.

Population genetics of apolipoprotein A-4, E, and H polymorphisms in Yanomami Indians of northwestern Brazil: associations with lipids, lipoproteins, and carbohydrate metabolism.

PubMed

Crews, D E; Kamboh, M I; Mancilha-Carvalho, J J; Kottke, B

1993-04-01

Using isoelectric focusing and immunoblotting techniques, we screened 96 serum samples from Yanomami Indians of northwestern Brazil to determine structural variation at three apolipoprotein loci: A4, E, and H. The APO-H locus, which is commonly polymorphic in white and black samples, was found to be monomorphic. At the APO-E locus only two alleles, APOE*3 and APOE*4, rather than the three-allele polymorphism commonly seen in Caucasians, was observed. At the APO-A4 locus no example of the APOA4*2 allele, found in Caucasians, was detected. However, the frequency of the less common APOA4*4 allele was above what has been observed in any other population. We investigated the impact of genetic variation at both polymorphic loci on quantitative differences in lipids, apolipoproteins, serum glucose, glycated hemoglobin, and uric acid. Contrary to the cholesterol-elevating effect of APOE*4 reported elsewhere, in both univariate analyses and after adjustments for age, sex, weight, and height, APOE*4 was associated with about a 4% lower mean serum cholesterol. Only after adjustment was this association statistically significant. The APOE*4 allele was significantly associated with unadjusted APO-A1 and APO-E levels but not with any other dependent variable; associations with adjusted APO-A1, APO-C2, and uric acid also approached standard levels of statistical significance (p < or = 0.05). In univariate analyses the APOA4*4 allele was significantly associated with APO-B, serum glucose, percent glycated hemoglobin, and uric acid, but no significant associations were observed after dependent variables were adjusted for age, sex, weight, and height. These results support the notion that apolipoprotein distributions and their associations with lipid and carbohydrate metabolism show ethnic variability.

Two-trait-locus linkage analysis: A powerful strategy for mapping complex genetic traits

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

Schork, N.J.; Boehnke, M.; Terwilliger, J.D.

1993-11-01

Nearly all diseases mapped to date follow clear Mendelian, single-locus segregation patterns. In contrast, many common familial diseases such as diabetes, psoriasis, several forms of cancer, and schizophrenia are familial and appear to have a genetic component but do not exhibit simple Mendelian transmission. More complex models are required to explain the genetics of these important diseases. In this paper, the authors explore two-trait-locus, two-marker-locus linkage analysis in which two trait loci are mapped simultaneously to separate genetic markers. The authors compare the utility of this approach to standard one-trait-locus, one-marker-locus linkage analysis with and without allowance for heterogeneity. Themore » authors also compare the utility of the two-trait-locus, two-marker-locus analysis to two-trait-locus, one-marker-locus linkage analysis. For common diseases, pedigrees are often bilineal, with disease genes entering via two or more unrelated pedigree members. Since such pedigrees often are avoided in linkage studies, the authors also investigate the relative information content of unilineal and bilineal pedigrees. For the dominant-or-recessive and threshold models that the authors consider, the authors find that two-trait-locus, two-marker-locus linkage analysis can provide substantially more linkage information, as measured by expected maximum lod score, than standard one-trait-locus, one-marker-locus methods, even allowing for heterogeneity, while, for a dominant-or-dominant generating model, one-locus models that allow for heterogeneity extract essentially as much information as the two-trait-locus methods. For these three models, the authors also find that bilineal pedigrees provide sufficient linkage information to warrant their inclusion in such studies. The authors discuss strategies for assessing the significance of the two linkages assumed in two-trait-locus, two-marker-locus models. 37 refs., 1 fig., 4 tabs.« less

An American termite in Paris: temporal colony dynamics.

PubMed

Baudouin, Guillaume; Dedeine, Franck; Bech, Nicolas; Bankhead-Dronnet, Stéphanie; Dupont, Simon; Bagnères, Anne-Geneviève

2017-12-01

Termites of the genus Reticulitermes are widespread invaders, particularly in urban habitats. Their cryptic and subterranean lifestyle makes them difficult to detect, and we know little about their colony dynamics over time. In this study we examined the persistence of Reticulitermes flavipes (Kollar) colonies in the city of Paris over a period of 15 years. The aim was (1) to define the boundaries of colonies sampled within the same four areas over two sampling periods, (2) to determine whether the colonies identified during the first sampling period persisted to the second sampling period, and (3) to compare the results obtained when colonies were delineated using a standard population genetic approach versus a Bayesian clustering method that combined both spatial and genetic information. Herein, colony delineations were inferred from genetic differences at nine microsatellite loci and one mitochondrial locus. Four of the 18 identified colonies did not show significant differences in their genotype distributions between the two sampling periods. While allelic richness was low, making it hard to reliably distinguish colony family type, most colonies appeared to retain the same breeding structure over time. These large and expansive colonies showed an important ability to fuse (39% were mixed-family colonies), contained hundreds of reproductives and displayed evidence of isolation-by-distance, suggesting budding dispersal. These traits, which favor colony persistence over time, present a challenge for pest control efforts, which apply treatment locally. The other colonies showed significant differences, but we cannot exclude the possibility that their genotype distributions simply changed over time.

Application of logistic regression to case-control association studies involving two causative loci.

PubMed

North, Bernard V; Curtis, David; Sham, Pak C

2005-01-01

Models in which two susceptibility loci jointly influence the risk of developing disease can be explored using logistic regression analysis. Comparison of likelihoods of models incorporating different sets of disease model parameters allows inferences to be drawn regarding the nature of the joint effect of the loci. We have simulated case-control samples generated assuming different two-locus models and then analysed them using logistic regression. We show that this method is practicable and that, for the models we have used, it can be expected to allow useful inferences to be drawn from sample sizes consisting of hundreds of subjects. Interactions between loci can be explored, but interactive effects do not exactly correspond with classical definitions of epistasis. We have particularly examined the issue of the extent to which it is helpful to utilise information from a previously identified locus when investigating a second, unknown locus. We show that for some models conditional analysis can have substantially greater power while for others unconditional analysis can be more powerful. Hence we conclude that in general both conditional and unconditional analyses should be performed when searching for additional loci.

First genetic characterisation of Giardia in human isolates from Jordan.

PubMed

Hijjawi, Nawal; Yang, Rongchang; Mukbel, Rami; Yassin, Yasmeen; Mharib, Taghrid; Ryan, Una

2016-10-01

Little is known about the epidemiology of Giardia in Jordan and to date, no genotyping studies have been conducted on Giardia isolates from Jordanians. In the present study, a total of 49 microscopy-positive faecal samples from Jordanian patients suffering from giardiasis were analysed at two loci: the triose phosphate isomerase (tpi) gene and the glutamate dehydrogenase (gdh) gene. At the tpi locus, a total of 28 samples amplified and assemblage A was identified in 46.4 % (13/28) samples, while assemblage B was identified in 50 % (14/28) samples and a mixed assemblage A and B was identified in one sample (3.6 %) (Table 1). At the gdh locus 48 isolates amplified and of these assemblages A was identified in 43.7 % (21/48) of isolates and assemblage B in 56.3 % (27/48) of isolates. No mixed infections were detected at the gdh locus. Subtyping at the gdh locus identified sub-assemblage AII in 43.7 % (21/48) of isolates and sub-assemblages BIII and BIV in 25 % (12/48) and 31.2 % (15/48) of isolates, respectively, with more genetic diversity in AII isolates than BIII or BIV isolates. Novel sub-types within each sub-assemblage were identified suggesting unique endemicity and anthroponotic transmission of Giardia in Jordanian patients suffering from giardiasis. Further studies are required to better understand the epidemiology and transmission of Giardia in Jordan.

cpDNA microsatellite markers for Lemna minor (Araceae): Phylogeographic implications1

PubMed Central

Wani, Gowher A.; Shah, Manzoor A.; Reshi, Zafar A.; Atangana, Alain R.; Khasa, Damase P.

2014-01-01

• Premise of the study: A lack of genetic markers impedes our understanding of the population biology of Lemna minor. Thus, the development of appropriate genetic markers for L. minor promises to be highly useful for population genetic studies and for addressing other life history questions regarding the species. • Methods and Results: For the first time, we characterized nine polymorphic and 24 monomorphic chloroplast microsatellite markers in L. minor using DNA samples of 26 individuals sampled from five populations in Kashmir and of 17 individuals from three populations in Quebec. Initially, we designed 33 primer pairs, which were tested on genomic DNA from natural populations. Nine loci provided markers with two alleles. Based on genotyping of the chloroplast DNA fragments from 43 sampled individuals, we identified one haplotype in Quebec and 11 haplotypes in Kashmir, of which one occurs in 56% of the genotypes, one in 8%, and nine in 4%, respectively. There was a maximum of two alleles per locus. • Conclusions: These new chloroplast microsatellite markers for L. minor and haplotype distribution patterns indicate a complex phylogeographic history that merits further investigation. PMID:25202636

cpDNA microsatellite markers for Lemna minor (Araceae): Phylogeographic implications.

PubMed

Wani, Gowher A; Shah, Manzoor A; Reshi, Zafar A; Atangana, Alain R; Khasa, Damase P

2014-07-01

A lack of genetic markers impedes our understanding of the population biology of Lemna minor. Thus, the development of appropriate genetic markers for L. minor promises to be highly useful for population genetic studies and for addressing other life history questions regarding the species. • For the first time, we characterized nine polymorphic and 24 monomorphic chloroplast microsatellite markers in L. minor using DNA samples of 26 individuals sampled from five populations in Kashmir and of 17 individuals from three populations in Quebec. Initially, we designed 33 primer pairs, which were tested on genomic DNA from natural populations. Nine loci provided markers with two alleles. Based on genotyping of the chloroplast DNA fragments from 43 sampled individuals, we identified one haplotype in Quebec and 11 haplotypes in Kashmir, of which one occurs in 56% of the genotypes, one in 8%, and nine in 4%, respectively. There was a maximum of two alleles per locus. • These new chloroplast microsatellite markers for L. minor and haplotype distribution patterns indicate a complex phylogeographic history that merits further investigation.

Analytical Framework for Identifying and Differentiating Recent Hitchhiking and Severe Bottleneck Effects from Multi-Locus DNA Sequence Data

DOE PAGES

Sargsyan, Ori

2012-05-25

Hitchhiking and severe bottleneck effects have impact on the dynamics of genetic diversity of a population by inducing homogenization at a single locus and at the genome-wide scale, respectively. As a result, identification and differentiation of the signatures of such events from DNA sequence data at a single locus is challenging. This study develops an analytical framework for identifying and differentiating recent homogenization events at multiple neutral loci in low recombination regions. The dynamics of genetic diversity at a locus after a recent homogenization event is modeled according to the infinite-sites mutation model and the Wright-Fisher model of reproduction withmore » constant population size. In this setting, I derive analytical expressions for the distribution, mean, and variance of the number of polymorphic sites in a random sample of DNA sequences from a locus affected by a recent homogenization event. Based on this framework, three likelihood-ratio based tests are presented for identifying and differentiating recent homogenization events at multiple loci. Lastly, I apply the framework to two data sets. First, I consider human DNA sequences from four non-coding loci on different chromosomes for inferring evolutionary history of modern human populations. The results suggest, in particular, that recent homogenization events at the loci are identifiable when the effective human population size is 50000 or greater in contrast to 10000, and the estimates of the recent homogenization events are agree with the “Out of Africa” hypothesis. Second, I use HIV DNA sequences from HIV-1-infected patients to infer the times of HIV seroconversions. The estimates are contrasted with other estimates derived as the mid-time point between the last HIV-negative and first HIV-positive screening tests. Finally, the results show that significant discrepancies can exist between the estimates.« less

Distribution of phlebotomine sand fly genotypes (Lutzomyia shannoni, Diptera: Psychodidae) across a highly heterogeneous landscape.

PubMed

Mukhopadhyay, J; Ghosh, K; Ferro, C; Munstermann, L E

2001-03-01

Genetic variability of eight Colombian field populations and two laboratory colonies of a tropical forest sand fly, Lutzomyia shannoni Dyar, was assessed by comparing allozyme frequencies at 20 enzyme loci. Substantial genetic variability was noted in all strains, with mean heterozygosities of 13-21% and alleles per locus of 2.0-2.8. Four loci were monomorphic. Six populations in north and central Colombia showed close genetic similarity (Nei's distances, 0.01-0.09), despite mountainous environment, discontinuous forest habitat, and elevation differences from 125 to 1,220 m. Two samples representing the Orinoco (near Villavicencio) and Amazon (near Leticia) river basins were similar (Nei's distance, 0.08) but diverged substantially from the central six samples (Nei's distances, 0.26-0.40). Although the range of L. shannoni extends from the southeastern United States to northern Argentina, three genetically distinct, geographically discrete, groups were discerned by the current analysis: Orinoco-Amazon river basins, north-central Colombia, and eastern United States.

QTL mapping for nine drought-responsive agronomic traits in bread wheat under irrigated and rain-fed environments

PubMed Central

Gahlaut, Vijay; Jaiswal, Vandana; Tyagi, Bhudeva S.; Singh, Gyanendra; Sareen, Sindhu; Balyan, Harindra S.

2017-01-01

In bread wheat, QTL interval mapping was conducted for nine important drought responsive agronomic traits. For this purpose, a doubled haploid (DH) mapping population derived from Kukri/Excalibur was grown over three years at four separate locations in India, both under irrigated and rain-fed environments. Single locus analysis using composite interval mapping (CIM) allowed detection of 98 QTL, which included 66 QTL for nine individual agronomic traits and 32 QTL, which affected drought sensitivity index (DSI) for the same nine traits. Two-locus analysis allowed detection of 19 main effect QTL (M-QTL) for four traits (days to anthesis, days to maturity, grain filling duration and thousand grain weight) and 19 pairs of epistatic QTL (E-QTL) for two traits (days to anthesis and thousand grain weight). Eight QTL were common in single locus analysis and two locus analysis. These QTL (identified both in single- and two-locus analysis) were distributed on 20 different chromosomes (except 4D). Important genomic regions on chromosomes 5A and 7A were also identified (5A carried QTL for seven traits and 7A carried QTL for six traits). Marker-assisted recurrent selection (MARS) involving pyramiding of important QTL reported in the present study, together with important QTL reported earlier, may be used for improvement of drought tolerance in wheat. In future, more closely linked markers for the QTL reported here may be developed through fine mapping, and the candidate genes may be identified and used for developing a better understanding of the genetic basis of drought tolerance in wheat. PMID:28793327

Rare Sequence Variation in the Genome Flanking a Short Tandem Repeat Locus Can Lead to a Question of “Nonmaternity”

PubMed Central

Deucher, Anne; Chiang, Tsoyu; Schrijver, Iris

2010-01-01

Typing of STR (short tandem repeat) alleles is used in a variety of applications in clinical molecular pathology, including evaluations for maternal cell contamination. Using a commercially available STR typing assay for maternal cell contamination performed in conjunction with prenatal diagnostic testing, we were posed with apparent nonmaternity when the two fetal samples did not demonstrate the expected maternal allele at one locus. By designing primers external to the region amplified by the primers from the commercial assay and by performing direct sequencing of the resulting amplicon, we were able to determine that a guanine to adenine sequence variation led to primer mismatch and allele dropout. This explained the apparent null allele shared between the maternal and fetal samples. Therefore, although rare, allele dropout must be considered whenever unexplained homozygosity at an STR locus is observed. PMID:20203001

Microsatellite variation and genetic structuring in Mugil liza (Teleostei: Mugilidae) populations from Argentina and Brazil

NASA Astrophysics Data System (ADS)

Mai, Ana C. G.; Miño, Carolina I.; Marins, Luis F. F.; Monteiro-Neto, Cassiano; Miranda, Laura; Schwingel, Paulo R.; Lemos, Valéria M.; Gonzalez-Castro, Mariano; Castello, Jorge P.; Vieira, João P.

2014-08-01

The mullet Mugil liza is distributed along the Atlantic coast of South America, from Argentina to Venezuela, and it is heavily exploited in Brazil. We assessed patterns of distribution of neutral nuclear genetic variation in 250 samples from the Brazilian states of Rio de Janeiro, São Paulo, Santa Catarina and Rio Grande do Sul (latitudinal range of 23-31°S) and from Buenos Aires Province in Argentina (36°S). Nine microsatellite loci revealed 131 total alleles, 3-23 alleles per locus, He: 0.69 and Ho: 0.67. Significant genetic differentiation was observed between Rio de Janeiro samples (23°S) and those from all other locations, as indicated by FST, hierarchical analyses of genetic structure, Bayesian cluster analyses and assignment tests. The presence of two different demographic clusters better explains the allelic diversity observed in mullets from the southernmost portion of the Atlantic coast of Brazil and from Argentina. This may be taken into account when designing fisheries management plans involving Brazilian, Uruguayan and Argentinean M. liza populations.

Capillary sample introduction of polymerase chain reaction (PCR) products separated in ultrathin slab gels.

PubMed

Bullard, K M; Hietpas, P B; Ewing, A G

1998-01-01

Polymerase chain reaction (PCR) amplified short tandem repeat (STR) samples from the HUMVWF locus have been analyzed using a unique sample introduction and separation technique. A single capillary is used to transfer samples onto an ultrathin slab gel (57 microm thin). This ultrathin nondenaturing polyacrylamide gel is used to separate the amplified fragments, and laser-induced fluorescence with ethidium bromide is used for detection. The feasibility of performing STR analysis using this system has been investigated by examining the reproducibility for repeated samples. Reproducibility is examined by comparing the migration of the 14 and 17 HUMVWF alleles on three consecutive separations on the ultrathin slab gel. Using one locus, separations match in migration time with the two alleles 42 s apart for each of the three consecutive separations. This technique shows potential to increase sample throughput in STR analysis techniques although separation resolution still needs to be improved.

Effectiveness of teaching cognitive-behavioral techniques on locus of control in hemodialysis patients.

PubMed

Mehrtak, Mohammad; Habibzadeh, Shahram; Farzaneh, Esmaeil; Rjaei-Khiavi, Abdollah

2017-10-01

Many of the cognitive behavioral models and therapeutic protocols developed so far for psychological disorders and chronic diseases have proved effective through clinical research. This study aimed to determine the effectiveness of teaching cognitive-behavioral techniques on locus of control in hemodialysis patients. This controlled clinical trial study was conducted in 2015 with 76 patients selected by census and treated with a hemodialysis machine in the dialysis department of Vali-Asr Hospital in the city of Meshkinshahr. A total of four patients were excluded because of their critical conditions while the rest, who were recruited, were randomly divided into two equal groups of 36 patients as the intervention and control groups. First, the locus of control was measured in both groups through a pretest, and cognitive-behavioral techniques were then taught to the intervention group during eight 45 to 90-minute sessions. The locus of control in patients of both groups was finally re-measured through a posttest. Data were collected using Rotter's Locus of Control Inventory. The Wilcoxon test and Mann-Whitney U test were respectively used in SPSS18 for data analysis. In the pretest and posttest stages respectively, 4.8% and 14.3% of samples in the control group as well as 14.3% and 33.3% of samples in the intervention group enjoyed internal locus of control. The difference between the pretest and posttest scores of internal locus of control in the intervention group was significant (p=0.004), which indicates the positive effect of cognitive-behavioral psychotherapeutic intervention on internalization of locus of control in this group. Given the external locus of control in most of the study patients and also the positive significant effect of cognitive-behavioral psychotherapy on internalization of locus of control in this group of patients, it appears necessary to have a psychology resident present in the hemodialysis department to teach the necessary cognitive-behavioral techniques to internalize the locus of control. The trial was registered at the Thai Clinical Trial Registry (http://www.clinicaltrials.in.th) with the TCTID: TCTR20170707003. The authors received no financial support for the research, authorship, and/or publication of this article.

Genome-wide association analysis of young onset stroke identifies a locus on chromosome 10q25 near HABP2

PubMed Central

Cheng, Yu-Ching; Stanne, Tara M.; Giese, Anne-Katrin; Ho, Weang Kee; Traylor, Matthew; Amouyel, Philippe; Holliday, Elizabeth G.; Malik, Rainer; Xu, Huichun; Kittner, Steven J.; Cole, John W.; O’Connell, Jeffrey R.; Danesh, John; Rasheed, Asif; Zhao, Wei; Engelter, Stefan; Grond-Ginsbach, Caspar; Kamatani, Yoichiro; Lathrop, Mark; Leys, Didier; Thijs, Vincent; Metso, Tiina M.; Tatlisumak, Turgut; Pezzini, Alessandro; Parati, Eugenio A.; Norrving, Bo; Bevan, Steve; Rothwell, Peter M; Sudlow, Cathie; Slowik, Agnieszka; Lindgren, Arne; Walters, Matthew R; Jannes, Jim; Shen, Jess; Crosslin, David; Doheny, Kimberly; Laurie, Cathy C.; Kanse, Sandip M.; Bis, Joshua C.; Fornage, Myriam; Mosley, Thomas H.; Hopewell, Jemma C.; Strauch, Konstantin; Müller-Nurasyid, Martina; Gieger, Christian; Waldenberger, Melanie; Peters, Annette; Meisinger, Christine; Ikram, M. Arfan; Longstreth, WT; Meschia, James F.; Seshadri, Sudha; Sharma, Pankaj; Worrall, Bradford; Jern, Christina; Levi, Christopher; Dichgans, Martin; Boncoraglio, Giorgio B.; Markus, Hugh S.; Debette, Stephanie; Rolfs, Arndt; Saleheen, Danish; Mitchell, Braxton D.

2015-01-01

Background and Purpose Although a genetic contribution to ischemic stroke is well recognized, only a handful of stroke loci have been identified by large-scale genetic association studies to date. Hypothesizing that genetic effects might be stronger for early- versus late-onset stroke, we conducted a two-stage meta-analysis of genome-wide association studies (GWAS), focusing on stroke cases with an age of onset < 60 years old. Methods The Discovery stage of our GWAS included 4,505 cases and 21,968 controls of European, South-Asian and African ancestry, drawn from 6 studies. In Stage 2, we selected the lead genetic variants at loci with association P<5×10−6 and performed in silico association analyses in an independent sample of up to 1,003 cases and 7,745 controls. Results One stroke susceptibility locus at 10q25 reached genome-wide significance in the combined analysis of all samples from the Discovery and Follow-up Stages (rs11196288, OR=1.41, P=9.5×10−9). The associated locus is in an intergenic region between TCF7L2 and HABP2. In a further analysis in an independent sample, we found that two SNPs in high linkage disequilibrium with rs11196288 were significantly associated with total plasma factor VII-activating protease levels, a product of HABP2. Conclusions HABP2, which encodes an extracellular serine protease involved in coagulation, fibrinolysis, and inflammatory pathways, may be a genetic susceptibility locus for early-onset stroke. PMID:26732560

Evidence for Sexual Reproduction: Identification, Frequency, and Spatial Distribution of Venturia effusa (Pecan Scab) Mating Type Idiomorphs.

PubMed

Young, Carolyn A; Bock, Clive H; Charlton, Nikki D; Mattupalli, Chakradhar; Krom, Nick; Bowen, Joanna K; Templeton, Matthew; Plummer, Kim M; Wood, Bruce W

2018-05-10

Venturia effusa (syn. Fusicladium effusum), causal agent of pecan scab, is the most prevalent pathogen of pecan (Carya illinoinensis), causing severe yield losses in the southeastern United States. V. effusa is currently known only by its asexual (conidial) stage. However, the degree and distribution of genetic diversity observed within and among populations of V. effusa are typical of a sexually reproducing fungal pathogen, and comparable with other dothideomycetes with a known sexual stage, including the closely related apple scab pathogen, V. inaequalis. Using the mating type (MAT) idiomorphs from V. inaequalis, we identified a single MAT gene, MAT1-1-1, in a draft genome of V. effusa. The MAT1-1-1 locus is flanked by two conserved genes encoding a DNA lyase (APN2) and a hypothetical protein. The MAT locus spanning the flanking genes was amplified and sequenced from a subset of 14 isolates, of which 7 contained MAT1-1-1 and the remaining samples contained MAT1-2-1. A multiplex polymerase chain reaction screen was developed to amplify MAT1-1-1, MAT1-2-1, and a conserved reference gene encoding β-tubulin, and used to screen 784 monoconidial isolates of V. effusa collected from 11 populations of pecan across the southeastern United States. A hierarchical sampling protocol representing region, orchard, and tree allowed for analysis of MAT structure at different spatial scales. Analysis of this collection revealed the frequency of the MAT idiomorphs is in a 1:1 equilibrium of MAT1-1:MAT1-2. The apparent equilibrium of the MAT idiomorphs provides impetus for a renewed effort to search for the sexual stage of V. effusa. [Formula: see text] Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

HYBRIDIZATION AND GEOGRAPHIC VARIATION IN TWO MEADOW KATYDID CONTACT ZONES.

PubMed

Shapiro, Leo H

1998-06-01

In this study, previously unrecognized hybridization was documented between two meadow katydids in each of two disjunct contact zones, in the southeastern United States and along the Potomac River near Washington, DC. These two zones have very different histories and dynamics of interaction between the two taxa. Orchelimum nigripes and O. pulchellum (Tettigoniidae: Conocephalinae) are distributed west and east, respectively, of the Appalachian Mountains, from the Great Lakes to the Gulf Coast and along the Atlantic Coastal Plain from New York to the Florida Keys, but are not found in the Appalachians themselves. In addition, during this century O. nigripes has become established in a small area east of the Appalachians, in the Potomac River basin, where it has completely replaced O. pulchellum along the river corridor above Washington, DC. I sampled katydids from 40 sites across both hybrid zones and mapped geographic patterns of genetic variation (allele frequencies at two diagnostic loci) and variation in a morphometric index for males. Although the two taxa are quite distinct over most of their extensive distributions, there is clear evidence of introgression in both contact zones. In the Deep South, samples from a transect along the Gulf Coast define a broad hybrid zone of about 50-100 km, while samples from a transect 200 km to the north define a zone of about 150-250 km in width. Only one Deep South population shows a deviation from Hardy-Weinberg equilibrium at either locus, and there is no evidence of linkage disequilibrium in any Deep South population. In the Potomac region, there is a narrow upstream-downstream hybrid zone along the river. Within the Potomac River floodplains downriver from Washington, DC, as well as outside the floodplains throughout the region, O. pulchellum is present in abundance, but O. nigripes markers are virtually absent. Within the floodplains upriver from Washington, DC, O. nigripes is abundant, but O. pulch***ellum markers are virtually absent. All four mixed ancestry Potomac populations sampled show strong and highly significant linkage disequilibrium, although only one clearly deviates from single-locus Hardy-Weinberg equilibrium. The position of the Deep South hybrid zone is generally consistent with interspecific and intraspecific phylogeographic patterns previously reported for numerous taxa from the southeastern United States. The observed genetic and morphometric clines appear to be the result of neutral introgression over thousands of years. In the much younger Potomac hybrid zone, O. nigripes appears to be spreading downriver, interbreeding with O. pulchellum, and replacing it. The mechanism for this replacement remains uncertain, but may be clarified by ongoing behavioral, genetic, and breeding studies. © 1998 The Society for the Study of Evolution.

A comparative genetic analysis of the Irish greyhound population using multilocus DNA fingerprinting, canine single locus minisatellites and canine microsatellites.

PubMed

Sutton, M D; Holmes, N G; Brennan, F B; Binns, M M; Kelly, E P; Duke, E J

1998-06-01

Pairwise analysis of HinfI/33.6 DNA fingerprints from a total of one hundred and fifty-three Irish greyhounds of known pedigree were used to determine band-share estimates of unrelated, first-degree and second-degree relationships. Forty-eight unrelated Irish greyhounds were used to determine allele frequencies for three single-locus minisatellites, and following a preliminary screen, eight of the most polymorphic tetra-nucleotide microsatellites from a panel of 15. The results indicated that both band-share estimates by DNA fingerprinting and microsatellite allele frequencies are highly effective in resolving parentage in this greyhound population, while single-locus minisatellites showed limited polymorphism and could not be used alone for routine parentage testing in this breed. The present study also demonstrated that, to obtain optimal resolution of parentage, sample sets of known pedigree status are required to determine the band-share distribution and/or microsatellite allele frequencies.

The effect of genetic variation of the serotonin 1B receptor gene on impulsive aggressive behavior and suicide.

PubMed

Zouk, Hana; McGirr, Alexander; Lebel, Véronique; Benkelfat, Chawky; Rouleau, Guy; Turecki, Gustavo

2007-12-05

Impulsive-aggressive behaviors (IABs) are regarded as possible suicide intermediate phenotypes, mediating the relationship between genes and suicide outcome. In this study, we aimed to investigate the putative relationship between genetic variation at the 5-HT1B receptor gene, which in animal models is involved in impulse-aggression control, IABs, and suicide risk. We investigated the relationship of variation at five 5-HT1B loci and IAB measures in a sample of 696 subjects, including 338 individuals who died by suicide and 358 normal epidemiological controls. We found that variation at the 5-HT1B promoter A-161T locus had a significant effect on levels of IABs, as measured by the Buss-Durkee Hostility Inventory (BDHI). Suicides also differed from controls in distribution of variants at this locus. The A-161T locus, which seems to impact 5-HT1B transcription, could play a role in suicide predisposition by means of mediating impulsive-aggressive behaviors. 2007 Wiley-Liss, Inc.

Genetic distribution of 15 autosomal STR markers in the Punjabi population of Pakistan.

PubMed

Shan, Muhammad Adnan; Hussain, Manzoor; Shafique, Muhammad; Shahzad, Muhammad; Perveen, Rukhsana; Idrees, Muhammad

2016-11-01

Genetic diversity of 15 autosomal short tandem repeat (STR) loci was evaluated in 713 unrelated individual samples of a Punjabi population of Pakistan. These loci were scrutinized to establish allelic frequencies and statistical parameters of forensic and paternity interests. A total of 165 alleles were observed with the corresponding allele frequencies ranging from 0.001 to 0.446. D2S1338 was found as the most informative locus while TPOX (0.611) was the least discriminating locus. The combined power of discrimination (CPD), the combined probability of exclusion (CPE), and cumulative probability of matching (CPM) were found equaled to 0.999999999999999998606227424808, 0.999995777557989, and 1.37543 × 10-18, respectively. All the loci followed the Hardy-Weinberg equilibrium after the Bonferroni correction (p < 0.0033) except one locus D3S1358. The study revealed that these STR loci are highly polymorphic, suitable for forensic and parentage analyses. In comparison to different populations (Asians and non-Asians), significant differences were recorded for these loci.

[Genetic aspects of species structure of the compost worm Eisenia foetida (Sav.) (Oligochaeta, Lumbricidae)].

PubMed

Bolotetskiĭ, N M; Kodolova, O P

2002-01-01

Distribution of frequencies alleles of polymorphous loci of peroxidase (Pox), leucineaminopeptidase (Lap), phosphoglucomutase (Pgm) and octanoldehydrogenase (Odh) were studied by electrophoresis in polyacrylamide gel in 22 local samples of Esenia foetida in Russia (European part), Ukraine, Kazakhstan and Kirghizia. The samples form two spatial groups--"northern" and "southern", distinguished by set of alleles in every studied locus. The "northern" groups is formed by local populations of European Russia from Murmansk region on the north to Smolensk region on the south, and also by cultivated population of selection line "red California hybrid". The "southern" group is formed by local populations on the territory of Russia from middle Volga to the North Caucasus, Ukraine, Kazakhstan, Kirghizia, cultivated populations from Kirghizia and Portugal. High degree of genetic difference between samples and independence of alleles frequencies distribution from geographical location and habitat allows to consider almost all studied groups as separate populations. Statistical processing of Nei genetic distances (Nei, 1972) revealed reliable differences between averages of within- and intergroup distances. Besides, discrete differences between intervals of significance of genetic distances were revealed. The results indicate that on the studied territory E. foetida has hierarchical two level structure. The first level is formed by local populations differed by frequency of the same alleles. The second level is formed by local populations, united into spatial groups, that are qualitatively distinguished by the set of alleles in the same loci.

The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions

PubMed Central

Jhunjhunwala, Suchit; van Zelm, Menno C.; Peak, Mandy M.; Cutchin, Steve; Riblet, Roy; van Dongen, Jacques J.M.; Grosveld, Frank G.; Knoch, Tobias A.; Murre, Cornelis

2009-01-01

SUMMARY The immunoglobulin heavy-chain (Igh) locus is organized into distinct regions that contain multiple variable (VH), diversity (DH), joining (JH) and constant (CH) coding elements. How the Igh locus is structured in 3D space is unknown. To probe the topography of the Igh locus, spatial distance distributions were determined between 12 genomic markers that span the entire Igh locus. Comparison of the distance distributions to computer simulations of alternative chromatin arrangements predicted that the Igh locus is organized into compartments containing clusters of loops separated by linkers. Trilateration and triple-point angle measurements indicated the mean relative 3D positions of the VH, DH, JH, and CH elements, showed compartmentalization and striking conformational changes involving VH and DH-JH elements during early B cell development. In pro-B cells, the entire repertoire of VH regions (2 Mbp) appeared to have merged and juxtaposed to the DH elements, mechanistically permitting long-range genomic interactions to occur with relatively high frequency. PMID:18423198

The Ties that Bind (the Igh Locus).

PubMed

Krangel, Michael S

2016-05-01

Immunoglobulin heavy-chain locus V(D)J recombination requires a 3D chromatin organization which permits widely distributed variable (V) gene segments to contact distant diversity (D) and joining (J) gene segments. A recent study has identified key nodes in the locus interactome, paving the way for new molecular insights into how the locus is configured for recombination. Copyright © 2016 Elsevier Ltd. All rights reserved.

Development of molecular method for sex identification in date palm (Phoenix dactylifera L.) plantlets using novel sex-linked microsatellite markers.

PubMed

Maryam; Jaskani, Muhammad Jafar; Awan, Faisal Saeed; Ahmad, Saeed; Khan, Iqrar A

2016-06-01

Microsatellite markers containing simple sequence repeats (SSRs) are a valuable tool for genetic analysis. Date palm is a dioecious and slow flowering and is very difficult to identify the gender of the trees until it reaches the reproductive age (5-10 years). A total of 12 microsatellite primers were used with 30 date palm samples, 14 parents (8 male + 6 females) and 16 progeny (developed from parents breeding) which showed that microsatellites were highly polymorphic, having a great number of alleles. A total of 124 alleles were characterized in 12 SSR loci. On average, there are 9.08 alleles per locus, with a range from 5 to 16 alleles, for primers mpdCIR15 and mpdCIR57, respectively. These primers produced 15 polymorphic loci specifically in male date palm samples and the seedlings harboring the unique fragments were further characterized as male plants. Increasingly, 38.46 % of these loci were scored as homozygous alleles while 61.53 % heterozygous allelic loci were determined. Primer mpdCIR48 produced a specific locus (250/250) in all male samples whereas the same locus was absent in female samples. Similarly, a locus of 300/310 bp reoccurred in 5 date palm male samples using marker DP-168 which indicated that these are the promising candidate marker to detect the sex in date palm seedlings at early stage. The data resulted from combination of 12 primers enabled the 16 seedling samples progeny (developed from parents breeding) of date palm cultivars to divide into two groups i.e., male and female regarding their sex expression comparative to the parents (male + female) using the principle coordinate analysis.

Characterization of 23 polymorphic SSR markers in Salix humboldtiana (Salicaceae) using next-generation sequencing and cross-amplification from related species1

PubMed Central

Bozzi, Jorge A.; Liepelt, Sascha; Ohneiser, Sebastian; Gallo, Leonardo A.; Marchelli, Paula; Leyer, Ilona; Ziegenhagen, Birgit; Mengel, Christina

2015-01-01

Premise of the study: We present a set of 23 polymorphic nuclear microsatellite loci, 18 of which are identified for the first time within the riparian species Salix humboldtiana (Salicaceae) using next-generation sequencing. Methods and Results To characterize the 23 loci, up to 60 individuals were sampled and genotyped at each locus. The number of alleles ranged from two to eight, with an average of 4.43 alleles per locus. The effective number of alleles ranged from 1.15 to 3.09 per locus, and allelic richness ranged from 2.00 to 7.73 alleles per locus. Conclusions The new marker set will be used for future studies of genetic diversity and differentiation as well as for unraveling spatial genetic structures in S. humboldtiana populations in northern Patagonia, Argentina. PMID:25909042

Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data.

PubMed

Bhaskar, Anand; Wang, Y X Rachel; Song, Yun S

2015-02-01

With the recent increase in study sample sizes in human genetics, there has been growing interest in inferring historical population demography from genomic variation data. Here, we present an efficient inference method that can scale up to very large samples, with tens or hundreds of thousands of individuals. Specifically, by utilizing analytic results on the expected frequency spectrum under the coalescent and by leveraging the technique of automatic differentiation, which allows us to compute gradients exactly, we develop a very efficient algorithm to infer piecewise-exponential models of the historical effective population size from the distribution of sample allele frequencies. Our method is orders of magnitude faster than previous demographic inference methods based on the frequency spectrum. In addition to inferring demography, our method can also accurately estimate locus-specific mutation rates. We perform extensive validation of our method on simulated data and show that it can accurately infer multiple recent epochs of rapid exponential growth, a signal that is difficult to pick up with small sample sizes. Lastly, we use our method to analyze data from recent sequencing studies, including a large-sample exome-sequencing data set of tens of thousands of individuals assayed at a few hundred genic regions. © 2015 Bhaskar et al.; Published by Cold Spring Harbor Laboratory Press.

Cluster analysis of European Y-chromosomal STR haplotypes using the discrete Laplace method.

PubMed

Andersen, Mikkel Meyer; Eriksen, Poul Svante; Morling, Niels

2014-07-01

The European Y-chromosomal short tandem repeat (STR) haplotype distribution has previously been analysed in various ways. Here, we introduce a new way of analysing population substructure using a new method based on clustering within the discrete Laplace exponential family that models the probability distribution of the Y-STR haplotypes. Creating a consistent statistical model of the haplotypes enables us to perform a wide range of analyses. Previously, haplotype frequency estimation using the discrete Laplace method has been validated. In this paper we investigate how the discrete Laplace method can be used for cluster analysis to further validate the discrete Laplace method. A very important practical fact is that the calculations can be performed on a normal computer. We identified two sub-clusters of the Eastern and Western European Y-STR haplotypes similar to results of previous studies. We also compared pairwise distances (between geographically separated samples) with those obtained using the AMOVA method and found good agreement. Further analyses that are impossible with AMOVA were made using the discrete Laplace method: analysis of the homogeneity in two different ways and calculating marginal STR distributions. We found that the Y-STR haplotypes from e.g. Finland were relatively homogeneous as opposed to the relatively heterogeneous Y-STR haplotypes from e.g. Lublin, Eastern Poland and Berlin, Germany. We demonstrated that the observed distributions of alleles at each locus were similar to the expected ones. We also compared pairwise distances between geographically separated samples from Africa with those obtained using the AMOVA method and found good agreement. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Two-locus diseas models with two marker loci: The power of affected-sib-pair tests

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

Knapp, M.; Seuchter, S.A.; Bauer, M.P.

1994-11-01

Recently, Schork et al. found that two-trait-locus, two-marker-locus (parametric) linkage analysis can provide substantially more linkage information than can standard one-trait-locus, one-marker-locus methods. However, because of the increased burden of computation, Schork et al. do not expect that their approach will be applied in an initial genome scan. Further, the specification of a suitable two-locus segregation model can be crucial. Affected-sib-pair tests are computationally simple and do not require an explicit specification of the disease model. In the past, however, these tests mainly have been applied to data with a single marker locus. Here, we consider sib-pair tests that makemore » it possible to analyze simultaneously two marker loci. The power of these tests is investigated for different (epistatic and heterogeneous) two-trait-locus models, each trait locus being linked to one of the marker loci. We compare these tests both with the test that is optimal for a certain model and with the strategy that analyzes each marker locus separately. The results indicate that a straightforward extension of the well-known mean test for two marker loci can be much more powerful than single-marker-locus analysis and that its power is only slightly inferior to the power of the optimal test. 21 refs., 5 figs., 2 tabs.« less

Diversification and Distribution of Ruminant Chlamydia abortus Clones Assessed by MLST and MLVA.

PubMed

Siarkou, Victoria I; Vorimore, Fabien; Vicari, Nadia; Magnino, Simone; Rodolakis, Annie; Pannekoek, Yvonne; Sachse, Konrad; Longbottom, David; Laroucau, Karine

2015-01-01

Chlamydia abortus, an obligate intracellular bacterium, is the most common infectious cause of abortion in small ruminants worldwide and has zoonotic potential. We applied multilocus sequence typing (MLST) together with multiple-locus variable-number tandem repeat analysis (MLVA) to genotype 94 ruminant C. abortus strains, field isolates and samples collected from 1950 to 2011 in diverse geographic locations, with the aim of delineating C. abortus lineages and clones. MLST revealed the previously identified sequence types (STs) ST19, ST25, ST29 and ST30, plus ST86, a recently-assigned type on the Chlamydiales MLST website and ST87, a novel type harbouring the hemN_21 allele, whereas MLVA recognized seven types (MT1 to MT7). Minimum-spanning-tree analysis suggested that all STs but one (ST30) belonged to a single clonal complex, possibly reflecting the short evolutionary timescale over which the predicted ancestor (ST19) has diversified into three single-locus variants (ST86, ST87 and ST29) and further, through ST86 diversification, into one double-locus variant (ST25). ST descendants have probably arisen through a point mutation evolution mode. Interestingly, MLVA showed that in the ST19 population there was a greater genetic diversity than in other STs, most of which exhibited the same MT over time and geographical distribution. However, the evolutionary pathways of C. abortus STs seem to be diverse across geographic distances with individual STs restricted to particular geographic locations. The ST30 singleton clone displaying geographic specificity and represented by the Greek strains LLG and POS was effectively distinguished from the clonal complex lineage, supporting the notion that possibly two separate host adaptations and hence independent bottlenecks of C. abortus have occurred through time. The combination of MLST and MLVA assays provides an additional level of C. abortus discrimination and may prove useful for the investigation and surveillance of emergent C. abortus clonal populations.

Worldwide genealogy of Entamoeba histolytica: an overview to understand haplotype distribution and infection outcome.

PubMed

Zermeño, Valeria; Ximénez, Cecilia; Morán, Patricia; Valadez, Alicia; Valenzuela, Olivia; Rascón, Edgar; Diaz, Daniel; Cerritos, René

2013-07-01

Although Entamoeba histolytica is one of the most prevalent intestinal parasites, how the different strains of this species are distributed all over the world and how different genotypes are associated with the infection outcome are yet to be fully understood. Recently, the use of a number of molecular markers has made the characterization of several genotypes in those regions with high incidence of amoebiasis possible. This work proposes the first genealogy of E. histolytica, with an haplotype network based on two tRNA gene-linked array of Short Tandem Repeats (STRs) reported until today, and 47 sequences from 39 new isolates of Mexican Amoebic Liver Abscesses (ALA) samples. One hundred and three sequences were obtained from D-A locus, their information about the geographic region of isolation as well as clinical diagnosis were also collected. One hundred and five sequences from N-K2 locus were also obtained as well as the region of isolation, but the information about clinical diagnosis was not available in all cases. The most abundant and widely distributed haplotype in the world is the one of E. histolytica HM1:IMSS strain. This was found in Mexico, Bangladesh, Japan, China and USA and is associated to symptomatic patients as well as asymptomatic cyst passers. Many other haplotypes were found only in a single country. Both genealogies suggest that there are no lineages within the networks that may be related to a particular geographic region or infection outcome. A concatenated analysis of the two molecular markers revealed 12 different combinations, which suggests the possibility of genetic recombination events. The present study is the first to propose a global genealogy of this species and suggests that there are still many genotypes to be discovered. The genotyping of new isolates will help to understand the great diversity and genetic structure of this parasite. Copyright © 2013 Elsevier B.V. All rights reserved.

Characterization of replication and conjugation of plasmid pWTY27 from a widely distributed Streptomyces species

PubMed Central

2012-01-01

Background Streptomyces species are widely distributed in natural habitats, such as soils, lakes, plants and some extreme environments. Replication loci of several Streptomyces theta-type plasmids have been reported, but are not characterized in details. Conjugation loci of some Streptomyces rolling-circle-type plasmids are identified and mechanism of conjugal transferring are described. Results We report the detection of a widely distributed Streptomyces strain Y27 and its indigenous plasmid pWTY27 from fourteen plants and four soil samples cross China by both culturing and nonculturing methods. The complete nucleotide sequence of pWTY27 consisted of 14,288 bp. A basic locus for plasmid replication comprised repAB genes and an adjacent iteron sequence, to a long inverted-repeat (ca. 105 bp) of which the RepA protein bound specifically in vitro, suggesting that RepA may recognize a second structure (e.g. a long stem-loop) of the iteron DNA. A plasmid containing the locus propagated in linear mode when the telomeres of a linear plasmid were attached, indicating a bi-directional replication mode for pWTY27. As for rolling-circle plasmids, a single traA gene and a clt sequence (covering 16 bp within traA and its adjacent 159 bp) on pWTY27 were required for plasmid transfer. TraA recognized and bound specifically to the two regions of the clt sequence, one containing all the four DC1 of 7 bp (TGACACC) and one DC2 (CCCGCCC) and most of IC1, and another covering two DC2 and part of IC1, suggesting formation of a high-ordered DNA-protein complex. Conclusions This work (i) isolates a widespread Streptomyces strain Y27 and sequences its indigenous theta-type plasmid pWTY27; (ii) identifies the replication and conjugation loci of pWTY27 and; (iii) characterizes the binding sequences of the RepA and TraA proteins. PMID:23134842

Effectiveness of teaching cognitive-behavioral techniques on locus of control in hemodialysis patients

PubMed Central

Mehrtak, Mohammad; Habibzadeh, Shahram; Farzaneh, Esmaeil; Rjaei-Khiavi, Abdollah

2017-01-01

Background Many of the cognitive behavioral models and therapeutic protocols developed so far for psychological disorders and chronic diseases have proved effective through clinical research. Objective This study aimed to determine the effectiveness of teaching cognitive-behavioral techniques on locus of control in hemodialysis patients. Methods This controlled clinical trial study was conducted in 2015 with 76 patients selected by census and treated with a hemodialysis machine in the dialysis department of Vali-Asr Hospital in the city of Meshkinshahr. A total of four patients were excluded because of their critical conditions while the rest, who were recruited, were randomly divided into two equal groups of 36 patients as the intervention and control groups. First, the locus of control was measured in both groups through a pretest, and cognitive-behavioral techniques were then taught to the intervention group during eight 45 to 90-minute sessions. The locus of control in patients of both groups was finally re-measured through a posttest. Data were collected using Rotter’s Locus of Control Inventory. The Wilcoxon test and Mann–Whitney U test were respectively used in SPSS18 for data analysis. Results In the pretest and posttest stages respectively, 4.8% and 14.3% of samples in the control group as well as 14.3% and 33.3% of samples in the intervention group enjoyed internal locus of control. The difference between the pretest and posttest scores of internal locus of control in the intervention group was significant (p=0.004), which indicates the positive effect of cognitive-behavioral psychotherapeutic intervention on internalization of locus of control in this group. Conclusions Given the external locus of control in most of the study patients and also the positive significant effect of cognitive-behavioral psychotherapy on internalization of locus of control in this group of patients, it appears necessary to have a psychology resident present in the hemodialysis department to teach the necessary cognitive-behavioral techniques to internalize the locus of control. Trial registration The trial was registered at the Thai Clinical Trial Registry (http://www.clinicaltrials.in.th) with the TCTID: TCTR20170707003. Funding The authors received no financial support for the research, authorship, and/or publication of this article. PMID:29238508

ABO blood group phenotype frequency estimation using molecular phenotyping in rhesus and cynomolgus macaques.

PubMed

Kanthaswamy, S; Ng, J; Oldt, R F; Valdivia, L; Houghton, P; Smith, D G

2017-11-01

A much larger sample (N = 2369) was used to evaluate a previously reported distribution of the A, AB and B blood group phenotypes in rhesus and cynomolgus macaques from six different regional populations. These samples, acquired from 15 different breeding and research facilities in the United States, were analyzed using a real-time quantitative polymerase chain reaction (qPCR) assay that targets single nucleotide polymorphisms (SNPs) responsible for the macaque A, B and AB phenotypes. The frequency distributions of blood group phenotypes of the two species differ significantly from each other and significant regional differentiation within the geographic ranges of each species was also observed. The B blood group phenotype was prevalent in rhesus macaques, especially those from India, while the frequencies of the A, B and AB phenotypes varied significantly among cynomolgus macaques from different geographic regions. The Mauritian cynomolgus macaques, despite having originated in Indonesia, showed significant (P ≪ .01) divergence from the Indonesian animals at the ABO blood group locus. Most Mauritian animals belonged to the B blood group while the Indonesian animals were mostly A. The close similarity in blood group frequency distributions between the Chinese rhesus and Indochinese cynomolgus macaques demonstrates that the introgression between these two species extends beyond the zone of intergradation in Indochina. This study underscores the importance of ABO blood group phenotyping of the domestic supply of macaques and their biospecimens. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Genetic diversity in Egyptian and Italian goat breeds measured with microsatellite polymorphism.

PubMed

Agha, S H; Pilla, F; Galal, S; Shaat, I; D'Andrea, M; Reale, S; Abdelsalam, A Z A; Li, M H

2008-06-01

Seven microsatellite markers were used to study genetic diversity of three Egyptian (Egyptian Baladi, Barki and Zaraibi) and two Italian (Maltese and Montefalcone) goat breeds. The microsatellites showed a high polymorphic information content (PIC) of more than 0.5 in most of the locus-breed combinations and indicated that the loci were useful in assessing within- and between-breed variability of domestic goat (Capra hircus). The expected heterozygosity of the breeds varied from 0.670 to 0.792. In the geographically wider distributed Egyptian Baladi breed there were indications for deviations from random breeding. Analysis of genetic distances and population structure grouped the three Egyptian goat breeds together, and separated them from the two Italian breeds. The studied Mediterranean breeds sampled from African and European populations seem to have differentiated from each other with only little genetic exchange between the geographically isolated populations.

A Narrow and Highly Significant Linkage Signal for Severe Bipolar Disorder in the Chromosome 5q33 Region in Latin American Pedigrees

PubMed Central

Jasinska, A.J.; Service, S.; Jawaheer, D.; DeYoung, J.; Levinson, M.; Zhang, Z.; Kremeyer, B.; Muller, H.; Aldana, I.; Garcia, J.; Restrepo, G.; Lopez, C.; Palacio, C.; Duque, C.; Parra, M.; Vega, J.; Ortiz, D.; Bedoya, G.; Mathews, C.; Davanzo, P.; Fournier, E.; Bejarano, J.; Ramirez, M.; Ortiz, C. Araya; Araya, X.; Molina, J.; Sabatti, C.; Reus, V.; Ospina, J.; Macaya, G.; Ruiz-Linares, A.; Freimer, N.B.

2016-01-01

We previously reported linkage of bipolar disorder to 5q33-q34 in families from two closely related population isolates, the Central Valley of Costa Rica (CVCR) and Antioquia, Colombia (CO). Here we present follow up results from fine-scale mapping in large CVCR and CO families segregating severe bipolar disorder, BP-I, and in 343 population trios/duos from CVCR and CO. Employing densely spaced SNPs to fine map the prior linkage peak region increases linkage evidence and clarifies the position of the putative BP-I locus. We performed two-point linkage analysis with 1134 SNPs in an approximately 9 Mb region between markers D5S410 and D5S422. Combining pedigrees from CVCR and CO yields a LOD score of 4.9 at SNP rs10035961. Two other SNPs (rs7721142 and rs1422795) within the same 94 kb region also displayed LOD scores greater than 4. This linkage peak coincides with our prior microsatellite results and suggests a narrowed BP-I susceptibility regions in these families. To investigate if the locus implicated in the familial form of BP-I also contributes to disease risk in the population, we followed up the family results with association analysis in duo and trio samples, obtaining signals within 2 Mb of the peak linkage signal in the pedigrees; rs12523547 and rs267015 (P = 0.00004 and 0.00016, respectively) in the CO sample and rs244960 in the CVCR sample and the combined sample, with P = 0.00032 and 0.00016, respectively. It remains unclear whether these association results reflect the same locus contributing to BP susceptibility within the extended pedigrees. PMID:19319892

Geographic structure of European anchovy: A nuclear-DNA study

NASA Astrophysics Data System (ADS)

Bouchenak-Khelladi, Yanis; Durand, Jean-Dominique; Magoulas, Antonios; Borsa, Philippe

2008-08-01

Atlantic-Mediterranean anchovies were genetically characterized at two polymorphic nuclear loci (intron 6 of two creatine-kinase genes) and compared to reference Engraulis albidus and E. encrasicolus samples from the northern Western Mediterranean to provide new insights into their geographic structure. Northeastern Atlantic anchovy, represented by one sample from the Canary archipelago and one sample from the Alboran Sea, were genetically distinct from Mediterranean E. encrasicolus (Weir and Cockerham's ^θ = 0.027-0.311), indicating geographic isolation from either side of the Almería-Oran oceanographic front. Generally smaller genetic differences were evident among anchovy populations from different sub-basins in the Mediterranean ( ^θ = - 0.019-0.116), the genetic differences between Black Sea and Ionian Sea/Aegean Sea anchovies being the strongest ( ^θ = 0.002-0.116). There was no evidence of the presence of E. albidus in our samples outside Camargue (northern shore of the Western Mediterranean). However, a sample from the southern Western Mediterranean appeared to be genetically intermediate between E. albidus and Mediterranean E. encrasicolus, indicating possible hybridization. Anchovy from the Benguela current system off southern Africa possessed allele frequencies characteristic of E. albidus at one locus and Northeastern Atlantic anchovy at the other locus, suggesting past introgression.

A Multiplex PCR assay to differentiate between dog and red fox.

PubMed

Weissenberger, M; Reichert, W; Mattern, R

2011-11-01

Foxes are frequently the cause of car accidents in Baden-Württemberg (BW, Germany). The domestic dog (Canis familiaris) is in close relation to the red fox (Vulpes vulpes) and the silver fox which is a coat colour variant of the red fox. As insurance claims that involve accidents with animals require authentication, we analyzed frequency distribution and allele sizes in two canine microsatellite loci in 26 dogs (different breeds) and 19 red foxes of the region of BW, Germany. Moreover, sequencing analysis was performed. Red foxes exhibited only 1 allele at each microsatellite locus, whereas in dog 7 alleles at the CPH4 locus and 6 alleles at the CPH12 locus were detected. Sequences of PCR products from the two species revealed several differences between dogs and foxes. We established a sequenced allelic ladder and give population data from dogs and red foxes from the region of BW, Germany. Using microsatellite polymorphisms is efficient in differentiating between dogs and foxes in forensic casework. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

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.

Detection of linkage between a quantitative trait and a marker locus by the lod score method: sample size and sampling considerations.

PubMed

Demenais, F; Lathrop, G M; Lalouel, J M

1988-07-01

A simulation study is here conducted to measure the power of the lod score method to detect linkage between a quantitative trait and a marker locus in various situations. The number of families necessary to detect such linkage with 80% power is assessed for different sets of parameters at the trait locus and different values of the recombination fraction. The effects of varying the mode of sampling families and the sibship size are also evaluated.

Multilocus genotyping of Giardia duodenalis in Brazilian children.

PubMed

Scalia, Luana A M; Fava, Natália M N; Soares, Rodrigo M; Limongi, Jean E; da Cunha, Maria Júlia R; Pena, Isabella F; Kalapothakis, Evanguedes; Cury, Márcia C

2016-06-01

Giardia duodenalis is a parasite of several mammalian species, including humans, distributed worldwide. This research aimed to identify the molecular assemblages/sub-assemblages of G. duodenalis and to determine the intra-assemblage genetic variation of the different genes of assemblages A and B in pre-school children in the cities of Araguari and Uberlândia, Minas Gerais, Brazil. The molecular characterization followed β-giardin (bg), glutamate dehydrogenase (gdh) and triose phosphate isomerase (tpi) protocols. Of 226 stool samples, G. duodenalis cysts were found in 45 (19.9%). The tpi gene was amplified in 34 samples: 16 assemblage A, 14 B and four mixed samples A/B. The gdh gene was amplified in 32 samples, including 14 A, 16 B and two A/B. For the bg gene, 19 samples were sequenced: nine assemblage A, five B, three E, and two mixed, A/E and B/E. Animal-specific assemblage E were identified by bg, but were not confirmed for other genes. Twelve samples were characterized by full agreement of the three genes. Two new multilocus genotyping (MLGs) for assemblage A and two new MLGs for assemblage B were also described. These findings substantiate the importance of using more than one gene protocol since the sensitivity and genetic variability changes with the locus used.Access numbers: The GenBank access numbers for the nucleotide sequences reported in this article are: JQ794877-JQ794890, JX033113-JX033118. © The Author 2016. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Molecular Identification of the Schwannomatosis Locus

DTIC Science & Technology

2006-07-01

DAMD17-03-1-0445 TITLE: Molecular Identification of the Schwannomatosis Locus PRINCIPAL INVESTIGATOR: Mia MacCollin, M.D...COVERED (From - To) 1 Jul 2005 – 30 Jun 2006 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Molecular Identification of the Schwannomatosis Locus 5b...Distribution Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Background: Schwannomatosis is a recently recognized third major type of

Molecular Identification of the Schwannomatosis Locus

DTIC Science & Technology

2004-07-01

AD Award Number: DAMD17-03-1-0445 TITLE: Molecular Identification of the Schwannomatosis Locus PRINCIPAL INVESTIGATOR: Mia M. MacCollin, M.D...COVERED (Leave blank) July 2004 Annual (1 Jul 2003 - 30 Jun 2004) 4. TITLE AND SUBTITLE 5. FUNDING NUMBERS Molecular Identification of the Schwannomatosis ...DISTRIBUTION CODE Approved for Public Release; Distribution Unlimited 13. ABSTRACT (Maximum 200 Words) Background: Schwannomatosis is a recently recognized

A Clonal Lineage of Fusarium oxysporum Circulates in the Tap Water of Different French Hospitals

PubMed Central

Sautour, Marc; Gautheron, Nadine; Laurent, Julie; Aho, Serge; Bonnin, Alain; Sixt, Nathalie; Hartemann, Philippe; Dalle, Frédéric; Steinberg, Christian

2016-01-01

ABSTRACT Fusarium oxysporum is typically a soilborne fungus but can also be found in aquatic environments. In hospitals, water distribution systems may be reservoirs for the fungi responsible for nosocomial infections. F. oxysporum was previously detected in the water distribution systems of five French hospitals. Sixty-eight isolates from water representative of all hospital units that were previously sampled and characterized by translation elongation factor 1α sequence typing were subjected to microsatellite analysis and full-length ribosomal intergenic spacer (IGS) sequence typing. All but three isolates shared common microsatellite loci and a common two-locus sequence type (ST). This ST has an international geographical distribution in both the water networks of hospitals and among clinical isolates. The ST dominant in water was not detected among 300 isolates of F. oxysporum that originated from surrounding soils. Further characterization of 15 isolates by vegetative compatibility testing allowed us to conclude that a clonal lineage of F. oxysporum circulates in the tap water of the different hospitals. IMPORTANCE We demonstrated that a clonal lineage of Fusarium oxysporum inhabits the water distribution systems of several French hospitals. This clonal lineage, which appears to be particularly adapted to water networks, represents a potential risk for human infection and raises questions about its worldwide distribution. PMID:27663024

Quantitative trait locus for reading disability on chromosome 6

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

Cardon, L.R.; Smith, S.D.; Kimberling, W.J.

1994-10-14

Interval mapping of data from two independent samples of sib pairs, at least one member of whom was reading disabled, revealed evidence for a quantitative trait locus (QTL) on chromosome 6. Results obtained from analyses of reading performance from 114 sib pairs genotyped for DNA markers localized the QTL to 6p21.3. Analyses of corresponding data from an independent sample of 50 dizygotic twin pairs provided evidence for linkage to the same region. In combination, the replicate samples yielded a x{sup 2} value of 16.73 (P = 0.0002). Examination of twin and kindred siblings with more extreme deficits in reading performancemore » yielded even stronger evidence for a QTL (x{sup 2} = 27.35, P < 0.00001). The position of the QTL was narrowly defined with a 100:1 confidence interval to a 2-centimorgan region within the human leukocyte antigen complex. 23 refs., 4 figs.« less

Sample design effects in landscape genetics

USGS Publications Warehouse

Oyler-McCance, Sara J.; Fedy, Bradley C.; Landguth, Erin L.

2012-01-01

An important research gap in landscape genetics is the impact of different field sampling designs on the ability to detect the effects of landscape pattern on gene flow. We evaluated how five different sampling regimes (random, linear, systematic, cluster, and single study site) affected the probability of correctly identifying the generating landscape process of population structure. Sampling regimes were chosen to represent a suite of designs common in field studies. We used genetic data generated from a spatially-explicit, individual-based program and simulated gene flow in a continuous population across a landscape with gradual spatial changes in resistance to movement. Additionally, we evaluated the sampling regimes using realistic and obtainable number of loci (10 and 20), number of alleles per locus (5 and 10), number of individuals sampled (10-300), and generational time after the landscape was introduced (20 and 400). For a simulated continuously distributed species, we found that random, linear, and systematic sampling regimes performed well with high sample sizes (>200), levels of polymorphism (10 alleles per locus), and number of molecular markers (20). The cluster and single study site sampling regimes were not able to correctly identify the generating process under any conditions and thus, are not advisable strategies for scenarios similar to our simulations. Our research emphasizes the importance of sampling data at ecologically appropriate spatial and temporal scales and suggests careful consideration for sampling near landscape components that are likely to most influence the genetic structure of the species. In addition, simulating sampling designs a priori could help guide filed data collection efforts.

Genetic variation of the bronze locus (MC1R) in turkeys from Southern Brazil

PubMed Central

Corso, Josmael; Hepp, Diego; Ledur, Mônica C.; Peixoto, Jane O.; Fagundes, Nelson J. R.; Freitas, Thales R. O.

2017-01-01

Abstract Domestic turkeys present several color phenotypes controlled by at least five genetic loci, but only one of these has been identified precisely: the bronze locus, which turned out to be the melanocortin-1 receptor (MC1R) gene. MC1R variation is important for breeders interested in maintaining or developing different color varieties. In this study, we sequenced most of the MC1R gene from 16 White Holland (the main commercial turkey variety) and 19 pigmented turkeys from southern Brazil with two purposes. The first was to describe the MC1R diversity in White Holland turkeys, which may serve as reservoirs of genetic diversity at this locus. The second was to test whether the traditional color classification used by Brazilian breeders is related to previously known MC1R alleles. White Holland turkeys had four different haplotypes corresponding to the bronze (b +) and black-winged bronze (b 1) alleles. Pigmented turkeys also had four haplotypes corresponding to the b + and b 1 alleles, but different haplotypes represent the most common b + allele in these two groups. The black (B) allele was absent from our samples. Overall, our results suggest that white and pigmented individuals form two different populations, and that the traditional color classification used by Brazilian breeders cannot accurately predict the genotypes at the bronze locus. PMID:28323301

Genetic variation of the bronze locus (MC1R) in turkeys from Southern Brazil.

PubMed

Corso, Josmael; Hepp, Diego; Ledur, Mônica C; Peixoto, Jane O; Fagundes, Nelson J R; Freitas, Thales R O

2017-01-01

Domestic turkeys present several color phenotypes controlled by at least five genetic loci, but only one of these has been identified precisely: the bronze locus, which turned out to be the melanocortin-1 receptor (MC1R) gene. MC1R variation is important for breeders interested in maintaining or developing different color varieties. In this study, we sequenced most of the MC1R gene from 16 White Holland (the main commercial turkey variety) and 19 pigmented turkeys from southern Brazil with two purposes. The first was to describe the MC1R diversity in White Holland turkeys, which may serve as reservoirs of genetic diversity at this locus. The second was to test whether the traditional color classification used by Brazilian breeders is related to previously known MC1R alleles. White Holland turkeys had four different haplotypes corresponding to the bronze (b+) and black-winged bronze (b1) alleles. Pigmented turkeys also had four haplotypes corresponding to the b+ and b1 alleles, but different haplotypes represent the most common b+ allele in these two groups. The black (B) allele was absent from our samples. Overall, our results suggest that white and pigmented individuals form two different populations, and that the traditional color classification used by Brazilian breeders cannot accurately predict the genotypes at the bronze locus.

DNA typing revealing high HLA-Cw polymorphism completes availability of major histocompatibility complex loci in forensic medicine.

PubMed

Keresztury, L; Rajczy, K; Tauszik, T; Gyódi, E; Petrányi, G G; Falus, A

2003-03-01

Studies of human population genetics in Hungary have revealed relevant heterogeneity in the major histocompatibility complex. In the present studies, two isolated ethnic groups were chosen: people living in the Káli Basin westward from the Danube River, and those living in Opusztaszer, a village eastward from Danube, who are known as native ancient Hungarians. Blood samples were collected from 70 people in the Káli Basin and from 45 people in Opusztaszer. The frequency of HLA-Cw alleles was determined by serology as well as by DNA typing in 46 and 32 samples of the two populations, respectively, and in 44 randomly selected subjects of Hungarian origin. Compared with a random population of cadaver donors (the deaths having resulted mostly from accidents or, in a smaller number, strokes or heart infarcts) and voluntary bone marrow donors (typed in the last 10 years) recruited from all parts of Hungary and representing the mixed Hungarian population, remarkable differences were found in haplotype and allele frequencies. HLA-A, -B, -Cw typing was performed by serology and, in the case of the HLA-Cw locus, by polymerase chain reaction (PCR)-SSP and/or PCR-SSOP techniques, as well. The PCR-SSO oligotyping procedure allowed the identification of 32 Cw alleles in contrast with the 9 serologically detectable types. Because of the combination of low antigen expression and the lack of specific serologic reagents of good quality, no HLA-Cw antigens were detectable in 41%, and only one was detected in 48%, of the investigated individuals by standard serologic typing. With PCR-SSO typing, however, 97% of the investigated individuals proved to be heterozygous for HLA-Cw alleles. The two isolated populations differed from each other, from mixed Hungarian and other Caucasian populations in HLA-Cw* allele frequencies, as well as in haplotype distribution. This newly recognized polymorphism at the HLA-Cw locus completes the availability of major histocompatibility complex typing in forensic science and practice.

Impacts of TNF-LTA SNPs/Haplotypes and Lifestyle Factors on Oral Carcinoma in an Indian Population.

PubMed

Bandil, Kapil; Singhal, Pallavi; Sharma, Upma; Hussain, Showket; Basu, Surojit; Parashari, Aditya; Singh, Veena; Sehgal, Ashok; Shivam, Animesh; Ahuja, Puneet; Bharadwaj, Mausumi; Banerjee, Basu Dev; Mehrotra, Ravi

2016-10-01

To investigate a potential association between single-nucleotide polymorphisms (SNPs) and  haplotypes at the TNFA-LTA locus and the development of oral cancer in an Indian population. In this study, 150 oral precancer/cancer samples (50 precancer and 100 cancer), along with an equal number of control samples, were genotyped. Six SNPs at the TNF-LTA locus (i.e., -238G/A, -308G/A, -857C/T, -863C/A, -1031T/C, and +252A/G) were analyzed by use of a polymerase chain reaction-restriction fragment length polymorphism method, the assay was validated by sequencing 10 % of samples. The allelic frequencies of TNFA and LTA SNPs were found to be significantly associated with the risk of oral cancer and precancerous lesions in comparison with controls (P < 0.0003). Further haplotypic analysis showed that two haplotypes (ATCTGG and ACACGG) served as risk haplotypes for oral cancer. These haplotypes were also found to be significantly and positively associated with lifestyle habits (tobacco chewing P = 0.04, odds ratio [OR] 3.4) and socioeconomic status (P = 0.01, OR 3.4). We noticed an increased percentage of risk haplotypes correlating with the aggressiveness of oral cancer. The percentages of risk haplotypes were found to be threefold higher in precancer and fourfold higher in advanced stages of oral cancer in comparison with controls. Five SNPs at the TNF-LTA locus (i.e., -308G>A, -857C>T, -863C>A, -1031T>C, and +252A>G) were found to be associated with the development of oral cancer. Two haplotypes (ATCTGG and ACACGG) emerged as major risk haplotypes for oral carcinoma progression and were also found to be associated with lifestyle factors and clinical aggressiveness. These findings make the TNF-LTA locus a suitable candidate for a future biomarker, which may be used either for early detection or for helping to improve treatment efficacy and effectiveness.

Measuring the Sensitivity of Single-locus “Neutrality Tests” Using a Direct Perturbation Approach

PubMed Central

Garrigan, Daniel; Lewontin, Richard; Wakeley, John

2010-01-01

A large number of statistical tests have been proposed to detect natural selection based on a sample of variation at a single genetic locus. These tests measure the deviation of the allelic frequency distribution observed within populations from the distribution expected under a set of assumptions that includes both neutral evolution and equilibrium population demography. The present study considers a new way to assess the statistical properties of these tests of selection, by their behavior in response to direct perturbations of the steady-state allelic frequency distribution, unconstrained by any particular nonequilibrium demographic scenario. Results from Monte Carlo computer simulations indicate that most tests of selection are more sensitive to perturbations of the allele frequency distribution that increase the variance in allele frequencies than to perturbations that decrease the variance. Simulations also demonstrate that it requires, on average, 4N generations (N is the diploid effective population size) for tests of selection to relax to their theoretical, steady-state distributions following different perturbations of the allele frequency distribution to its extremes. This relatively long relaxation time highlights the fact that these tests are not robust to violations of the other assumptions of the null model besides neutrality. Lastly, genetic variation arising under an example of a regularly cycling demographic scenario is simulated. Tests of selection performed on this last set of simulated data confirm the confounding nature of these tests for the inference of natural selection, under a demographic scenario that likely holds for many species. The utility of using empirical, genomic distributions of test statistics, instead of the theoretical steady-state distribution, is discussed as an alternative for improving the statistical inference of natural selection. PMID:19744997

Analysis of meiotic segregation, using single-sperm typing: Meiotic drive at the myotonic dystrophy locus

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

Leeflang, E.P.; Arnheim, N.; McPeek, M.S.

Meiotic drive at the myotonic dystrophy (DM) locus has recently been suggested as being responsible for maintaining the frequency, in the human population, of DM chromosomes capable of expansion to the disease state. In order to test this hypothesis, we have studied samples of single sperm from three individuals heterozygous at the DM locus, each with one allele larger and one allele smaller than 19 CTG repeats. To guard against the possible problem of differential PCR amplification rates based on the lengths of the alleles, the sperm were also typed at another closely linked marker whose allele size was unrelatedmore » to the allele size at the DM locus. Using statistical models specifically designed to study single-sperm segregation data, we find no evidence of meiotic segregation distortion. The upper limit of the two-sided 95% confidence interval for the estimate of the common segregation probability for the three donors is at or below .515 for all models considered, and no statistically significant difference from .5 is detected in any of the models. This suggests that any greater amount of segregation distortion at the myotonic dystrophy locus must result from events following sperm ejaculation. The mathematical models developed make it possible to study segregation distortion with high resolution by using sperm-typing data from any locus. 26 refs., 1 fig., 8 tabs.« less

Conclusion of LOD-score analysis for family data generated under two-locus models.

PubMed

Dizier, M H; Babron, M C; Clerget-Darpoux, F

1996-06-01

The power to detect linkage by the LOD-score method is investigated here for diseases that depend on the effects of two genes. The classical strategy is, first, to detect a major-gene (MG) effect by segregation analysis and, second, to seek for linkage with genetic markers by the LOD-score method using the MG parameters. We already showed that segregation analysis can lead to evidence for a MG effect for many two-locus models, with the estimates of the MG parameters being very different from those of the two genes involved in the disease. We show here that use of these MG parameter estimates in the LOD-score analysis may lead to a failure to detect linkage for some two-locus models. For these models, use of the sib-pair method gives a non-negligible increase of power to detect linkage. The linkage-homogeneity test among subsamples differing for the familial disease distribution provides evidence of parameter misspecification, when the MG parameters are used. Moreover, for most of the models, use of the MG parameters in LOD-score analysis leads to a large bias in estimation of the recombination fraction and sometimes also to a rejection of linkage for the true recombination fraction. A final important point is that a strong evidence of an MG effect, obtained by segregation analysis, does not necessarily imply that linkage will be detected for at least one of the two genes, even with the true parameters and with a close informative marker.

Empirical Bayes Estimation of Coalescence Times from Nucleotide Sequence Data.

PubMed

King, Leandra; Wakeley, John

2016-09-01

We demonstrate the advantages of using information at many unlinked loci to better calibrate estimates of the time to the most recent common ancestor (TMRCA) at a given locus. To this end, we apply a simple empirical Bayes method to estimate the TMRCA. This method is both asymptotically optimal, in the sense that the estimator converges to the true value when the number of unlinked loci for which we have information is large, and has the advantage of not making any assumptions about demographic history. The algorithm works as follows: we first split the sample at each locus into inferred left and right clades to obtain many estimates of the TMRCA, which we can average to obtain an initial estimate of the TMRCA. We then use nucleotide sequence data from other unlinked loci to form an empirical distribution that we can use to improve this initial estimate. Copyright © 2016 by the Genetics Society of America.

Linkage of mating-type loci distinguishes bipolar from tetrapolar mating in basidiomycetous smut fungi.

PubMed Central

Bakkeren, G; Kronstad, J W

1994-01-01

Sexual compatibility requires self vs. non-self recognition. Genetically, two compatibility or mating-type systems govern recognition in heterothallic basidiomycete fungi such as the edible and woodrotting mushrooms and the economically important rust and smut phytopathogens. A bipolar system is defined by a single genetic locus (MAT) that can have two or multiple alleles. A tetrapolar system has two loci, each with two or more specificities. We have employed two species from the genus Ustilago (smut fungi) to discover a molecular explanation for the genetic difference in mating systems. Ustilago maydis, a tetrapolar species, has two genetically unlinked loci that encode the distinct mating functions of cell fusion (a locus) and subsequent sexual development and pathogenicity (b locus). We have recently described a b locus in a bipolar species, Ustilago hordei, wherein the existence of an a locus has been suspected, but not demonstrated. We report here the cloning of an allele of the a locus (a1) from U. hordei and the discovery that physical linkage of the a and b loci in this bipolar fungus accounts for the distinct mating system. Linkage establishes a large complex MAT locus in U. hordei; this locus appears to be in a region suppressed for recombination. Images PMID:7913746

Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters

PubMed Central

Zanni, Vanessa; Eymery, Angéline; Coiffet, Michael; Zytnicki, Matthias; Luyten, Isabelle; Quesneville, Hadi; Vaury, Chantal; Jensen, Silke

2013-01-01

Most of our understanding of Drosophila heterochromatin structure and evolution has come from the annotation of heterochromatin from the isogenic y; cn bw sp strain. However, almost nothing is known about the heterochromatin’s structural dynamics and evolution. Here, we focus on a 180-kb heterochromatic locus producing Piwi-interacting RNAs (piRNA cluster), the flamenco (flam) locus, known to be responsible for the control of at least three transposable elements (TEs). We report its detailed structure in three different Drosophila lines chosen according to their capacity to repress or not to repress the expression of two retrotransposons named ZAM and Idefix, and we show that they display high structural diversity. Numerous rearrangements due to homologous and nonhomologous recombination, deletions and segmental duplications, and loss and gain of TEs are diverse sources of active genomic variation at this locus. Notably, we evidence a correlation between the presence of ZAM and Idefix in this piRNA cluster and their silencing. They are absent from flam in the strain where they are derepressed. We show that, unexpectedly, more than half of the flam locus results from recent TE insertions and that most of the elements concerned are prone to horizontal transfer between species of the melanogaster subgroup. We build a model showing how such high and constant dynamics of a piRNA master locus open the way to continual emergence of new patterns of piRNA biogenesis leading to changes in the level of transposition control. PMID:24248389

Speaking rate effects on locus equation slope.

PubMed

Berry, Jeff; Weismer, Gary

2013-11-01

A locus equation describes a 1st order regression fit to a scatter of vowel steady-state frequency values predicting vowel onset frequency values. Locus equation coefficients are often interpreted as indices of coarticulation. Speaking rate variations with a constant consonant-vowel form are thought to induce changes in the degree of coarticulation. In the current work, the hypothesis that locus slope is a transparent index of coarticulation is examined through the analysis of acoustic samples of large-scale, nearly continuous variations in speaking rate. Following the methodological conventions for locus equation derivation, data pooled across ten vowels yield locus equation slopes that are mostly consistent with the hypothesis that locus equations vary systematically with coarticulation. Comparable analyses between different four-vowel pools reveal variations in the locus slope range and changes in locus slope sensitivity to rate change. Analyses across rate but within vowels are substantially less consistent with the locus hypothesis. Taken together, these findings suggest that the practice of vowel pooling exerts a non-negligible influence on locus outcomes. Results are discussed within the context of articulatory accounts of locus equations and the effects of speaking rate change.

[Allelic variation at high-molecular-weight glutenin subunit loci in Aegilops biuncialis Vis].

PubMed

Kozub, N A; Sozinov, I A; Ksinias, I N; Sozinov, A A

2011-09-01

Alleles at the high-molecular-weight glutenin subunit loci Glu-U1 and Glu-M(b)1 were analyzed in the tetraploid species Aegilops biuncialis (UUM(b)M(b)). The material for the investigation included the collection of 39 accessions of Ae. biuncialis from Ukraine (the Crimea), one Hellenic accession, one accession of unknown origin, F2 seeds from different crosses, as well as samples from natural populations from the Crimea. Ae. umbellulata and Ae. comosa accessions were used to allocate components of the HMW glutenin subunit patterns of Ae. biuncialis to U or M(b) genomes. Eight alleles were identified at the Glu-U1 locus and ten alleles were revealed at the Glu-M(b) 1 locus. Among alleles at the Glu-M(b) 1 locus ofAe. biuncialis there were two alleles controlling the y-type subunit only and one allele encoding the x-subunit only.

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.

The Discovery of Single-Nucleotide Polymorphisms—and Inferences about Human Demographic History

PubMed Central

Wakeley, John; Nielsen, Rasmus; Liu-Cordero, Shau Neen; Ardlie, Kristin

2001-01-01

A method of historical inference that accounts for ascertainment bias is developed and applied to single-nucleotide polymorphism (SNP) data in humans. The data consist of 84 short fragments of the genome that were selected, from three recent SNP surveys, to contain at least two polymorphisms in their respective ascertainment samples and that were then fully resequenced in 47 globally distributed individuals. Ascertainment bias is the deviation, from what would be observed in a random sample, caused either by discovery of polymorphisms in small samples or by locus selection based on levels or patterns of polymorphism. The three SNP surveys from which the present data were derived differ both in their protocols for ascertainment and in the size of the samples used for discovery. We implemented a Monte Carlo maximum-likelihood method to fit a subdivided-population model that includes a possible change in effective size at some time in the past. Incorrectly assuming that ascertainment bias does not exist causes errors in inference, affecting both estimates of migration rates and historical changes in size. Migration rates are overestimated when ascertainment bias is ignored. However, the direction of error in inferences about changes in effective population size (whether the population is inferred to be shrinking or growing) depends on whether either the numbers of SNPs per fragment or the SNP-allele frequencies are analyzed. We use the abbreviation “SDL,” for “SNP-discovered locus,” in recognition of the genomic-discovery context of SNPs. When ascertainment bias is modeled fully, both the number of SNPs per SDL and their allele frequencies support a scenario of growth in effective size in the context of a subdivided population. If subdivision is ignored, however, the hypothesis of constant effective population size cannot be rejected. An important conclusion of this work is that, in demographic or other studies, SNP data are useful only to the extent that their ascertainment can be modeled. PMID:11704929

Genetic profile of scrapie codons 146, 211 and 222 in the PRNP gene locus in three breeds of dairy goats.

PubMed

Vouraki, Sotiria; Gelasakis, Athanasios I; Alexandri, Panoraia; Boukouvala, Evridiki; Ekateriniadou, Loukia V; Banos, Georgios; Arsenos, Georgios

2018-01-01

Polymorphisms at PRNP gene locus have been associated with resistance against classical scrapie in goats. Genetic selection on this gene within appropriate breeding programs may contribute to the control of the disease. The present study characterized the genetic profile of codons 146, 211 and 222 in three dairy goat breeds in Greece. A total of 766 dairy goats from seven farms were used. Animals belonged to two indigenous Greek, Eghoria (n = 264) and Skopelos (n = 287) and a foreign breed, Damascus (n = 215). Genomic DNA was extracted from blood samples from individual animals. Polymorphisms were detected in these codons using Real-Time PCR analysis and four different Custom TaqMan® SNP Genotyping Assays. Genotypic, allelic and haplotypic frequencies were calculated based on individual animal genotypes. Chi-square tests were used to examine Hardy-Weinberg equilibrium state and compare genotypic distribution across breeds. Genetic distances among the three breeds, and between these and 30 breeds reared in other countries were estimated based on haplotypic frequencies using fixation index FST with Arlequin v3.1 software; a Neighbor-Joining tree was created using PHYLIP package v3.695. Level of statistical significance was set at P = 0.01. All scrapie resistance-associated alleles (146S, 146D, 211Q and 222K) were detected in the studied population. Significant frequency differences were observed between the indigenous Greek and Damascus breeds. Alleles 222K and 146S had the highest frequency in the two indigenous and the Damascus breed, respectively (ca. 6.0%). The studied breeds shared similar haplotypic frequencies with most South Italian and Turkish breeds but differed significantly from North-Western European, Far East and some USA goat breeds. Results suggest there is adequate variation in the PRNP gene locus to support breeding programs for enhanced scrapie resistance in goats reared in Greece. Genetic comparisons among goat breeds indicate that separate breeding programs should apply to the two indigenous and the imported Damascus breeds.

Competitiveness: relations with GPA, locus of control, sex, and athletic status.

PubMed

Frederick, C M

2000-04-01

A sample of college students and college athletes completed measures of competitiveness and locus of control. In addition, self-reports of GPA and sex were provided. Negative correlations among scores on competitiveness, GPA, and scores on internal locus of control were significant. Also, there were sex and athletic status differences in competitiveness.

Absence of Interference in Association with Gene Conversion in SORDARIA FIMICOLA, and Presence of Interference in Association with Ordinary Recombination

PubMed Central

Kitani, Y.

1978-01-01

From the analysis of large samples of gene conversion asci in the g locus of Sordaria fimicola, it was found that neither the conversion event itself nor conversion-associated recombination of flanking markers cause either chiasma or chromatid interference with crossing over in a neighboring interval. The presence of more than one kind of crossover event, one causing interference the other not, is considered. The existence of two kinds of gene loci, one of single-cistron composition and the other of multiple-cistron composition, is discussed in relation to reciprocal recombination within a locus. PMID:17176535

Absence of interference in association with gene conversion in Sordaria fimicola, and presence of interference in association with ordinary recombination.

PubMed

Kitani, Y

1978-07-01

From the analysis of large samples of gene conversion asci in the g locus of Sordaria fimicola, it was found that neither the conversion event itself nor conversion-associated recombination of flanking markers cause either chiasma or chromatid interference with crossing over in a neighboring interval. The presence of more than one kind of crossover event, one causing interference the other not, is considered. The existence of two kinds of gene loci, one of single-cistron composition and the other of multiple-cistron composition, is discussed in relation to reciprocal recombination within a locus.

High-Density SNP Genotyping to Define β-Globin Locus Haplotypes

PubMed Central

Liu, Li; Muralidhar, Shalini; Singh, Manisha; Sylvan, Caprice; Kalra, Inderdeep S.; Quinn, Charles T.; Onyekwere, Onyinye C.; Pace, Betty S.

2014-01-01

Five major β-globin locus haplotypes have been established in individuals with sickle cell disease (SCD) from the Benin, Bantu, Senegal, Cameroon, and Arab-Indian populations. Historically, β-haplotypes were established using restriction fragment length polymorphism (RFLP) analysis across the β-locus, which consists of five functional β-like globin genes located on chromosome 11. Previous attempts to correlate these haplotypes as robust predictors of clinical phenotypes observed in SCD have not been successful. We speculate that the coverage and distribution of the RFLP sites located proximal to or within the globin genes are not sufficiently dense to accurately reflect the complexity of this region. To test our hypothesis, we performed RFLP analysis and high-density single nucleotide polymorphism (SNP) genotyping across the β-locus using DNA samples from either healthy African Americans with normal hemoglobin A (HbAA) or individuals with homozygous SS (HbSS) disease. Using the genotyping data from 88 SNPs and Haploview analysis, we generated a greater number of haplotypes than that observed with RFLP analysis alone. Furthermore, a unique pattern of long-range linkage disequilibrium between the locus control region and the β-like globin genes was observed in the HbSS group. Interestingly, we observed multiple SNPs within the HindIII restriction site located in the Gγ-globin intervening sequence II which produced the same RFLP pattern. These findings illustrated the inability of RFLP analysis to decipher the complexity of sequence variations that impacts genomic structure in this region. Our data suggest that high density SNP mapping may be required to accurately define β-haplotypes that correlate with the different clinical phenotypes observed in SCD. PMID:18829352

Age differences in coping and locus of control: a study of managerial stress in Hong Kong.

PubMed

Siu, O; Cooper, C L; Spector, P E; Donald, I

2001-12-01

The present study involved data collection from 3 samples of Hong Kong managers to examine mechanisms by which age would relate to work well-being. A total of 634 managers was drawn by random sampling and purposive sampling methods. The results showed that age was positively related to well-being (job satisfaction and mental well-being). Furthermore, older managers reported fewer sources of stress, better coping, and a more internal locus of control. Multiple regression analyses suggested that the relations of age with 2 well-being indicators can be attributed to various combinations of coping, work locus of control, sources of stress, managerial level, and organizational tenure.

Lateralization in Alpha-Band Oscillations Predicts the Locus and Spatial Distribution of Attention.

PubMed

Ikkai, Akiko; Dandekar, Sangita; Curtis, Clayton E

2016-01-01

Attending to a task-relevant location changes how neural activity oscillates in the alpha band (8-13Hz) in posterior visual cortical areas. However, a clear understanding of the relationships between top-down attention, changes in alpha oscillations in visual cortex, and attention performance are still poorly understood. Here, we tested the degree to which the posterior alpha power tracked the locus of attention, the distribution of attention, and how well the topography of alpha could predict the locus of attention. We recorded magnetoencephalographic (MEG) data while subjects performed an attention demanding visual discrimination task that dissociated the direction of attention from the direction of a saccade to indicate choice. On some trials, an endogenous cue predicted the target's location, while on others it contained no spatial information. When the target's location was cued, alpha power decreased in sensors over occipital cortex contralateral to the attended visual field. When the cue did not predict the target's location, alpha power again decreased in sensors over occipital cortex, but bilaterally, and increased in sensors over frontal cortex. Thus, the distribution and the topography of alpha reliably indicated the locus of covert attention. Together, these results suggest that alpha synchronization reflects changes in the excitability of populations of neurons whose receptive fields match the locus of attention. This is consistent with the hypothesis that alpha oscillations reflect the neural mechanisms by which top-down control of attention biases information processing and modulate the activity of neurons in visual cortex.

Linkage and association study of late-onset Alzheimer disease families linked to 9p21.3.

PubMed

Züchner, S; Gilbert, J R; Martin, E R; Leon-Guerrero, C R; Xu, P-T; Browning, C; Bronson, P G; Whitehead, P; Schmechel, D E; Haines, J L; Pericak-Vance, M A

2008-11-01

A chromosomal locus for late-onset Alzheimer disease (LOAD) has previously been mapped to 9p21.3. The most significant results were reported in a sample of autopsy-confirmed families. Linkage to this locus has been independently confirmed in AD families from a consanguineous Israeli-Arab community. In the present study we analyzed an expanded clinical sample of 674 late-onset AD families, independently ascertained by three different consortia. Sample subsets were stratified by site and autopsy-confirmation. Linkage analysis of a dense array of SNPs across the chromosomal locus revealed the most significant results in the 166 autopsy-confirmed families of the NIMH sample. Peak HLOD scores of 4.95 at D9S741 and 2.81 at the nearby SNP rs2772677 were obtained in a dominant model. The linked region included the cyclin-dependent kinase inhibitor 2A gene (CDKN2A), which has been suggested as an AD candidate gene. By re-sequencing all exons in the vicinity of CDKN2A in 48 AD cases, we identified and genotyped four novel SNPs, including a non-synonymous, a synonymous, and two variations located in untranslated RNA sequences. Family-based allelic and genotypic association analysis yielded significant results in CDKN2A (rs11515: PDT p = 0.003, genotype-PDT p = 0.014). We conclude that CDKN2A is a promising new candidate gene potentially contributing to AD susceptibility on chromosome 9p.

Multilocus phylogeny and cryptic diversity in Asian shrew-like moles (Uropsilus, Talpidae): implications for taxonomy and conservation

PubMed Central

2013-01-01

Background The genus Uropsilus comprises a group of terrestrial, montane mammals endemic to the Hengduan and adjacent mountains. These animals are the most primitive living talpids. The taxonomy has been primarily based on cursory morphological comparisons and the evolutionary affinities are little known. To provide insight into the systematics of this group, we estimated the first multi-locus phylogeny and conducted species delimitation, including taxon sampling throughout their distribution range. Results We obtained two mitochondrial genes (~1, 985 bp) and eight nuclear genes (~4, 345 bp) from 56 specimens. Ten distinct evolutionary lineages were recovered from the three recognized species, eight of which were recognized as species/putative species. Five of these putative species were found to be masquerading as the gracile shrew mole. The divergence time estimation results indicated that climate change since the last Miocene and the uplift of the Himalayas may have resulted in the diversification and speciation of Uropsilus. Conclusions The cryptic diversity found in this study indicated that the number of species is strongly underestimated under the current taxonomy. Two synonyms of gracilis (atronates and nivatus) should be given full species status, and the taxonomic status of another three potential species should be evaluated using extensive taxon sampling, comprehensive morphological, and morphometric approaches. Consequently, the conservation status of Uropsilus spp. should also be re-evaluated, as most of the species/potential species have very limited distribution. PMID:24161152

The Children's Perceived Locus of Causality Scale for Physical Education

ERIC Educational Resources Information Center

Pannekoek, Linda; Piek, Jan P.; Hagger, Martin S.

2014-01-01

A mixed methods design was applied to evaluate the application of the Perceived Locus of Causality scale (PLOC) to preadolescent samples in physical education settings. Subsequent to minor item adaptations to accommodate the assessment of younger samples, qualitative pilot tests were performed (N = 15). Children's reports indicated the need…

A Clonal Lineage of Fusarium oxysporum Circulates in the Tap Water of Different French Hospitals.

PubMed

Edel-Hermann, Véronique; Sautour, Marc; Gautheron, Nadine; Laurent, Julie; Aho, Serge; Bonnin, Alain; Sixt, Nathalie; Hartemann, Philippe; Dalle, Frédéric; Steinberg, Christian

2016-11-01

Fusarium oxysporum is typically a soilborne fungus but can also be found in aquatic environments. In hospitals, water distribution systems may be reservoirs for the fungi responsible for nosocomial infections. F. oxysporum was previously detected in the water distribution systems of five French hospitals. Sixty-eight isolates from water representative of all hospital units that were previously sampled and characterized by translation elongation factor 1α sequence typing were subjected to microsatellite analysis and full-length ribosomal intergenic spacer (IGS) sequence typing. All but three isolates shared common microsatellite loci and a common two-locus sequence type (ST). This ST has an international geographical distribution in both the water networks of hospitals and among clinical isolates. The ST dominant in water was not detected among 300 isolates of F. oxysporum that originated from surrounding soils. Further characterization of 15 isolates by vegetative compatibility testing allowed us to conclude that a clonal lineage of F. oxysporum circulates in the tap water of the different hospitals. We demonstrated that a clonal lineage of Fusarium oxysporum inhabits the water distribution systems of several French hospitals. This clonal lineage, which appears to be particularly adapted to water networks, represents a potential risk for human infection and raises questions about its worldwide distribution. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Association of High Myopia with Crystallin Beta A4 (CRYBA4) Gene Polymorphisms in the Linkage-Identified MYP6 Locus

PubMed Central

Ho, Daniel W. H.; Yap, Maurice K. H.; Ng, Po Wah; Fung, Wai Yan; Yip, Shea Ping

2012-01-01

Background Myopia is the most common ocular disorder worldwide and imposes tremendous burden on the society. It is a complex disease. The MYP6 locus at 22 q12 is of particular interest because many studies have detected linkage signals at this interval. The MYP6 locus is likely to contain susceptibility gene(s) for myopia, but none has yet been identified. Methodology/Principal Findings Two independent subject groups of southern Chinese in Hong Kong participated in the study an initial study using a discovery sample set of 342 cases and 342 controls, and a follow-up study using a replication sample set of 316 cases and 313 controls. Cases with high myopia were defined by spherical equivalent ≤ -8 dioptres and emmetropic controls by spherical equivalent within ±1.00 dioptre for both eyes. Manual candidate gene selection from the MYP6 locus was supported by objective in silico prioritization. DNA samples of discovery sample set were genotyped for 178 tagging single nucleotide polymorphisms (SNPs) from 26 genes. For replication, 25 SNPs (tagging or located at predicted transcription factor or microRNA binding sites) from 4 genes were subsequently examined using the replication sample set. Fisher P value was calculated for all SNPs and overall association results were summarized by meta-analysis. Based on initial and replication studies, rs2009066 located in the crystallin beta A4 (CRYBA4) gene was identified to be the most significantly associated with high myopia (initial study: P = 0.02; replication study: P = 1.88e-4; meta-analysis: P = 1.54e-5) among all the SNPs tested. The association result survived correction for multiple comparisons. Under the allelic genetic model for the combined sample set, the odds ratio of the minor allele G was 1.41 (95% confidence intervals, 1.21-1.64). Conclusions/Significance A novel susceptibility gene (CRYBA4) was discovered for high myopia. Our study also signified the potential importance of appropriate gene prioritization in candidate selection. PMID:22792142

Improved amplification results following episodes of failure to amplify at the Amelogenin Locus using PowerPlex® ESI 16 Fast System.

PubMed

Berlyne, Sigal; Oz, Carla; Einot, Naftaly; Avraham, Shlomit; Ram, Tanya; Goldberg, Miri D; Gafny, Ron

2017-07-01

In 2012 the Israel Police DNA Casework laboratory adopted the 16 STR PowerPlex ® ESI kit for routine use. The Promega Company updated this kit and developed the PowerPlex ® ESI 16 Fast System in which all autosomal primer pairs remained identical to the original set, except at the amelogenin site. The master mix was improved and optimized which allowed for direct, faster and more robust amplification. Prior to implementing the PowerPlex ® ESI 16 Fast System in our lab, we conducted a preliminary assay where 213 casework samples were amplified using the new kit. These samples had previously been extracted by one of two extraction kits employed by our lab. (the PrepFiler ExpressTM and PrepFiler BTATM Forensic DNA Extraction Kits). The amplification results from these samples were compared to samples amplified using the original PowerPlex ® ESI 16 kit. Multiple incidents of failure to amplify at the amelogenin locus were noted using the new system with the recommended protocol at a rate of 13% (28 of 213 samples). Experiments were performed to understand whether these amplification failures could be a result of primer binding site mutations, extraction method reagents and/or inhibitors. The conclusions reached following these experiments, in conjunction with consultation with the manufacturer, led to the trial of a modified amplification protocol where the suggested annealing temperature was reduced by 2 degrees. To evaluate the efficiency of this altered protocol, a comparison study was undertaken where 88 additional casework samples were chosen and amplified using both the modified 58°C and the recommended 60°C annealing temperatures. We concluded that the most effective method in our laboratory for achieving a consistent and balanced amplification at the amelogenin locus was to reduce the annealing temperature from the manufacturer's recommended 60°C to 58°C. This modification resulted in a reduction of the failure to amplify at the amelogenin locus from 13% (28/213) to 1.1% (1/88) without any observed changes to the autosomal STR amplification results. Copyright © 2017 Elsevier B.V. All rights reserved.

The locus control region is required for association of the murine β-globin locus with engaged transcription factories during erythroid maturation

PubMed Central

Ragoczy, Tobias; Bender, M.A.; Telling, Agnes; Byron, Rachel; Groudine, Mark

2006-01-01

We have examined the relationship between nuclear localization and transcriptional activity of the endogenous murine β-globin locus during erythroid differentiation. Murine fetal liver cells were separated into distinct erythroid maturation stages by fluorescence-activated cell sorting, and the nuclear position of the locus was determined at each stage. We find that the β-globin locus progressively moves away from the nuclear periphery with increasing maturation. Contrary to the prevailing notion that the nuclear periphery is a repressive compartment in mammalian cells, βmajor-globin expression begins at the nuclear periphery prior to relocalization. However, relocation of the locus to the nuclear interior with maturation is accompanied by an increase in βmajor-globin transcription. The distribution of nuclear polymerase II (Pol II) foci also changes with erythroid differentiation: Transcription factories decrease in number and contract toward the nuclear interior. Moreover, both efficient relocalization of the β-globin locus from the periphery and its association with hyperphosphorylated Pol II transcription factories require the locus control region (LCR). These results suggest that the LCR-dependent association of the β-globin locus with transcriptionally engaged Pol II foci provides the driving force for relocalization of the locus toward the nuclear interior during erythroid maturation. PMID:16705039

Evolution of IFN-λ in tetrapod vertebrates and its functional characterization in green anole lizard (Anolis carolinensis).

PubMed

Chen, Shan Nan; Zhang, Xiao Wen; Li, Li; Ruan, Bai Ye; Huang, Bei; Huang, Wen Shu; Zou, Peng Fei; Fu, Jian Ping; Zhao, Li Juan; Li, Nan; Nie, Pin

2016-08-01

IFN-λ (IFNL), i.e. type III IFN genes were found in a conserved gene locus in tetrapod vertebrates. But, a unique locus containing IFNL was found in avian. In turtle and crocodile, IFNL genes were distributed in these two separate loci. As revealed in phylogenetic trees, IFN-λs in these two different loci and other amniotes were grouped into two different clades. The conservation in gene presence and gene locus was also observed for the receptors of IFN-λ, IFN-λR1 and IL-10RB in tetrapods. It is further revealed that in North American green anole lizard Anolis carolinensis, a single IFNL gene was situated collinearly in the conserved locus as in other tetrapods, together with its receptors IFN-λR1 and IL-10RB also identified in this study. The IFN-λ and its receptors were expressed in all examined organs/tissues, and their expression was stimulated following the injection of polyI:polyC. The ISREs in promoter of IFN-λ in lizard were responsible to IRF3 as demonstrated using luciferase report system, and IFN-λ in lizard functioned through the receptors, IFN-λR1 and IL-10RB, as the up-regulation of ISGs was observed in ligand-receptor transfected, and also in recombinant IFN-λ stimulated, cell lines. Taken together, it is concluded that the mechanisms involved in type III IFN ligand-receptor system, and in its signalling pathway and its down-stream genes may be conserved in green anole lizard, and may even be so in tetrapods from xenopus to human. Copyright © 2016. Published by Elsevier Ltd.

Personality and Locus of Control among School Children

ERIC Educational Resources Information Center

Pandya, Archana A.; Jogsan, Yogesh A.

2013-01-01

The main purpose of this investigation is to find out the sex differences in personality traits and locus of control among school children. A total 60 children (30 boys and 30 girls) were taken as a sample. The research tool for personality, children personality questionnaire was used, which was made by Cattell and Porter. Locus of control was…

Metacognition: As a Predictor of One's Academic Locus of Control

ERIC Educational Resources Information Center

Arslan, Serhat; Akin, Ahmet

2014-01-01

The purpose of this study is to examine the effect of metacognition on one's academic locus of control. The study's sample group consists of 451 university students enrolled in various programs at Sakarya University, Turkey. In this study, the Metacognitive Awareness Inventory and the Academic Locus of Control Scale were used. The correlations and…

Relation of organizational citizenship behavior and locus of control.

PubMed

Turnipseed, David L; Bacon, Calvin M

2009-12-01

The relation of organizational citizenship behavior and locus of control was assessed in a sample of 286 college students (52% men; M age = 24 yr.) who worked an average of 26 hr. per week. Measures were Spector's Work Locus of Control Scale and Podsakoff, et al.'s Organization Citizenship Behavior scale. Hierarchical multiple regressions indicated positive association of scores on work locus of control with scores on each of the four tested dimensions of organizational citizenship, as well as total organizational citizenship behavior.

Individualism and collectivism: cultural orientation in locus of control and moral attribution under conditions of social change.

PubMed

Santiago, Jose H; Tarantino, Santo J

2002-12-01

This study examined the validity of the view that the constructs of individualism and collectivism are coherent cultural manifestations necessarily reflected in an individual's attribution patterns. It was hypothesized that the attribution patterns of locus of control and moral accountability would show divergent individualistic and collectivistic influences in a culture during change from a collectivist culture to an individualist culture. 98 university students from the United States and Puerto Rico were administered the Singelis Individualism-Collectivism Scale, Rotter's Locus of Control Scale, and Miller and Luthar's justice-related moral accountability vignettes. Contrary to expectation, the Puerto Rican sample scored less external in locus of control than the United States sample. No cultural differences in moral accountability were found. No strong correlations were found among the variables at the individual level of analysis. Accounting for these results included the lack of representativeness of the samples, the independence of relation between variables at different levels of analysis, and social change.

Conclusion of LOD-score analysis for family data generated under two-locus models.

PubMed Central

Dizier, M. H.; Babron, M. C.; Clerget-Darpoux, F.

1996-01-01

The power to detect linkage by the LOD-score method is investigated here for diseases that depend on the effects of two genes. The classical strategy is, first, to detect a major-gene (MG) effect by segregation analysis and, second, to seek for linkage with genetic markers by the LOD-score method using the MG parameters. We already showed that segregation analysis can lead to evidence for a MG effect for many two-locus models, with the estimates of the MG parameters being very different from those of the two genes involved in the disease. We show here that use of these MG parameter estimates in the LOD-score analysis may lead to a failure to detect linkage for some two-locus models. For these models, use of the sib-pair method gives a non-negligible increase of power to detect linkage. The linkage-homogeneity test among subsamples differing for the familial disease distribution provides evidence of parameter misspecification, when the MG parameters are used. Moreover, for most of the models, use of the MG parameters in LOD-score analysis leads to a large bias in estimation of the recombination fraction and sometimes also to a rejection of linkage for the true recombination fraction. A final important point is that a strong evidence of an MG effect, obtained by segregation analysis, does not necessarily imply that linkage will be detected for at least one of the two genes, even with the true parameters and with a close informative marker. PMID:8651311

Bovine Polledness – An Autosomal Dominant Trait with Allelic Heterogeneity

PubMed Central

Medugorac, Ivica; Seichter, Doris; Graf, Alexander; Russ, Ingolf; Blum, Helmut; Göpel, Karl Heinrich; Rothammer, Sophie; Förster, Martin; Krebs, Stefan

2012-01-01

The persistent horns are an important trait of speciation for the family Bovidae with complex morphogenesis taking place briefly after birth. The polledness is highly favourable in modern cattle breeding systems but serious animal welfare issues urge for a solution in the production of hornless cattle other than dehorning. Although the dominant inhibition of horn morphogenesis was discovered more than 70 years ago, and the causative mutation was mapped almost 20 years ago, its molecular nature remained unknown. Here, we report allelic heterogeneity of the POLLED locus. First, we mapped the POLLED locus to a ∼381-kb interval in a multi-breed case-control design. Targeted re-sequencing of an enlarged candidate interval (547 kb) in 16 sires with known POLLED genotype did not detect a common allele associated with polled status. In eight sires of Alpine and Scottish origin (four polled versus four horned), we identified a single candidate mutation, a complex 202 bp insertion-deletion event that showed perfect association to the polled phenotype in various European cattle breeds, except Holstein-Friesian. The analysis of the same candidate interval in eight Holsteins identified five candidate variants which segregate as a 260 kb haplotype also perfectly associated with the POLLED gene without recombination or interference with the 202 bp insertion-deletion. We further identified bulls which are progeny tested as homozygous polled but bearing both, 202 bp insertion-deletion and Friesian haplotype. The distribution of genotypes of the two putative POLLED alleles in large semi-random sample (1,261 animals) supports the hypothesis of two independent mutations. PMID:22737241

Contrasted patterns of selection on MHC-linked microsatellites in natural populations of the Malagasy plague reservoir.

PubMed

Tollenaere, Charlotte; Ivanova, Svilena; Duplantier, Jean-Marc; Loiseau, Anne; Rahalison, Lila; Rahelinirina, Soanandrasana; Brouat, Carine

2012-01-01

Plague (Yersinia pestis infection) is a highly virulent rodent disease that persists in many natural ecosystems. The black rat (Rattus rattus) is the main host involved in the plague focus of the central highlands of Madagascar. Black rat populations from this area are highly resistant to plague, whereas those from areas in which the disease is absent (low altitude zones of Madagascar) are susceptible. Various lines of evidence suggest a role for the Major Histocompatibility Complex (MHC) in plague resistance. We therefore used the MHC region as a candidate for detecting signatures of plague-mediated selection in Malagasy black rats, by comparing population genetic structures for five MHC-linked microsatellites and neutral markers in two sampling designs. We first compared four pairs of populations, each pair including one population from the plague focus and one from the disease-free zone. Plague-mediated selection was expected to result in greater genetic differentiation between the two zones than expected under neutrality and this was observed for one MHC-class I-linked locus (D20Img2). For this marker as well as for four other MHC-linked loci, a geographic pattern of genetic structure was found at local scale within the plague focus. This pattern would be expected if plague selection pressures were spatially variable. Finally, another MHC-class I-linked locus (D20Rat21) showed evidences of balancing selection, but it seems more likely that this selection would be related to unknown pathogens more widely distributed in Madagascar than plague.

Assignment of the gene locus for severe congenital neutropenia to chromosome 1q22 in the original Kostmann family from Northern Sweden.

PubMed

Melin, M; Entesarian, M; Carlsson, G; Garwicz, D; Klein, C; Fadeel, B; Nordenskjöld, M; Palmblad, J; Henter, J I; Dahl, N

2007-02-16

Autosomal recessive severe congenital neutropenia (SCN) or Kostmann syndrome is characterised by reduced neutrophil counts and subsequent recurrent bacterial infections. The disease was originally described in a large consanguineous pedigree from Northern Sweden. A genome-wide autozygosity scan was initiated on samples from four individuals in the original pedigree using high density single nucleotide polymorphism (SNP) genotyping arrays in order to map the disease locus. Thirty candidate regions were identified and the ascertainment of samples from two additional patients confirmed a single haplotype with significant association to the disorder (p<0.01) on chromosome 1q22. One affected individual from the original Kostmann pedigree was confirmed as a phenocopy. The minimal haplotype shared by affected individuals spans a candidate region of 1.2 Mb, containing several potential candidate genes.

A Meta-Analysis of Genome-Wide Association Studies of Growth Differentiation Factor-15 Concentration in Blood

PubMed Central

Jiang, Jiyang; Thalamuthu, Anbupalam; Ho, Jennifer E.; Mahajan, Anubha; Ek, Weronica E.; Brown, David A.; Breit, Samuel N.; Wang, Thomas J.; Gyllensten, Ulf; Chen, Ming-Huei; Enroth, Stefan; Januzzi, James L.; Lind, Lars; Armstrong, Nicola J.; Kwok, John B.; Schofield, Peter R.; Wen, Wei; Trollor, Julian N.; Johansson, Åsa; Morris, Andrew P.; Vasan, Ramachandran S.; Sachdev, Perminder S.; Mather, Karen A.

2018-01-01

Blood levels of growth differentiation factor-15 (GDF-15), also known as macrophage inhibitory cytokine-1 (MIC-1), have been associated with various pathological processes and diseases, including cardiovascular disease and cancer. Prior studies suggest genetic factors play a role in regulating blood MIC-1/GDF-15 concentration. In the current study, we conducted the largest genome-wide association study (GWAS) to date using a sample of ∼5,400 community-based Caucasian participants, to determine the genetic variants associated with MIC-1/GDF-15 blood concentration. Conditional and joint (COJO), gene-based association, and gene-set enrichment analyses were also carried out to identify novel loci, genes, and pathways. Consistent with prior results, a locus on chromosome 19, which includes nine single nucleotide polymorphisms (SNPs) (top SNP, rs888663, p = 1.690 × 10-35), was significantly associated with blood MIC-1/GDF-15 concentration, and explained 21.47% of its variance. COJO analysis showed evidence for two independent signals within this locus. Gene-based analysis confirmed the chromosome 19 locus association and in addition, a putative locus on chromosome 1. Gene-set enrichment analyses showed that the“COPI-mediated anterograde transport” gene-set was associated with MIC-1/GDF15 blood concentration with marginal significance after FDR correction (p = 0.067). In conclusion, a locus on chromosome 19 was associated with MIC-1/GDF-15 blood concentration with genome-wide significance, with evidence for a new locus (chromosome 1). Future studies using independent cohorts are needed to confirm the observed associations especially for the chromosomes 1 locus, and to further investigate and identify the causal SNPs that contribute to MIC-1/GDF-15 levels. PMID:29628937

A Meta-Analysis of Genome-Wide Association Studies of Growth Differentiation Factor-15 Concentration in Blood.

PubMed

Jiang, Jiyang; Thalamuthu, Anbupalam; Ho, Jennifer E; Mahajan, Anubha; Ek, Weronica E; Brown, David A; Breit, Samuel N; Wang, Thomas J; Gyllensten, Ulf; Chen, Ming-Huei; Enroth, Stefan; Januzzi, James L; Lind, Lars; Armstrong, Nicola J; Kwok, John B; Schofield, Peter R; Wen, Wei; Trollor, Julian N; Johansson, Åsa; Morris, Andrew P; Vasan, Ramachandran S; Sachdev, Perminder S; Mather, Karen A

2018-01-01

Blood levels of growth differentiation factor-15 (GDF-15), also known as macrophage inhibitory cytokine-1 (MIC-1), have been associated with various pathological processes and diseases, including cardiovascular disease and cancer. Prior studies suggest genetic factors play a role in regulating blood MIC-1/GDF-15 concentration. In the current study, we conducted the largest genome-wide association study (GWAS) to date using a sample of ∼5,400 community-based Caucasian participants, to determine the genetic variants associated with MIC-1/GDF-15 blood concentration. Conditional and joint (COJO), gene-based association, and gene-set enrichment analyses were also carried out to identify novel loci, genes, and pathways. Consistent with prior results, a locus on chromosome 19, which includes nine single nucleotide polymorphisms (SNPs) (top SNP, rs888663, p = 1.690 × 10 -35 ), was significantly associated with blood MIC-1/GDF-15 concentration, and explained 21.47% of its variance. COJO analysis showed evidence for two independent signals within this locus. Gene-based analysis confirmed the chromosome 19 locus association and in addition, a putative locus on chromosome 1. Gene-set enrichment analyses showed that the"COPI-mediated anterograde transport" gene-set was associated with MIC-1/GDF15 blood concentration with marginal significance after FDR correction ( p = 0.067). In conclusion, a locus on chromosome 19 was associated with MIC-1/GDF-15 blood concentration with genome-wide significance, with evidence for a new locus (chromosome 1). Future studies using independent cohorts are needed to confirm the observed associations especially for the chromosomes 1 locus, and to further investigate and identify the causal SNPs that contribute to MIC-1/GDF-15 levels.

Low Cost Upper Atmosphere Sounder (LOCUS)

NASA Astrophysics Data System (ADS)

Gerber, Daniel; Swinyard, Bruce M.; Ellison, Brian N.; Aylward, Alan D.; Aruliah, Anasuya; Plane, John M. C.; Feng, Wuhu; Saunders, Christopher; Friend, Jonathan; Bird, Rachel; Linfield, Edmund H.; Davies, A. Giles; Parkes, Steve

2014-05-01

The Mesosphere - Lower Thermosphere region (MLT) is often quoted as being the least well known region of the atmosphere, meaning that measurements of this altitude range are sparser than for the neighbouring layers. The reason for this apparent lack of observations can be traced back to a combination of two facts - A) the MLT is ill suited for in-situ sampling on a global scale because the residual air drag is prohibitive for suborbital vehicles (rockets are traditionally used to sample the MLT region, but they only provide snapshot measurements both geographically, as well as temporally), and B) Some of the most important trace gases in the MLT have spectral emission lines in the THz range, a frequency band which has only just become accessible to conventional remote sensing technologies (i.e. passive heterodyne detection) thanks to ongoing technology development, but which still poses massive - often prohibitive - demands on the complexity, weight and power consumption of satellite borne remote sensing detectors. To mitigate the substantial power requirements of a Local Oscillator (LO) able to pump a heterodyne receiver at THZ frequencies, we are suggesting the use of Quantum Cascade Laser diodes (QCL). Combining a QCL LO with a sub-harmonic Schottky mixer in an integrated receiver system would allow us to build a THz passive heterodyne detector for atmospheric remote sensing that is both very compact and power efficient, and could therefore be built and launched much more cheaply than competitive systems. Many of the technologies required for such an instrument already exist at technology readiness levels (TRL) of 3-5. A consortium of RAL Space, University College London (UCL), University of Leeds, Surrey Satellite Technology Ltd (SSTL) and STAR-Dundee have been awarded a grant through the ESA In Orbit Demonstration Programme (IOD) to start developing an integrated, sub-harmonic heterodyne receiver with a QCL LO up to a TRL that would allow IOD hopefully in the near future. We describe the current instrument configuration of LOCUS, and give a first preview of the expected science return such a mission would yield. The LOCUS instrument concept calls for four spectral bands, a first band at 4.7 THz to target atomic oxygen (O), a second band at 3.5 THz to target hydroxyl (OH), a third band at 1.1 THz to cover several diatomic species (NO, CO, O3, H2O) and finally a fourth band at 0.8 THz to retrieve pointing information from molecular oxygen (O2). LOCUS would be the first satellite instrument to measure atomic oxygen on a global scale with a precision that will allow the retrieval of the global O distribution. It would also be the first time that annual and diurnal changes in O are measured. This will be a significant step forward in understanding the chemistry and dynamics of the MLT. Current indications (derived from CRISTA measurement) lead us to believe that current models only give a poor representation of upper atmospheric O. The secondary target species can help us to address additional scientific questions related to both Climate (distribution of climate relevant gases, highly geared cooling of the MLT in response to Climate change, increased occurrence of Polar Mesospheric Clouds (PMC), etc) and Space Weather (precipitation of electrically charged particles and impact on NOx chemistry, fluctuations of solar Lyman-alpha flux through shown in the the distribution of photochemically active species, etc).

Testing comparative phylogeographic models of marine vicariance and dispersal using a hierarchical Bayesian approach

PubMed Central

2008-01-01

Background Marine allopatric speciation is an enigma because pelagic larval dispersal can potentially connect disjunct populations thereby preventing reproductive and morphological divergence. Here we present a new hierarchical approximate Bayesian computation model (HABC) that tests two hypotheses of marine allopatric speciation: 1.) "soft vicariance", where a speciation involves fragmentation of a large widespread ancestral species range that was previously connected by long distance gene flow; and 2.) peripatric colonization, where speciations in peripheral archipelagos emerge from sweepstakes colonizations from central source regions. The HABC approach analyzes all the phylogeographic datasets at once in order to make across taxon-pair inferences about biogeographic processes while explicitly allowing for uncertainty in the demographic differences within each taxon-pair. Our method uses comparative phylogeographic data that consists of single locus mtDNA sequences from multiple co-distributed taxa containing pairs of central and peripheral populations. We use the method on two comparative phylogeographic data sets consisting of cowrie gastropod endemics co-distributed in the Hawaiian (11 taxon-pairs) and Marquesan archipelagos (7 taxon-pairs). Results Given the Marquesan data, we find strong evidence of simultaneous colonization across all seven cowrie gastropod endemics co-distributed in the Marquesas. In contrast, the lower sample sizes in the Hawaiian data lead to greater uncertainty associated with the Hawaiian estimates. Although, the hyper-parameter estimates point to soft vicariance in a subset of the 11 Hawaiian taxon-pairs, the hyper-prior and hyper-posterior are too similar to make a definitive conclusion. Both results are not inconsistent with what is known about the geologic history of the archipelagos. Simulations verify that our method can successfully distinguish these two histories across a wide range of conditions given sufficient sampling. Conclusion Although soft vicariance and colonization are likely to produce similar genetic patterns when a single taxon-pair is used, our hierarchical Bayesian model can potentially detect if either history is a dominant process across co-distributed taxon-pairs. As comparative phylogeographic datasets grow to include > 100 co-distributed taxon-pairs, the HABC approach will be well suited to dissect temporal patterns in community assembly and evolution, thereby providing a bridge linking comparative phylogeography with community ecology. PMID:19038027

Getting to the core of locus of control: Is it an evaluation of the self or the environment?

PubMed

Johnson, Russell E; Rosen, Christopher C; Chang, Chu-Hsiang Daisy; Lin, Szu-Han Joanna

2015-09-01

Responding to criticisms surrounding the structural validity of the higher order core self-evaluations (CSE) construct, in the current study we examined the appropriateness of including locus of control as an indicator of CSE. Drawing from both theoretical and empirical evidence, we argue that locus of control is more heavily influenced by evaluations of the environment compared with the other CSE traits. Using data from 4 samples, we demonstrate that model fit for the higher order CSE construct is better when locus of control is excluded versus included as a trait indicator and that the shared variance between locus of control and CSE is nominal. This does not mean that locus of control is irrelevant for CSE theory though. We propose that evaluations of the environment moderate the relations that CSE has with its outcomes. To test this proposition, we collected data from 4 unique samples that included a mix of student and employee participants, self- and other-ratings, and cross-sectional and longitudinal data. Our results revealed that locus of control moderated relations of CSE with life and job satisfaction, and supervisor-rated job performance. CSE had stronger, positive relations with these outcomes when locus of control is internal versus external. These findings broaden CSE theory by demonstrating one way in which evaluations of the environment interface with evaluations of the self. (PsycINFO Database Record (c) 2015 APA, all rights reserved).

Forensic parameters of the X-STR Decaplex system in Mexican populations.

PubMed

Mariscal Ramos, C; Martínez-Cortes, G; Ramos-González, B; Rangel-Villalobos, H

2018-03-01

We studied the X-STR decaplex system in 529 DNA female samples of Mexican populations from five geographic regions. Allele frequencies and forensic parameters were estimated in each region and in the pooled Mexican population. Genotype distribution by locus was in agreement with Hardy-Weinberg expectations in each Mexican population sample. Similarly, linkage equilibrium was demonstrated between pair of loci. Pairwise comparisons and genetic distances between Mexican, Iberoamerican and one African populations were estimated and graphically represented. Interestingly, a non-significant interpopulation differentiation was detected (Fst = 0.0021; p = .74389), which allows using a global Mexican database for forensic interpretation of X-STR genotypes. Copyright © 2017 Elsevier B.V. All rights reserved.

Lateralization in Alpha-Band Oscillations Predicts the Locus and Spatial Distribution of Attention

PubMed Central

Ikkai, Akiko; Dandekar, Sangita; Curtis, Clayton E.

2016-01-01

Attending to a task-relevant location changes how neural activity oscillates in the alpha band (8–13Hz) in posterior visual cortical areas. However, a clear understanding of the relationships between top-down attention, changes in alpha oscillations in visual cortex, and attention performance are still poorly understood. Here, we tested the degree to which the posterior alpha power tracked the locus of attention, the distribution of attention, and how well the topography of alpha could predict the locus of attention. We recorded magnetoencephalographic (MEG) data while subjects performed an attention demanding visual discrimination task that dissociated the direction of attention from the direction of a saccade to indicate choice. On some trials, an endogenous cue predicted the target’s location, while on others it contained no spatial information. When the target’s location was cued, alpha power decreased in sensors over occipital cortex contralateral to the attended visual field. When the cue did not predict the target’s location, alpha power again decreased in sensors over occipital cortex, but bilaterally, and increased in sensors over frontal cortex. Thus, the distribution and the topography of alpha reliably indicated the locus of covert attention. Together, these results suggest that alpha synchronization reflects changes in the excitability of populations of neurons whose receptive fields match the locus of attention. This is consistent with the hypothesis that alpha oscillations reflect the neural mechanisms by which top-down control of attention biases information processing and modulate the activity of neurons in visual cortex. PMID:27144717

Genetic variation at the MHC DRB1 locus is similar across Gunnison's prairie dog (Cynomys gunnisoni) colonies regardless of plague history.

PubMed

Cobble, Kacy R; Califf, Katy J; Stone, Nathan E; Shuey, Megan M; Birdsell, Dawn N; Colman, Rebecca E; Schupp, James M; Aziz, Maliha; Van Andel, Roger; Rocke, Tonie E; Wagner, David M; Busch, Joseph D

2016-04-01

Yersinia pestis was introduced to North America around 1900 and leads to nearly 100% mortality in prairie dog (Cynomys spp.) colonies during epizootic events, which suggests this pathogen may exert a strong selective force. We characterized genetic diversity at an MHC class II locus (DRB1) in Gunnison's prairie dog (C. gunnisoni) and quantified population genetic structure at the DRB1 versus 12 microsatellite loci in three large Arizona colonies. Two colonies, Seligman (SE) and Espee Ranch (ES), have experienced multiple plague-related die-offs in recent years, whereas plague has never been documented at Aubrey Valley (AV). We found fairly low allelic diversity at the DRB1 locus, with one allele (DRB1*01) at high frequency (0.67-0.87) in all colonies. Two other DRB1 alleles appear to be trans-species polymorphisms shared with the black-tailed prairie dog (C. ludovicianus), indicating that these alleles have been maintained across evolutionary time frames. Estimates of genetic differentiation were generally lower at the MHC locus (F ST = 0.033) than at microsatellite markers (F ST = 0.098). The reduced differentiation at DRB1 may indicate that selection has been important for shaping variation at MHC loci, regardless of the presence or absence of plague in recent decades. However, genetic drift has probably also influenced the DRB1 locus because its level of differentiation was not different from that of microsatellites in an F ST outlier analysis. We then compared specific MHC alleles to plague survivorship in 60 C. gunnisoni that had been experimentally infected with Y. pestis. We found that survival was greater in individuals that carried at least one copy of the most common allele (DRB1*01) compared to those that did not (60% vs. 20%). Although the sample sizes of these two groups were unbalanced, this result suggests the possibility that this MHC class II locus, or a nearby linked gene, could play a role in plague survival.

Genetic variation at the MHC DRB1 locus is similar across Gunnison's prairie dog (Cynomys gunnisoni) colonies regardless of plague history

USGS Publications Warehouse

Cobble, Kacy R.; Califf, Katy J.; Stone, Nathan E.; Shuey, Megan M.; Birdsell, Dawn; Colman, Rebecca E.; Schupp, James M.; Aziz, Maliha; Van Andel, Roger; Rocke, Tonie E.; Wagner, David M.; Busch, Joseph D.

2016-01-01

Yersinia pestis was introduced to North America around 1900 and leads to nearly 100% mortality in prairie dog (Cynomys spp.) colonies during epizootic events, which suggests this pathogen may exert a strong selective force. We characterized genetic diversity at an MHC class II locus (DRB1) in Gunnison's prairie dog (C. gunnisoni) and quantified population genetic structure at the DRB1versus 12 microsatellite loci in three large Arizona colonies. Two colonies, Seligman (SE) and Espee Ranch (ES), have experienced multiple plague-related die-offs in recent years, whereas plague has never been documented at Aubrey Valley (AV). We found fairly low allelic diversity at the DRB1 locus, with one allele (DRB1*01) at high frequency (0.67–0.87) in all colonies. Two otherDRB1 alleles appear to be trans-species polymorphisms shared with the black-tailed prairie dog (C. ludovicianus), indicating that these alleles have been maintained across evolutionary time frames. Estimates of genetic differentiation were generally lower at the MHC locus (FST = 0.033) than at microsatellite markers (FST = 0.098). The reduced differentiation at DRB1 may indicate that selection has been important for shaping variation at MHC loci, regardless of the presence or absence of plague in recent decades. However, genetic drift has probably also influenced theDRB1 locus because its level of differentiation was not different from that of microsatellites in anFST outlier analysis. We then compared specific MHC alleles to plague survivorship in 60C. gunnisoni that had been experimentally infected with Y. pestis. We found that survival was greater in individuals that carried at least one copy of the most common allele (DRB1*01) compared to those that did not (60% vs. 20%). Although the sample sizes of these two groups were unbalanced, this result suggests the possibility that this MHC class II locus, or a nearby linked gene, could play a role in plague survival.

An improved and validated RNA HLA class I SBT approach for obtaining full length coding sequences.

PubMed

Gerritsen, K E H; Olieslagers, T I; Groeneweg, M; Voorter, C E M; Tilanus, M G J

2014-11-01

The functional relevance of human leukocyte antigen (HLA) class I allele polymorphism beyond exons 2 and 3 is difficult to address because more than 70% of the HLA class I alleles are defined by exons 2 and 3 sequences only. For routine application on clinical samples we improved and validated the HLA sequence-based typing (SBT) approach based on RNA templates, using either a single locus-specific or two overlapping group-specific polymerase chain reaction (PCR) amplifications, with three forward and three reverse sequencing reactions for full length sequencing. Locus-specific HLA typing with RNA SBT of a reference panel, representing the major antigen groups, showed identical results compared to DNA SBT typing. Alleles encountered with unknown exons in the IMGT/HLA database and three samples, two with Null and one with a Low expressed allele, have been addressed by the group-specific RNA SBT approach to obtain full length coding sequences. This RNA SBT approach has proven its value in our routine full length definition of alleles. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Protein variants in Hiroshima and Nagasaki: tales of two cities.

PubMed Central

Neel, J V; Satoh, C; Smouse, P; Asakawa, J; Takahashi, N; Goriki, K; Fujita, M; Kageoka, T; Hazama, R

1988-01-01

The results of 1,465,423 allele product determinations based on blood samples from Hiroshima and Nagasaki, involving 30 different proteins representing 32 different gene products, are analyzed in a variety of ways, with the following conclusions: (1) Sibships and their parents are included in the sample. Our analysis reveals that statistical procedures designed to reduce the sample to equivalent independent genomes do not in population comparisons compensate for the familial cluster effect of rare variants. Accordingly, the data set was reduced to one representative of each sibship (937,427 allele products). (2) Both chi 2-type contrasts and a genetic distance measure (delta) reveal that rare variants (P less than .01) are collectively as effective as polymorphisms in establishing genetic differences between the two cities. (3) We suggest that rare variants that individually exhibit significant intercity differences are probably the legacy of tribal private polymorphisms that occurred during prehistoric times. (4) Despite the great differences in the known histories of the two cities, both the overall frequency of rare variants and the number of different rare variants are essentially identical in the two cities. (5) The well-known differences in locus variability are confirmed, now after adjustment for sample size differences for the various locus products; in this large series we failed to detect variants at only three of 29 loci for which sample size exceeded 23,000. (6) The number of alleles identified per locus correlates positively with subunit molecular weight. (7) Loci supporting genetic polymorphisms are characterized by more rare variants than are loci at which polymorphisms were not encountered. (8) Loci whose products do not appear to be essential for health support more variants than do loci the absence of whose product is detrimental to health. (9) There is a striking excess of rare variants over the expectation under the neutral mutation/drift/equilibrium theory. We suggest that this finding is primarily due to the relatively recent (in genetic time) agglomeration of previously separated tribal populations; efforts to test for agreement with the expectations of this theory by using data from modern cosmopolitan populations are exercises in futility. (10) All of these findings should characterize DNA variants in exons as more data become available, since the finding are the protein expression of such variants. PMID:3195587

Protein variants in Hiroshima and Nagasaki: tales of two cities.

PubMed

Neel, J V; Satoh, C; Smouse, P; Asakawa, J; Takahashi, N; Goriki, K; Fujita, M; Kageoka, T; Hazama, R

1988-12-01

The results of 1,465,423 allele product determinations based on blood samples from Hiroshima and Nagasaki, involving 30 different proteins representing 32 different gene products, are analyzed in a variety of ways, with the following conclusions: (1) Sibships and their parents are included in the sample. Our analysis reveals that statistical procedures designed to reduce the sample to equivalent independent genomes do not in population comparisons compensate for the familial cluster effect of rare variants. Accordingly, the data set was reduced to one representative of each sibship (937,427 allele products). (2) Both chi 2-type contrasts and a genetic distance measure (delta) reveal that rare variants (P less than .01) are collectively as effective as polymorphisms in establishing genetic differences between the two cities. (3) We suggest that rare variants that individually exhibit significant intercity differences are probably the legacy of tribal private polymorphisms that occurred during prehistoric times. (4) Despite the great differences in the known histories of the two cities, both the overall frequency of rare variants and the number of different rare variants are essentially identical in the two cities. (5) The well-known differences in locus variability are confirmed, now after adjustment for sample size differences for the various locus products; in this large series we failed to detect variants at only three of 29 loci for which sample size exceeded 23,000. (6) The number of alleles identified per locus correlates positively with subunit molecular weight. (7) Loci supporting genetic polymorphisms are characterized by more rare variants than are loci at which polymorphisms were not encountered. (8) Loci whose products do not appear to be essential for health support more variants than do loci the absence of whose product is detrimental to health. (9) There is a striking excess of rare variants over the expectation under the neutral mutation/drift/equilibrium theory. We suggest that this finding is primarily due to the relatively recent (in genetic time) agglomeration of previously separated tribal populations; efforts to test for agreement with the expectations of this theory by using data from modern cosmopolitan populations are exercises in futility. (10) All of these findings should characterize DNA variants in exons as more data become available, since the finding are the protein expression of such variants.

Inference on the Strength of Balancing Selection for Epistatically Interacting Loci

PubMed Central

Buzbas, Erkan Ozge; Joyce, Paul; Rosenberg, Noah A.

2011-01-01

Existing inference methods for estimating the strength of balancing selection in multi-locus genotypes rely on the assumption that there are no epistatic interactions between loci. Complex systems in which balancing selection is prevalent, such as sets of human immune system genes, are known to contain components that interact epistatically. Therefore, current methods may not produce reliable inference on the strength of selection at these loci. In this paper, we address this problem by presenting statistical methods that can account for epistatic interactions in making inference about balancing selection. A theoretical result due to Fearnhead (2006) is used to build a multi-locus Wright-Fisher model of balancing selection, allowing for epistatic interactions among loci. Antagonistic and synergistic types of interactions are examined. The joint posterior distribution of the selection and mutation parameters is sampled by Markov chain Monte Carlo methods, and the plausibility of models is assessed via Bayes factors. As a component of the inference process, an algorithm to generate multi-locus allele frequencies under balancing selection models with epistasis is also presented. Recent evidence on interactions among a set of human immune system genes is introduced as a motivating biological system for the epistatic model, and data on these genes are used to demonstrate the methods. PMID:21277883

The APOE locus advances disease progression in late onset familial Alzheimer`s disease but is not causative

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

Crawford, F.; Bennett, C.; Osborne, A.

1994-09-01

An association has been observed in several independent data sets between late onset Alzheimer`s disease (AD) and the APOE locus on chromosomes 19. We have examined the genotype in family history positive (FHP) and family history negative (FHN) cases and find a distortion of the APOE allele frequencies in accord with previous studies. However, when we examined the allele distribution of the at-risk siblings of the FHP group we found an excess of the {epsilon}4 allele which also differs significantly from historic controls but not from the affected siblings. The age distribution of the affected and unaffected siblings was similar,more » suggesting that the allelic frequency distortion in the unaffected siblings was not due to their being below the mean age of onset. Lod score linkage analysis, with age dependent onset and nonstringent specification of the genetic parameters, did not suggest linkage to the APOE locus. Furthermore, an analysis of variance of the age of disease-free survival suggested that APOE genotype contributes a small fraction of the total variance, indicating that the APOE locus is a poor predictor of disease-free survival time within late onset families. We suggest that the APOE locus enhances the rate of progression of the disease in otherwise predisposed individuals and that variation at this locus is not able in and of itself to cause this disease.« less

Characterization of arrangement and expression of the beta-2 microglobulin locus in the sandbar and nurse shark.

PubMed

Chen, Hao; Kshirsagar, Sarika; Jensen, Ingvill; Lau, Kevin; Simonson, Caitlin; Schluter, Samuel F

2010-02-01

Beta 2 microglobulin (beta2m) is an essential subunit of major histocompatibility complex (MHC) type I molecules. In this report, beta2m cDNAs were identified and sequenced from sandbar shark spleen cDNA library. Sandbar shark beta2m gene encodes one amino acid less than most teleost beta2m genes, and 3 amino acids less than mammal beta2m genes. Although sandbar shark beta2m protein contains one beta sheet less than that of human in the predicted protein structure, the overall structure of beta2m proteins is conserved during evolution. Germline gene for the beta2m in sandbar and nurse shark is present as a single locus. It contains three exons and two introns. CpG sites are evenly distributed in the shark beta2m loci. Several DNA repeat elements were also identified in the shark beta2m loci. Sequence analysis suggests that the beta2m locus is not linked to the MHC I loci in the shark genome.

Inferring Demographic History Using Two-Locus Statistics.

PubMed

Ragsdale, Aaron P; Gutenkunst, Ryan N

2017-06-01

Population demographic history may be learned from contemporary genetic variation data. Methods based on aggregating the statistics of many single loci into an allele frequency spectrum (AFS) have proven powerful, but such methods ignore potentially informative patterns of linkage disequilibrium (LD) between neighboring loci. To leverage such patterns, we developed a composite-likelihood framework for inferring demographic history from aggregated statistics of pairs of loci. Using this framework, we show that two-locus statistics are more sensitive to demographic history than single-locus statistics such as the AFS. In particular, two-locus statistics escape the notorious confounding of depth and duration of a bottleneck, and they provide a means to estimate effective population size based on the recombination rather than mutation rate. We applied our approach to a Zambian population of Drosophila melanogaster Notably, using both single- and two-locus statistics, we inferred a substantially lower ancestral effective population size than previous works and did not infer a bottleneck history. Together, our results demonstrate the broad potential for two-locus statistics to enable powerful population genetic inference. Copyright © 2017 by the Genetics Society of America.

ULTRAVIOLET+INFRARED STAR FORMATION RATES: HICKSON COMPACT GROUPS WITH SWIFT AND SPITZER

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

Tzanavaris, P.; Hornschemeier, A. E.; Immler, S.

2010-06-10

We present Swift UVOT ultraviolet (UV; 1600-3000 A) data with complete three-band UV photometry for a sample of 41 galaxies in 11 nearby (<4500 km s{sup -1}) Hickson Compact Groups (HCGs) of galaxies. We use UVOT uvw2-band (2000 A) photometry to estimate the dust-unobscured component, SFR{sub UV}, of the total star formation rate, SFR{sub TOTAL}. We use Spitzer MIPS 24 {mu}m photometry to estimate SFR{sub IR}, the component of SFR{sub TOTAL} that suffers dust extinction in the UV and is re-emitted in the IR. By combining the two components, we obtain SFR{sub TOTAL} estimates for all HCG galaxies. We obtainmore » total stellar mass, M {sub *}, estimates by means of Two Micron All Sky Survey K{sub s} -band luminosities, and use them to calculate specific star formation rates, SSFR {identical_to} SFR{sub TOTAL}/M {sub *}. SSFR values show a clear and significant bimodality, with a gap between low ({approx}<3.2 x 10{sup -11} yr{sup -1}) and high-SSFR ({approx_gt}1.2 x 10{sup -10} yr{sup -1}) systems. We compare this bimodality to the previously discovered bimodality in {alpha}{sub IRAC}, the MIR activity index from a power-law fit to the Spitzer IRAC 4.5-8 {mu}m data for these galaxies. We find that all galaxies with {alpha}{sub IRAC} {<=} 0 ( >0) are in the high- (low-) SSFR locus, as expected if high levels of star-forming activity power MIR emission from polycyclic aromatic hydrocarbon molecules and a hot dust continuum. Consistent with this finding, all elliptical/S0 galaxies are in the low-SSFR locus, while 22 out of 24 spirals/irregulars are in the high-SSFR locus, with two borderline cases. We further divide our sample into three subsamples (I, II, and III) according to decreasing H I richness of the parent galaxy group to which a galaxy belongs. Consistent with the SSFR and {alpha}{sub IRAC} bimodality, 12 out of 15 type I (11 out of 12 type III) galaxies are in the high- (low-) SSFR locus, while type II galaxies span almost the full range of SSFR values. We use the Spitzer Infrared Nearby Galaxy Survey (SINGS) to construct a comparison subsample of galaxies that (1) match HCG galaxies in J-band total galaxy luminosity and (2) are not strongly interacting and largely isolated. This selection eliminates mostly low-luminosity dwarfs and galaxies with some degree of peculiarity, providing a substantially improved, quiescent control sample. Unlike HCG galaxies, galaxies in the comparison SINGS subsample are continuously distributed both in SSFR and {alpha}{sub IRAC}, although they show ranges in SFR{sub TOTAL} values, morphologies and stellar masses similar to those for HCG systems. We test the SSFR bimodality against a number of uncertainties, and find that these can only lead to its further enhancement. Excluding galaxies belonging to HCGs with three giant galaxies (triplets) leaves both the SSFR and the {alpha}{sub IRAC} bimodality completely unaffected. We interpret these results as further evidence that an environment characterized by high galaxy number densities and low galaxy velocity dispersions, such as the one found in compact groups, plays a key role in accelerating galaxy evolution by enhancing star formation processes in galaxies and favoring a fast transition to quiescence.« less

Ultraviolet+Infrared Star Formation Rates: Hickson Compact Groups with Swift and SPitzer

NASA Technical Reports Server (NTRS)

Tzanavaris, P.; Hornschemeier, A. E.; Gallagher, S. C.; Johnson, K. E.; Gronwall, C.; Immler, S.; Reines, A. E.; Hoversten, E.; Charlton, J. C.

2010-01-01

We present Swift UVOT ultraviolet (UV; 1600-3000 A) data with complete three-band UV photometry for a sample of 41 galaxies in 11 nearby (<4500 km/s) Hickson Compact Groups (HCGs) of galaxies. We use UVOT uvw2-band (2000A) photometry to estimate the dust-unobscured component, SFR(sub uv), of the total star formation rate, SFR(sub TOTAL). We use Spitzer MIPS 24 micron photometry to estimate SFR(sub IR), the component of SFR(sub TOTAL) that suffers dust extinction in the UV and is re-emitted in the IR. By combining the two components, we obtain SFR(sub TOTAL) estimates for all HCG galaxies. We obtain total stellar mass, M(sub *) estimates by means of Two Micron All Sky Survey K(sub s)-band luminosities, and use them to calculate specific star formation rates, SSFR is identical with SFR(sub TOTAL)/ M (sub *). SSFR values show a clear and significant bimodality, with a gap between low (approximately <3.2 x 10(exp -11) / yr) and high-SSFR (approximately > 1.2 x lO)exp -10)/yr) systems. We compare this bimodality to the previously discovered bimodality in alpha-IRAC, the MIR activity index from a power-law fit to the Spitzer IRAC 4.5-8 micron data for these galaxies. We find that all galaxies with alpha-IRAC <= 0 (> 0) are in the high- (low-) SSFR locus, as expected if high levels of star-forming activity power MIR emission from polycyclic aromatic hydrocarbon molecules and a hot dust continuum. Consistent with this finding, all elliptical/SO galaxies are in the low-SSFR locus, while 22 out of 24 spirals / irregulars are in the high-SSFR locus, with two borderline cases. We further divide our sample into three subsamples (I, II, and III) according to decreasing H I richness of the parent galaxy group to which a galaxy belongs. Consistent with the SSFR and alpha-IRAC bimodality, 12 out of 15 type I (11 out of 12 type III) galaxies are in the high- (low-) SSFR locus, while type II galaxies span almost the full range of SSFR values. We use the Spitzer Infrared Nearby Galaxy Survey (SINGS) to construct a comparison subsample of galaxies that (1) match HCG galaxies in J-band total galaxy luminosity and (2) are not strongly interacting and largely isolated. This selection eliminates mostly low-luminosity dwarfs and galaxies with some degree of peculiarity, providing a substantially improved, quiescent control sample. Unlike HCG galaxies, galaxies in the comparison SINGS subsample are continuously distributed both in SSFR and alpha-IRAC, although they show ranges in SFR(sub TOTAL) values, morphologies and stellar masses similar to those for HCG systems. We test the SSFR bimodality against a number of uncertainties, and find that these can only lead to its further enhancement. Excluding galaxies belonging to HCGs with three giant galaxies (triplets) leaves both the SSFR and the alpha-IRAC bimodality completely unaffected. We interpret these results as further evidence that an environment characterized by high galaxy number densities and low galaxy velocity dispersions, such as the one found in compact groups, plays a key role in accelerating galaxy evolution by enhancing star formation processes in galaxies and favoring a fast transition to quiescence.

HLA-A*02 allele frequencies and haplotypic associations in Koreans.

PubMed

Park, M H; Whang, D H; Kang, S J; Han, K S

2000-03-01

We have investigated the frequencies of HLA-A*02 alleles and their haplotypic associations with HLA-B and -DRB1 loci in 439 healthy unrelated Koreans, including 214 parents from 107 families. All of the 227 samples (51.7%) typed as A2 by serology were analyzed for A*02 alleles using polymerase chain reaction (PCR)-low ionic strength-single-strand conformation polymorphism (LIS-SSCP) method. A total of six different A*02 alleles were detected (A*02 allele frequency 29.6%): A*0201/9 (16.6%), *0203 (0.5%), *0206 (9.3%), *0207 (3.0%), and one each case of *0210 and *02 undetermined type. Two characteristic haplotypes showing the strongest linkage disequilibrium were A*0203-B38-DRB]*1502 and A*0207-B46-DRB1*0803. Besides these strong associations, significant two-locus associations (P<0.001) were observed for A*0201 with B61, DRB1*0901 and DRB1*1401, and for A*0206 with B48 and B61. HLA haplotypes carrying HLA-A2 showed a variable distribution of A*02 alleles, and all of the eight most common A2-B-DR haplotypes occurring at frequencies of > or =1% were variably associated with two different A*02 alleles. These results demonstrate that substantial heterogeneity is present in the distribution of HLA-A*02 alleles and related haplotypes in Koreans.

The influence of DNA degradation in formalin-fixed, paraffin-embedded (FFPE) tissue on locus-specific methylation assessment by MS-HRM.

PubMed

Daugaard, Iben; Kjeldsen, Tina E; Hager, Henrik; Hansen, Lise Lotte; Wojdacz, Tomasz K

2015-12-01

Readily accessible formalin-fixed paraffin embedded (FFPE) tissues are a highly valuable source of genetic material for molecular analyses in both research and in vitro diagnostics but frequently genetic material in those samples is highly degraded. With locus-specific methylation changes being widely investigated for use as biomarkers in various aspects of clinical disease management, we aimed to evaluate to what extent standard laboratory procedures can approximate the quality of the DNA extracted from FFPE samples prior to methylation analyses. DNA quality in 107 FFPE non-small cell lung cancer (NSCLC) samples was evaluated using spectrophotometry and gel electrophoresis. Subsequently, the quality assessment results were correlated with the results of locus specific methylation assessment with methylation sensitive high resolution melting (MS-HRM). The correlation of template quality with PCR amplification performance and HRM based methylation detection indicated a significant influence of DNA quality on PCR amplification but not on methylation assessment. In conclusion, standard laboratory procedures fairly well approximate DNA degradation of FFPE samples and DNA degradation does not seem to considerably affect locus-specific methylation assessment by MS-HRM. Copyright © 2015 Elsevier Inc. All rights reserved.

Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris.

PubMed

García-Gil, M R; Mikkonen, M; Savolainen, O

2003-05-01

Forest tree species provide many examples of well-studied adaptive differentiation, where the search for the underlying genes might be possible. In earlier studies and in our common conditions in a greenhouse, northern populations set bud earlier than southern ones. A difference in latitude of origin of one degree corresponded to a change of 1.4 days in number of days to terminal bud set of seedlings. Earlier physiological and ecological genetics work in conifers and other plants have suggested that such variation could be governed by phytochromes. Nucleotide variation was examined at two phytochrome loci (PHYP and PHYO, homologues of the Arabidopsis thaliana PHYB and PHYA, respectively) in three populations: northern Finland, southern Finland and northern Spain. In our samples of 12-15 sequences (2980 and 1156 base pairs at the two loci) we found very low nonsynonymous variation; pi was 0.0003 and 0.0002 at PHYP and PHYO loci, respectively. There was no functional differentiation between populations at the photosensory domains of either locus. The overall silent variation was also low, only 0.0024 for the PHYP locus. The low estimates of silent variation are consistent with the estimated low synonymous substitution rates between Pinus sylvestris and Picea abies at the PHYO locus. Despite the low level of nucleotide variation, haplotypic diversity was relatively high (0.42 and 0.41 for fragments of 1156 nucleotides) at the two loci.

Genome-Wide Meta-Analyses of Plasma Renin Activity and Concentration Reveal Association with the Kininogen 1 and Prekallikrein Genes

PubMed Central

Lieb, Wolfgang; Chen, Ming-Huei; Teumer, Alexander; de Boer, Rudolf A.; Lin, Honghuang; Fox, Ervin R.; Musani, Solomon K.; Wilson, James G.; Wang, Thomas J.; Völzke, Henry; Petersen, Ann-Kristin; Meisinger, Christine; Nauck, Matthias; Schlesinger, Sabrina; Li, Yong; Menard, Jöel; Hercberg, Serge; Wichmann, H.-Erich; Völker, Uwe; Rawal, Rajesh; Bidlingmaier, Martin; Hannemann, Anke; Dörr, Marcus; Rettig, Rainer; van Gilst, Wiek H.; van Veldhuisen, Dirk J.; Bakker, Stephan J.L.; Navis, Gerjan; Wallaschofski, Henri; Meneton, Pierre; van der Harst, Pim; Reincke, Martin; Vasan, Ramachandran S.; Consortium, CKDGen

2015-01-01

Background The renin-angiotensin-aldosterone-system (RAAS) is critical for regulation of blood pressure and fluid balance and influences cardiovascular remodeling. Dysregulation of the RAAS contributes to cardiovascular and renal morbidity. The genetic architecture of circulating RAAS components is incompletely understood. Methods and Results We meta-analyzed genome-wide association data for plasma renin activity (n=5,275), plasma renin concentrations (n=8,014) and circulating aldosterone (n=13,289) from up to four population-based cohorts of European and European-American ancestry, and assessed replication of the top results in an independent sample (n=6,487). Single nucleotide polymorphisms (SNPs) in two independent loci displayed associations with plasma renin activity atgenome-wide significance (p<5×10-8). A third locus was close to this threshold (rs4253311 in kallikrein B [KLKB1], p=5.5×10-8). Two of these loci replicated in an independent sample for both plasma renin and aldosterone concentrations (SNP rs5030062 in kininogen 1 [KNG1]: p=0.001 for plasma renin, p=0.024 for plasma aldosterone concentration; rs4253311 with p<0.001 for both plasma renin and aldosterone concentration). SNPs in the NEBL gene reached genome-wide significance for plasma renin concentration in the discovery sample (top SNP rs3915911, p= 8.81×10-9), but did not replicate (p=0.81). No locus reached genome-wide significance for aldosterone. SNPs rs5030062 and rs4253311 were not related to blood pressure or renal traits; in a companion study, variants in the kallikrein B locus were associated with B-type natriuretic peptide concentrations in African-Americans. Conclusions We identified two genetic loci (kininogen 1 and kallikrein B) influencing key components of the RAAS, consistent with the close interrelation between the kallikrein-kinin system and the RAAS. PMID:25477429

Locus of control, sources of motivation, and mental boundaries as antecedents of leader-member exchange quality.

PubMed

Barbuto, John E; Finch, Weltmer Dayna; Pennisi, Lisa A

2010-02-01

In this study were examined leaders' and members' scores on locus of control, sources of motivation, and mental boundaries to predict the quality of leader-member exchanges. 80 elected officials and their 388 direct reports were sampled in a field study. Analysis indicated followers' scores on locus of control, leaders' scores of self-concept internal motivation, leaders' scores on locus of control, and followers' rated goal-internalization motivation were positively related to leader-member exchanges. Implications and directions for research are discussed.

Association in Long-Evans hooded rats of red cell 2,3-diphosphoglycerate levels with hemoglobin types.

PubMed

Brewer, G; Gilman, J; Noble, N; Crews, V

1978-08-01

Two sublines of commercially available Long-Evans hooded rats have been developed by genetic selection. These sublines have widely differing levels of erythrocyte 2,3-diphosphoglycerate (DPG) due to different alleles at a single genetic locus. In the present work, it is shown that rats from the commercial population are also polymorphic at a hemoglobin locus, probably involving two alleles of the IIIbeta-globin chain locus. Particular hemoglobin types have been found to be strongly associated with certain DPG types, not only in the high-DPG and low-DPG lines but also in the commercial population. Two explanations for this association are considered. One is a single-locus hypothesis, with hemoglobin allelic variation causing DPG variation, and the other is a two-locus hypothesis, with marked linkage disequilibrium.

A comparative analysis of genetic variation in rootstocks and scions of old olive trees - a window into the history of olive cultivation practices and past genetic variation.

PubMed

Barazani, Oz; Westberg, Erik; Hanin, Nir; Dag, Arnon; Kerem, Zohar; Tugendhaft, Yizhar; Hmidat, Mohammed; Hijawi, Thameen; Kadereit, Joachim W

2014-05-28

Past clonal propagation of olive trees is intimately linked to grafting. However, evidence on grafting in ancient trees is scarce, and not much is known about the source of plant material used for rootstocks. Here, the Simple Sequence Repeat (SSR) marker technique was used to study genetic diversity of rootstocks and scions in ancient olive trees from the Levant and its implications for past cultivation of olives. Leaf samples were collected from tree canopies (scions) and shoots growing from the trunk base (suckers). A total of 310 trees were sampled in 32 groves and analyzed with 14 SSR markers. In 82.7% of the trees in which both scion and suckers could be genotyped, these were genetically different, and thus suckers were interpreted to represent the rootstock of grafted trees. Genetic diversity values were much higher among suckers than among scions, and 194 and 87 multi-locus genotypes (MLGs) were found in the two sample groups, respectively. Only five private alleles were found among scions, but 125 among suckers. A frequency analysis revealed a bimodal distribution of genetic distance among MLGs, indicating the presence of somatic mutations within clones. When assuming that MLGs differing by one mutation are identical, scion and sucker MLGs were grouped in 20 and 147 multi-locus lineages (MLLs). The majority of scions (90.0%) belonged to a single common MLL, whereas 50.5% of the suckers were single-sample MLLs. However, one MLL was specific to suckers and found in 63 (22.6%) of the samples. Our results provide strong evidence that the majority of olive trees in the study are grafted, that the large majority of scions belong to a single ancient cultivar containing somatic mutations, and that the widespread occurrence of one sucker genotype may imply rootstock selection. For the majority of grafted trees it seems likely that saplings were used as rootstocks; their genetic diversity probably is best explained as the result of a long history of sexual reproduction involving cultivated, feral and wild genotypes.

A comparative analysis of genetic variation in rootstocks and scions of old olive trees – a window into the history of olive cultivation practices and past genetic variation

PubMed Central

2014-01-01

Background Past clonal propagation of olive trees is intimately linked to grafting. However, evidence on grafting in ancient trees is scarce, and not much is known about the source of plant material used for rootstocks. Here, the Simple Sequence Repeat (SSR) marker technique was used to study genetic diversity of rootstocks and scions in ancient olive trees from the Levant and its implications for past cultivation of olives. Leaf samples were collected from tree canopies (scions) and shoots growing from the trunk base (suckers). A total of 310 trees were sampled in 32 groves and analyzed with 14 SSR markers. Results In 82.7% of the trees in which both scion and suckers could be genotyped, these were genetically different, and thus suckers were interpreted to represent the rootstock of grafted trees. Genetic diversity values were much higher among suckers than among scions, and 194 and 87 multi-locus genotypes (MLGs) were found in the two sample groups, respectively. Only five private alleles were found among scions, but 125 among suckers. A frequency analysis revealed a bimodal distribution of genetic distance among MLGs, indicating the presence of somatic mutations within clones. When assuming that MLGs differing by one mutation are identical, scion and sucker MLGs were grouped in 20 and 147 multi-locus lineages (MLLs). The majority of scions (90.0%) belonged to a single common MLL, whereas 50.5% of the suckers were single-sample MLLs. However, one MLL was specific to suckers and found in 63 (22.6%) of the samples. Conclusions Our results provide strong evidence that the majority of olive trees in the study are grafted, that the large majority of scions belong to a single ancient cultivar containing somatic mutations, and that the widespread occurrence of one sucker genotype may imply rootstock selection. For the majority of grafted trees it seems likely that saplings were used as rootstocks; their genetic diversity probably is best explained as the result of a long history of sexual reproduction involving cultivated, feral and wild genotypes. PMID:24886387

Meta-analysis of Parkinson disease: Identification of a novel locus, RIT2

PubMed Central

Pankratz, Nathan; Beecham, Gary W.; DeStefano, Anita L.; Dawson, Ted M.; Doheny, Kimberly F.; Factor, Stewart A.; Hamza, Taye H.; Hung, Albert Y.; Hyman, Bradley T.; Ivinson, Adrian J.; Krainc, Dmitri; Latourelle, Jeanne C.; Clark, Lorraine N.; Marder, Karen; Martin, Eden R.; Mayeux, Richard; Ross, Owen A.; Scherzer, Clemens R.; Simon, David K.; Tanner, Caroline; Vance, Jeffery M.; Wszolek, Zbigniew K.; Zabetian, Cyrus P.; Myers, Richard H.; Payami, Haydeh; Scott, William K.; Foroud, Tatiana

2011-01-01

Objective Genome-wide association (GWAS) methods have identified genes contributing to Parkinson disease (PD); we sought to identify additional genes associated with PD susceptibility. Methods A two stage design was used. First, individual level genotypic data from five recent PD GWAS (Discovery Sample: 4,238 PD cases and 4,239 controls) were combined. Following imputation, a logistic regression model was employed in each dataset to test for association with PD susceptibility and results from each dataset were meta-analyzed. Second, 768 SNPs were genotyped in an independent Replication Sample (3,738 cases and 2,111 controls). Results Genome-wide significance was reached for SNPs in SNCA (rs356165, G: odds ratio (OR)=1.37; p=9.3 × 10−21), MAPT (rs242559, C: OR=0.78; p=1.5 × 10−10), GAK/DGKQ (rs11248051, T:OR=1.35; p=8.2 × 10−9/ rs11248060, T: OR=1.35; p=2.0×10−9), and the HLA region (rs3129882, A: OR=0.83; p=1.2 × 10−8), which were previously reported. The Replication Sample confirmed the associations with SNCA, MAPT, and the HLA region and also with GBA (E326K OR=1.71; p=5 × 10−8 Combined Sample) (N370 OR=3.08; p=7 × 10−5 Replication sample). A novel PD susceptibility locus, RIT2, on chromosome 18 (rs12456492; p=5 × 10−5 Discovery Sample; p=1.52 × 10−7 Replication sample; p=2 × 10−10 Combined Sample) was replicated. Conditional analyses within each of the replicated regions identified distinct SNP associations within GBA and SNCA, suggesting that there may be multiple risk alleles within these genes. Interpretation We identified a novel PD susceptibility locus, RIT2, replicated several previously identified loci, and identified more than one risk allele within SNCA and GBA. PMID:22451204

Distribution of HLA-A,B alleles in 13 panels of blood donors in France.

PubMed

Prevost, P; Busson, M; Marcelli-Barge, A

1984-05-01

In this study, we analysed 13 samples of the French population--4147 non-related individuals living in Bordeaux, Brest, Caen, Dijon, Limoges, Lyon, Marseille, Nancy, Paris, Poitiers, Rennes, Strasbourg and Toulouse--all of whom were typed for 10 alleles of the HLA-A locus and 16 alleles of the HLA-B locus. The results showed a strong heterogeneity (chi 2 = 675.13 for 324 df, p less than 10(5)). A diagram has been drawn up, showing the matrix of genetic distances obtained thanks to the B2 of Balkrishnan & Sanghvi (1968). This diagram enables us to envisage the hypothesis of 6 homogeneous clusters. A partition of chi 2 was used to test this 6 luster hypothesis: Paris and Caen (p = 0.98); Nancy, Strasbourg (p less than 5%); Rennes, Brest (p less than 1%); Dijon, Lyon, Marseille (p = 0.89); Limoges, Poitiers (p = 0.18); Toulouse, Bordeaux (p less than 10(-5)). The heterogeneity within these clusters represents only 1/43 of the total heterogeneity.

Perceived health promotion practice by older women: use of herbal products.

PubMed

Yoon, Saunjoo Lee; Horne, Claydell H

2004-07-01

Women age 65 and older appear to use herbal products as well as multiple prescribed and non-prescribed drugs as part of their health-promoting practice. The purpose of this study was to identify changes in herbal-product use in a sample of older women during an 18-month period and to explore differences in locus of control and perceived health competence between herbal-product users and non-users. A longitudinal and descriptive study design was used. Instruments used to guide the two sets of structured interviews included the Multidimensional Health Locus of Control (MHLC), the Perceived Health Competence Scale (PHCS), and a questionnaire about herbal-product use. The prevalence of herbal-product usage and the number of products used remained consistent between the initial and follow-up interviews, with 43% of the participants using an average of 2.6 herbal products. Neither MHLC nor PHCS scores differed between herbal-product users and non-users. Mean scores of women in the study indicated higher internal than external locus of control.

Sexually Antagonistic Selection in Human Male Homosexuality

PubMed Central

Camperio Ciani, Andrea; Cermelli, Paolo; Zanzotto, Giovanni

2008-01-01

Several lines of evidence indicate the existence of genetic factors influencing male homosexuality and bisexuality. In spite of its relatively low frequency, the stable permanence in all human populations of this apparently detrimental trait constitutes a puzzling ‘Darwinian paradox’. Furthermore, several studies have pointed out relevant asymmetries in the distribution of both male homosexuality and of female fecundity in the parental lines of homosexual vs. heterosexual males. A number of hypotheses have attempted to give an evolutionary explanation for the long-standing persistence of this trait, and for its asymmetric distribution in family lines; however a satisfactory understanding of the population genetics of male homosexuality is lacking at present. We perform a systematic mathematical analysis of the propagation and equilibrium of the putative genetic factors for male homosexuality in the population, based on the selection equation for one or two diallelic loci and Bayesian statistics for pedigree investigation. We show that only the two-locus genetic model with at least one locus on the X chromosome, and in which gene expression is sexually antagonistic (increasing female fitness but decreasing male fitness), accounts for all known empirical data. Our results help clarify the basic evolutionary dynamics of male homosexuality, establishing this as a clearly ascertained sexually antagonistic human trait. PMID:18560521

CoLIde

PubMed Central

Mohorianu, Irina; Stocks, Matthew Benedict; Wood, John; Dalmay, Tamas; Moulton, Vincent

2013-01-01

Small RNAs (sRNAs) are 20–25 nt non-coding RNAs that act as guides for the highly sequence-specific regulatory mechanism known as RNA silencing. Due to the recent increase in sequencing depth, a highly complex and diverse population of sRNAs in both plants and animals has been revealed. However, the exponential increase in sequencing data has also made the identification of individual sRNA transcripts corresponding to biological units (sRNA loci) more challenging when based exclusively on the genomic location of the constituent sRNAs, hindering existing approaches to identify sRNA loci.   To infer the location of significant biological units, we propose an approach for sRNA loci detection called CoLIde (Co-expression based sRNA Loci Identification) that combines genomic location with the analysis of other information such as variation in expression levels (expression pattern) and size class distribution. For CoLIde, we define a locus as a union of regions sharing the same pattern and located in close proximity on the genome. Biological relevance, detected through the analysis of size class distribution, is also calculated for each locus. CoLIde can be applied on ordered (e.g., time-dependent) or un-ordered (e.g., organ, mutant) series of samples both with or without biological/technical replicates. The method reliably identifies known types of loci and shows improved performance on sequencing data from both plants (e.g., A. thaliana, S. lycopersicum) and animals (e.g., D. melanogaster) when compared with existing locus detection techniques. CoLIde is available for use within the UEA Small RNA Workbench which can be downloaded from: http://srna-workbench.cmp.uea.ac.uk. PMID:23851377

CoLIde: a bioinformatics tool for CO-expression-based small RNA Loci Identification using high-throughput sequencing data.

PubMed

Mohorianu, Irina; Stocks, Matthew Benedict; Wood, John; Dalmay, Tamas; Moulton, Vincent

2013-07-01

Small RNAs (sRNAs) are 20-25 nt non-coding RNAs that act as guides for the highly sequence-specific regulatory mechanism known as RNA silencing. Due to the recent increase in sequencing depth, a highly complex and diverse population of sRNAs in both plants and animals has been revealed. However, the exponential increase in sequencing data has also made the identification of individual sRNA transcripts corresponding to biological units (sRNA loci) more challenging when based exclusively on the genomic location of the constituent sRNAs, hindering existing approaches to identify sRNA loci. To infer the location of significant biological units, we propose an approach for sRNA loci detection called CoLIde (Co-expression based sRNA Loci Identification) that combines genomic location with the analysis of other information such as variation in expression levels (expression pattern) and size class distribution. For CoLIde, we define a locus as a union of regions sharing the same pattern and located in close proximity on the genome. Biological relevance, detected through the analysis of size class distribution, is also calculated for each locus. CoLIde can be applied on ordered (e.g., time-dependent) or un-ordered (e.g., organ, mutant) series of samples both with or without biological/technical replicates. The method reliably identifies known types of loci and shows improved performance on sequencing data from both plants (e.g., A. thaliana, S. lycopersicum) and animals (e.g., D. melanogaster) when compared with existing locus detection techniques. CoLIde is available for use within the UEA Small RNA Workbench which can be downloaded from: http://srna-workbench.cmp.uea.ac.uk.

Identification and typing of Brucella spp. in stranded harbour porpoises (Phocoena phocoena) on the Dutch coast.

PubMed

Maio, Elisa; Begeman, Lineke; Bisselink, Yvette; van Tulden, Peter; Wiersma, Lidewij; Hiemstra, Sjoukje; Ruuls, Robin; Gröne, Andrea; Roest, Hendrik-Ido-Jan; Willemsen, Peter; van der Giessen, Joke

2014-09-17

The presence of Brucella (B.) spp. in harbour porpoises stranded between 2008 and 2011 along the Dutch coast was studied. A selection of 265 tissue samples from 112 animals was analysed using conventional and molecular methods. In total, 4.5% (5/112) of the animals corresponding with 2.3% (6/265) Brucella positive tissue samples were Brucella positive by culture and these were all confirmed by real-time polymerase chain reaction (real-time PCR) based on the insertion element 711 (IS711). In addition, two more Brucella-positive tissue samples from two animals collected in 2011 were identified using real-time PCR resulting in an overall Brucella prevalence of 6.3% (7/112 animals). Brucella spp. were obtained from lungs (n=3), pulmonary lymph node (n=3) and lungworms (n=2). Multi Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) typing based on the MLVA-16 showed that the Brucella isolates were B. ceti. Additional in silico Multi Locus Sequence typing (MLST) after whole genome sequencing of the 6 Brucella isolates confirmed B. ceti ST 23. According to the Brucella 2010 MLVA database, the isolated Brucella strains encountered were of five genotypes, in two distinct subclusters divided in two different time periods of harbour porpoises collection. This study is the first population based analyses for Brucella spp. infections in cetaceans stranded along the Dutch coast. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Genome-Wide Association Study of Multiple Sclerosis Confirms a Novel Locus at 5p13.1

PubMed Central

Sanna, Serena; Gayán, Javier; Urcelay, Elena; Zara, Ilenia; Pitzalis, Maristella; Cavanillas, María L.; Arroyo, Rafael; Zoledziewska, Magdalena; Marrosu, Marisa; Fernández, Oscar; Leyva, Laura; Alcina, Antonio; Fedetz, Maria; Moreno-Rey, Concha; Velasco, Juan; Real, Luis M.; Ruiz-Peña, Juan Luis; Cucca, Francesco

2012-01-01

Multiple Sclerosis (MS) is the most common progressive and disabling neurological condition affecting young adults in the world today. From a genetic point of view, MS is a complex disorder resulting from the combination of genetic and non-genetic factors. We aimed to identify previously unidentified loci conducting a new GWAS of Multiple Sclerosis (MS) in a sample of 296 MS cases and 801 controls from the Spanish population. Meta-analysis of our data in combination with previous GWAS was done. A total of 17 GWAS-significant SNPs, corresponding to three different loci were identified:HLA, IL2RA, and 5p13.1. All three have been previously reported as GWAS-significant. We confirmed our observation in 5p13.1 for rs9292777 using two additional independent Spanish samples to make a total of 4912 MS cases and 7498 controls (ORpooled = 0.84; 95%CI: 0.80–0.89; p = 1.36×10-9). This SNP differs from the one reported within this locus in a recent GWAS. Although it is unclear whether both signals are tapping the same genetic association, it seems clear that this locus plays an important role in the pathogenesis of MS. PMID:22570697

Genetic variation in a compound short tandem repeat/Alu haplotype system at the SB19.3 locus: properties and interpretation.

PubMed

Gaspar, Paulo; Seixas, Susana; Rocha, Jorge

2004-04-01

The genetic variation at a compound nonrecombining haplotype system, consisting of the previously reported SB19.3 Alu insertion polymorphism and a newly identified adjacent short tandem repeat (STR), was studied in population samples from Portugal and São Tomé (Gulf of Guinea, West Africa). Age estimates based on the linked microsatellite variation suggest that the Alu insertion occurred about 190,000 years ago. In accordance with the global patterns of distribution of human genetic variation, the highest haplotype diversity was found in the African sample. This excess in African diversity was due to both a substantial reduction in heterozygosity at the Alu polymorphism and a lower STR variability associated with the predominant Alu insertion allele in the Portuguese sample. The high level of interpopulation differentiation observed at the Alu locus (F(ST) = 0.43) was interpreted under alternative selective and demographic scenarios. The need for compatibility between patterns of variation at the STR and Alu loci could be used to restrict the range of selection coefficients in selection-driven genetic hitchhiking frameworks and to favor demographic scenarios dominated by larger pre-expansion African population sizes. Taken together, the data show that the SB19.3 Alu-STR system is an informative marker that can be included in more extended batteries of compound haplotypes used in human evolutionary studies.

Polymorphism at the merozoite surface protein-3alpha locus of Plasmodium vivax: global and local diversity.

PubMed

Bruce, M C; Galinski, M R; Barnwell, J W; Snounou, G; Day, K P

1999-10-01

Allelic diversity at the Plasmodium vivax merozoite surface protein-3alpha (PvMsp-3alpha) locus was investigated using a combined polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP) protocol. Symptomatic patient isolates from global geographic origins showed a high level of polymorphism at the nucleotide level. These samples were used to validate the sensitivity, specificity, and reproducibility of the PCR/RFLP method. It was then used to investigate PvMsp3alpha diversity in field samples from children living in a single village in a malaria-endemic region of Papua New Guinea, with the aim of assessing the usefulness of this locus as an epidemiologic marker of P. vivax infections. Eleven PvMsp-3alpha alleles were distinguishable in 16 samples with single infections, revealing extensive parasite polymorphism within this restricted area. Multiple infections were easily detected and accounted for 5 (23%) of 22 positive samples. Pairs of samples from individual children provided preliminary evidence for high turnover of P. vivax populations.

The population genetics of the alpha-2 globin locus of orangutans (Pongo pygmaeus).

PubMed

Steiper, Michael E; Wolfe, Nathan D; Karesh, William B; Kilbourn, Annelisa M; Bosi, Edwin J; Ruvolo, Maryellen

2005-03-01

In this study, the molecular population genetics of the orangutan's alpha-2 globin (HBA2) gene were investigated in order to test for the action of natural selection. Haplotypes from 28 orangutan chromosomes were collected from a 1.46-kilobase region of the alpha-2 globin locus. While many aspects of the data were consistent with neutrality, the observed heterogeneous distribution of polymorphisms was inconsistent with neutral expectations. Furthermore, a single amino acid variant, found in both the Bornean and the Sumatran orangutan subspecies, was associated with different alternative synonymous variants in each subspecies, suggesting that the allele may have spread separately through the two subspecies after two distinct origination events. This variant is not in Hardy-Weinberg equilibrium (HWE). These observations are consistent with neutral models that incorporate population structure and models that invoke selection. The orangutan Plasmodium parasite is a plausible selective agent that may underlie the variation at alpha-2 globin in orangutans.

Artemisinin Resistance-Associated Polymorphisms at the K13-Propeller Locus Are Absent in Plasmodium falciparum Isolates from Haiti

PubMed Central

Carter, Tamar E.; Boulter, Alexis; Existe, Alexandre; Romain, Jean R.; St. Victor, Jean Yves; Mulligan, Connie J.; Okech, Bernard A.

2015-01-01

Antimalarial drugs are a key tool in malaria elimination programs. With the emergence of artemisinin resistance in southeast Asia, an effort to identify molecular markers for surveillance of resistant malaria parasites is underway. Non-synonymous mutations in the kelch propeller domain (K13-propeller) in Plasmodium falciparum have been associated with artemisinin resistance in samples from southeast Asia, but additional studies are needed to characterize this locus in other P. falciparum populations with different levels of artemisinin use. Here, we sequenced the K13-propeller locus in 82 samples from Haiti, where limited government oversight of non-governmental organizations may have resulted in low-level use of artemisinin-based combination therapies. We detected a single-nucleotide polymorphism (SNP) at nucleotide 1,359 in a single isolate. Our results contribute to our understanding of the global genomic diversity of the K13-propeller locus in P. falciparum populations. PMID:25646258

A methylation status analysis of the apomixis-specific region in Paspalum spp. suggests an epigenetic control of parthenogenesis.

PubMed

Podio, Maricel; Cáceres, Maria E; Samoluk, Sergio S; Seijo, José G; Pessino, Silvina C; Ortiz, Juan Pablo A; Pupilli, Fulvio

2014-12-01

Apomixis, a clonal plant reproduction by seeds, is controlled in Paspalum spp. by a single locus which is blocked in terms of recombination. Partial sequence analysis of the apomixis locus revealed structural features of heterochromatin, namely the presence of repetitive elements, gene degeneration, and de-regulation. To test the epigenetic control of apomixis, a study on the distribution of cytosine methylation at the apomixis locus and the effect of artificial DNA demethylation on the mode of reproduction was undertaken in two apomictic Paspalum species. The 5-methylcytosine distribution in the apomixis-controlling genomic region was studied in P. simplex by methylation-sensitive restriction fragment length polymorphism (RFLP) analysis and in P. notatum by fluorescene in situ hybridization (FISH). The effect of DNA demethylation was studied on the mode of reproduction of P. simplex by progeny test analysis of apomictic plants treated with the demethylating agent 5'-azacytidine. A high level of cytosine methylation was detected at the apomixis-controlling genomic region in both species. By analysing a total of 374 open pollination progeny, it was found that artificial demethylation had little or no effect on apospory, whereas it induced a significant depression of parthenogenesis. The results suggested that factors controlling repression of parthenogenesis might be inactivated in apomictic Paspalum by DNA methylation. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Principal component analysis and the locus of the Fréchet mean in the space of phylogenetic trees.

PubMed

Nye, Tom M W; Tang, Xiaoxian; Weyenberg, Grady; Yoshida, Ruriko

2017-12-01

Evolutionary relationships are represented by phylogenetic trees, and a phylogenetic analysis of gene sequences typically produces a collection of these trees, one for each gene in the analysis. Analysis of samples of trees is difficult due to the multi-dimensionality of the space of possible trees. In Euclidean spaces, principal component analysis is a popular method of reducing high-dimensional data to a low-dimensional representation that preserves much of the sample's structure. However, the space of all phylogenetic trees on a fixed set of species does not form a Euclidean vector space, and methods adapted to tree space are needed. Previous work introduced the notion of a principal geodesic in this space, analogous to the first principal component. Here we propose a geometric object for tree space similar to the [Formula: see text]th principal component in Euclidean space: the locus of the weighted Fréchet mean of [Formula: see text] vertex trees when the weights vary over the [Formula: see text]-simplex. We establish some basic properties of these objects, in particular showing that they have dimension [Formula: see text], and propose algorithms for projection onto these surfaces and for finding the principal locus associated with a sample of trees. Simulation studies demonstrate that these algorithms perform well, and analyses of two datasets, containing Apicomplexa and African coelacanth genomes respectively, reveal important structure from the second principal components.

Microsatellite markers for northern red oak (Fagaceae: Quercus rubra)

Treesearch

Preston R. Aldrich; Charles H. Michler; Weilin Sun; Jeanne Romero-Severson

2002-01-01

We provide primer sequences for 14 (GA)n microsatellite loci developed from northern red oak, an important timber species. We screened loci using two sets of samples. A parent-offspring set included DNA from seven acorns collected from one mother tree along with maternal DNA, to determine that all progeny carried a maternal allele at each locus....

Investigating the Latent Structure of the Teacher Efficacy Scale

ERIC Educational Resources Information Center

Wagler, Amy; Wagler, Ron

2013-01-01

This article reevaluates the latent structure of the Teacher Efficacy Scale using confirmatory factor analyses (CFAs) on a sample of preservice teachers from a public university in the U.S. Southwest. The fit of a proposed two-factor CFA model with an error correlation structure consistent with internal/ external locus of control is compared to…

Low Variation in the Polymorphic Clock Gene Poly-Q Region Despite Population Genetic Structure across Barn Swallow (Hirundo rustica) Populations

PubMed Central

Dor, Roi; Lovette, Irby J.; Safran, Rebecca J.; Billerman, Shawn M.; Huber, Gernot H.; Vortman, Yoni; Lotem, Arnon; McGowan, Andrew; Evans, Matthew R.; Cooper, Caren B.; Winkler, David W.

2011-01-01

Recent studies of several species have reported a latitudinal cline in the circadian clock gene, Clock, which influences rhythms in both physiology and behavior. Latitudinal variation in this gene may hence reflect local adaptation to seasonal variation. In some bird populations, there is also an among-individual association between Clock poly-Q genotype and clutch initiation date and incubation period. We examined Clock poly-Q allele variation in the Barn Swallow (Hirundo rustica), a species with a cosmopolitan geographic distribution and considerable variation in life-history traits that may be influenced by the circadian clock. We genotyped Barn Swallows from five populations (from three subspecies) and compared variation at the Clock locus to that at microsatellite loci and mitochondrial DNA (mtDNA). We found very low variation in the Clock poly-Q region, as >96% of individuals were homozygous, and the two other alleles at this locus were globally rare. Genetic differentiation based on the Clock poly-Q locus was not correlated with genetic differentiation based on either microsatellite loci or mtDNA sequences. Our results show that high diversity in Clock poly-Q is not general across avian species. The low Clock variation in the background of heterogeneity in microsatellite and mtDNA loci in Barn Swallows may be an outcome of stabilizing selection on the Clock locus. PMID:22216124

Factor Specific Differences in Locus of Control for Emotionally Disturbed and Normal Children

ERIC Educational Resources Information Center

Kendall, Philip C.; And Others

1976-01-01

Institutionalized emotionally disturbed boys and noninstitutionalized normal boys were administered the Nowicki-Strickland Locus of Control Scale for Children. Locus of control and separate factor scores were calculated. Helplessness factor scores, but not overall locus of control scores, differentiated the two groups. (BJG)

Globally dispersed Y chromosomal haplotypes in wild and domestic sheep.

PubMed

Meadows, J R S; Hanotte, O; Drögemüller, C; Calvo, J; Godfrey, R; Coltman, D; Maddox, J F; Marzanov, N; Kantanen, J; Kijas, J W

2006-10-01

To date, investigations of genetic diversity and the origins of domestication in sheep have utilised autosomal microsatellites and variation in the mitochondrial genome. We present the first analysis of both domestic and wild sheep using genetic markers residing on the ovine Y chromosome. Analysis of a single nucleotide polymorphism (oY1) in the SRY promoter region revealed that allele A-oY1 was present in all wild bighorn sheep (Ovis canadensis), two subspecies of thinhorn sheep (Ovis dalli), European Mouflon (Ovis musimon) and the Barbary (Ammontragis lervia). A-oY1 also had the highest frequency (71.4%) within 458 domestic sheep drawn from 65 breeds sampled from Africa, Asia, Australia, the Caribbean, Europe, the Middle East and Central Asia. Sequence analysis of a second locus, microsatellite SRYM18, revealed a compound repeat array displaying fixed differences, which identified bighorn and thinhorn sheep as distinct from the European Mouflon and domestic animals. Combined genotypic data identified 11 male-specific haplotypes that represented at least two separate lineages. Investigation of the geographical distribution of each haplotype revealed that one (H6) was both very common and widespread in the global sample of domestic breeds. The remaining haplotypes each displayed more restricted and informative distributions. For example, H5 was likely founded following the domestication of European breeds and was used to trace the recent transportation of animals to both the Caribbean and Australia. A high rate of Y chromosomal dispersal appears to have taken place during the development of domestic sheep as only 12.9% of the total observed variation was partitioned between major geographical regions.

New development and validation of 50 SSR markers in breadfruit (Artocarpus altilis, Moraceae) by next-generation sequencing.

PubMed

De Bellis, Fabien; Malapa, Roger; Kagy, Valérie; Lebegin, Stéphane; Billot, Claire; Labouisse, Jean-Pierre

2016-08-01

Using next-generation sequencing technology, new microsatellite loci were characterized in Artocarpus altilis (Moraceae) and two congeners to increase the number of available markers for genotyping breadfruit cultivars. A total of 47,607 simple sequence repeat loci were obtained by sequencing a library of breadfruit genomic DNA with an Illumina MiSeq system. Among them, 50 single-locus markers were selected and assessed using 41 samples (39 A. altilis, one A. camansi, and one A. heterophyllus). All loci were polymorphic in A. altilis, 44 in A. camansi, and 21 in A. heterophyllus. The number of alleles per locus ranged from two to 19. The new markers will be useful for assessing the identity and genetic diversity of breadfruit cultivars on a small geographical scale, gaining a better understanding of farmer management practices, and will help to optimize breadfruit genebank management.

Gender differences in the roles of religion and locus of control on alcohol use and smoking among African Americans.

PubMed

Holt, Cheryl L; Roth, David L; Huang, Jin; Clark, Eddie M

2015-05-01

Spiritual health locus of control reflects a person's beliefs about the role of a higher power in one's health and can take an active or a passive perspective. The purpose of this study was to examine the moderating role of active and passive spiritual health locus of control beliefs on select health risk behaviors--alcohol use and smoking--in a national sample of African Americans. A national U.S. probability sample of study participants (N = 2,370; 906 men; 1,464 women) completed a telephone survey assessing religious involvement, active and passive spiritual health locus of control beliefs, and alcohol consumption and smoking status. Because of previous research suggesting gender-specific associations among these variables, moderation analyses were conducted separately for men and women. For women, higher religious behaviors were associated with less alcohol use, and this effect was more pronounced among those high in active spiritual health locus of control. For men, the combination of lower religious beliefs and higher passive spiritual health locus of control was associated with more alcohol consumption and more days of consuming five or more alcoholic drinks. No moderation effects were found for smoking. This study identified unique patterns of religious involvement and spiritual health locus of control beliefs that are associated with alcohol use, including heavy drinking, among African Americans. These findings have implications for pastoral counseling and other faith-based approaches for addressing heavy drinking in African Americans.

The association of genome-wide significant spirometric loci with chronic obstructive pulmonary disease susceptibility.

PubMed

Castaldi, Peter J; Cho, Michael H; Litonjua, Augusto A; Bakke, Per; Gulsvik, Amund; Lomas, David A; Anderson, Wayne; Beaty, Terri H; Hokanson, John E; Crapo, James D; Laird, Nan; Silverman, Edwin K

2011-12-01

Two recent metaanalyses of genome-wide association studies conducted by the CHARGE and SpiroMeta consortia identified novel loci yielding evidence of association at or near genome-wide significance (GWS) with FEV(1) and FEV(1)/FVC. We hypothesized that a subset of these markers would also be associated with chronic obstructive pulmonary disease (COPD) susceptibility. Thirty-two single-nucleotide polymorphisms (SNPs) in or near 17 genes in 11 previously identified GWS spirometric genomic regions were tested for association with COPD status in four COPD case-control study samples (NETT/NAS, the Norway case-control study, ECLIPSE, and the first 1,000 subjects in COPDGene; total sample size, 3,456 cases and 1,906 controls). In addition to testing the 32 spirometric GWS SNPs, we tested a dense panel of imputed HapMap2 SNP markers from the 17 genes located near the 32 GWS SNPs and in a set of 21 well studied COPD candidate genes. Of the previously identified GWS spirometric genomic regions, three loci harbored SNPs associated with COPD susceptibility at a 5% false discovery rate: the 4q24 locus including FLJ20184/INTS12/GSTCD/NPNT, the 6p21 locus including AGER and PPT2, and the 5q33 locus including ADAM19. In conclusion, markers previously associated at or near GWS with spirometric measures were tested for association with COPD status in data from four COPD case-control studies, and three loci showed evidence of association with COPD susceptibility at a 5% false discovery rate.

A genome-wide association study identifies multiple loci associated with mathematics ability and disability

PubMed Central

Docherty, S J; Davis, O S P; Kovas, Y; Meaburn, E L; Dale, P S; Petrill, S A; Schalkwyk, L C; Plomin, R

2010-01-01

Numeracy is as important as literacy and exhibits a similar frequency of disability. Although its etiology is relatively poorly understood, quantitative genetic research has demonstrated mathematical ability to be moderately heritable. In this first genome-wide association study (GWAS) of mathematical ability and disability, 10 out of 43 single nucleotide polymorphism (SNP) associations nominated from two high- vs. low-ability (n = 600 10-year-olds each) scans of pooled DNA were validated (P < 0.05) in an individually genotyped sample of *2356 individuals spanning the entire distribution of mathematical ability, as assessed by teacher reports and online tests. Although the effects are of the modest sizes now expected for complex traits and require further replication, interesting candidate genes are implicated such as NRCAM which encodes a neuronal cell adhesion molecule. When combined into a set, the 10 SNPs account for 2.9% (F = 56.85; df = 1 and 1881; P = 7.277e–14) of the phenotypic variance. The association is linear across the distribution consistent with a quantitative trait locus (QTL) hypothesis; the third of children in our sample who harbour 10 or more of the 20 risk alleles identified are nearly twice as likely (OR = 1.96; df = 1; P = 3.696e–07) to be in the lowest performing 15% of the distribution. Our results correspond with those of quantitative genetic research in indicating that mathematical ability and disability are influenced by many genes generating small effects across the entire spectrum of ability, implying that more highly powered studies will be needed to detect and replicate these QTL associations. PMID:20039944

A genome-wide association study identifies multiple loci associated with mathematics ability and disability.

PubMed

Docherty, S J; Davis, O S P; Kovas, Y; Meaburn, E L; Dale, P S; Petrill, S A; Schalkwyk, L C; Plomin, R

2010-03-01

Numeracy is as important as literacy and exhibits a similar frequency of disability. Although its etiology is relatively poorly understood, quantitative genetic research has demonstrated mathematical ability to be moderately heritable. In this first genome-wide association study (GWAS) of mathematical ability and disability, 10 out of 43 single nucleotide polymorphism (SNP) associations nominated from two high- vs. low-ability (n = 600 10-year-olds each) scans of pooled DNA were validated (P < 0.05) in an individually genotyped sample of (*)2356 individuals spanning the entire distribution of mathematical ability, as assessed by teacher reports and online tests. Although the effects are of the modest sizes now expected for complex traits and require further replication, interesting candidate genes are implicated such as NRCAM which encodes a neuronal cell adhesion molecule. When combined into a set, the 10 SNPs account for 2.9% (F = 56.85; df = 1 and 1881; P = 7.277e-14) of the phenotypic variance. The association is linear across the distribution consistent with a quantitative trait locus (QTL) hypothesis; the third of children in our sample who harbour 10 or more of the 20 risk alleles identified are nearly twice as likely (OR = 1.96; df = 1; P = 3.696e-07) to be in the lowest performing 15% of the distribution. Our results correspond with those of quantitative genetic research in indicating that mathematical ability and disability are influenced by many genes generating small effects across the entire spectrum of ability, implying that more highly powered studies will be needed to detect and replicate these QTL associations.

Locus of Control, Attribution Theory, and the Five Deadly Sins of Aviation

DTIC Science & Technology

2006-05-01

1989), using a path-analytic model, found only two variables, distractibility and general social maladjustment , to be directly related to frequency of...May 2006 20060811005 United States Army Research Institute for the Behavioral and Social Sciences Approved for public release; distribution is unlimited...U.S. Army Research Institute for the Behavioral and Social Sciences A Directorate of the Department of the Army Deputy Chief of Staff, G1 Authorized

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...

Microsatellite-based phylogeny of Indian domestic goats

PubMed Central

Rout, Pramod K; Joshi, Manjunath B; Mandal, Ajoy; Laloe, D; Singh, Lalji; Thangaraj, Kumarasamy

2008-01-01

Background The domestic goat is one of the important livestock species of India. In the present study we assess genetic diversity of Indian goats using 17 microsatellite markers. Breeds were sampled from their natural habitat, covering different agroclimatic zones. Results The mean number of alleles per locus (NA) ranged from 8.1 in Barbari to 9.7 in Jakhrana goats. The mean expected heterozygosity (He) ranged from 0.739 in Barbari to 0.783 in Jakhrana goats. Deviations from Hardy-Weinberg Equilibrium (HWE) were statistically significant (P < 0.05) for 5 loci breed combinations. The DA measure of genetic distance between pairs of breeds indicated that the lowest distance was between Marwari and Sirohi (0.135). The highest distance was between Pashmina and Black Bengal. An analysis of molecular variance indicated that 6.59% of variance exists among the Indian goat breeds. Both a phylogenetic tree and Principal Component Analysis showed the distribution of breeds in two major clusters with respect to their geographic distribution. Conclusion Our study concludes that Indian goat populations can be classified into distinct genetic groups or breeds based on the microsatellites as well as mtDNA information. PMID:18226239

Lessons from a Phenotyping Center Revealed by the Genome-Guided Mapping of Powdery Mildew Resistance Loci.

PubMed

Cadle-Davidson, Lance; Gadoury, David; Fresnedo-Ramírez, Jonathan; Yang, Shanshan; Barba, Paola; Sun, Qi; Demmings, Elizabeth M; Seem, Robert; Schaub, Michelle; Nowogrodzki, Anna; Kasinathan, Hema; Ledbetter, Craig; Reisch, Bruce I

2016-10-01

The genomics era brought unprecedented opportunities for genetic analysis of host resistance, but it came with the challenge that accurate and reproducible phenotypes are needed so that genomic results appropriately reflect biology. Phenotyping host resistance by natural infection in the field can produce variable results due to the uncontrolled environment, uneven distribution and genetics of the pathogen, and developmentally regulated resistance among other factors. To address these challenges, we developed highly controlled, standardized methodologies for phenotyping powdery mildew resistance in the context of a phenotyping center, receiving samples of up to 140 grapevine progeny per F 1 family. We applied these methodologies to F 1 families segregating for REN1- or REN2-mediated resistance and validated that some but not all bioassays identified the REN1 or REN2 locus. A point-intercept method (hyphal transects) to quantify colony density objectively at 8 or 9 days postinoculation proved to be the phenotypic response most reproducibly predicted by these resistance loci. Quantitative trait locus (QTL) mapping with genotyping-by-sequencing maps defined the REN1 and REN2 loci at relatively high resolution. In the reference PN40024 genome under each QTL, nucleotide-binding site-leucine-rich repeat candidate resistance genes were identified-one gene for REN1 and two genes for REN2. The methods described here for centralized resistance phenotyping and high-resolution genetic mapping can inform strategies for breeding resistance to powdery mildews and other pathogens on diverse, highly heterozygous hosts.

Examining maternal age, breastfeeding self-efficacy and health locus of control in psychological wellbeing of mothers.

PubMed

Lawal, Abiodun Musbau; Idemudia, Erhabor Sunday

2017-12-01

We investigated the direct and interaction influence of maternal age, breastfeeding self-efficacy (BSE), health locus of control (HLOC) on six dimensions of psychological wellbeing of breastfeeding mothers in Lagos, Nigeria. Data were collected from a convenience sample of 291 mothers attending health facilities in two suburb local government areas. The survey included socio-demographics (maternal age, marital status, ethnicity, education level and position of the baby currently breastfeeding), breastfeeding self-efficacy, health locus of control and psychological wellbeing scales. Independent variables were tested against sense of autonomy, positive relations with others, purpose in life, self-acceptance, environmental mastery and personal growth using factorial Multivariate Analysis of Variance. Results showed direct influence of BSE, HLOC and maternal age on various dimensions of psychological wellbeing. Interaction influences indicate BSE and HLOC on environmental mastery; BSE and maternal age on self-acceptance and HLOC and maternal age on sense of autonomy, positive relationship with others and self-acceptance respectively. In conclusion, maternal age, breastfeeding self-efficacy and health locus of control are vital for mothers to enjoy plenty dimensions of psychological wellbeing. Breastfeeding mothers need to be confident in their abilities to breastfeed and have control over their health-related behaviour in order to enjoy sufficient dimensions of psychological wellbeing.

A silent allele in the locus D5S818 contained within the PowerPlex®21 PCR Amplification Kit.

PubMed

Chen, Ling; Tai, Yunchun; Qiu, Pingming; Du, Weian; Liu, Chao

2015-11-01

Three paternity tests cases were found with a single locus mismatch at the locus D5S818 with PowerPlex®21 PCR Amplification Kit (Promega). Forward and reverse primers were redesigned to type the samples again and to evaluate if there were alleles dropped out. The results showed the existence of a silent allele 12 in all the three families, due to a point mutation that changed cytosine to adenine at 90 nucleotides upstream from the 5' end of the AGAT repeat sequences in all the six individuals. A single locus mismatch due to a silent allele may occur in any locus using any kit. Therefore, we recommend using multiple kits to confirm the results in paternity testing cases with mismatches, especially when there is a single locus mismatch with homozygote involved. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Identification of genetic aberrations on chromosome 22 outside the NF2 locus in schwannomatosis and neurofibromatosis type 2.

PubMed

Buckley, Patrick G; Mantripragada, Kiran K; Díaz de Ståhl, Teresita; Piotrowski, Arkadiusz; Hansson, Caisa M; Kiss, Hajnalka; Vetrie, David; Ernberg, Ingemar T; Nordenskjöld, Magnus; Bolund, Lars; Sainio, Markku; Rouleau, Guy A; Niimura, Michihito; Wallace, Andrew J; Evans, D Gareth R; Grigelionis, Gintautas; Menzel, Uwe; Dumanski, Jan P

2005-12-01

Schwannomatosis is characterized by multiple peripheral and cranial nerve schwannomas that occur in the absence of bilateral 8th cranial nerve schwannomas. The latter is the main diagnostic criterion of neurofibromatosis type 2 (NF2), which is a related but distinct disorder. The genetic factors underlying the differences between schwannomatosis and NF2 are poorly understood, although available evidence implicates chromosome 22 as the primary location of the gene(s) of interest. To investigate this, we comprehensively profiled the DNA copy number in samples from sporadic and familial schwannomatosis, NF2, and a large cohort of normal controls. Using a tiling-path chromosome 22 genomic array, we identified two candidate regions of copy number variation, which were further characterized by a PCR-based array with higher resolution. The latter approach allows the detection of minute alterations in total genomic DNA, with as little as 1.5 kb per measurement point of nonredundant sequence on the array. In DNA derived from peripheral blood from a schwannomatosis patient and a sporadic schwannoma sample, we detected rearrangements of the immunoglobulin lambda (IGL) locus, which is unlikely to be due to a B-cell specific somatic recombination of IGL. Analysis of normal controls indicated that these IGL rearrangements were restricted to schwannomatosis/schwannoma samples. In the second candidate region spanning GSTT1 and CABIN1 genes, we observed a frequent copy number polymorphism at the GSTT1 locus. We further describe missense mutations in the CABIN1 gene that are specific to samples from schwannomatosis and NF2 and make this gene a plausible candidate for contributing to the pathogenesis of these disorders. Copyright 2005 Wiley-Liss, Inc.

Molecular Test to Assign Individuals within the Cacopsylla pruni Complex

PubMed Central

Peccoud, Jean; Labonne, Gérard; Sauvion, Nicolas

2013-01-01

Crop protection requires the accurate identification of disease vectors, a task that can be made difficult when these vectors encompass cryptic species. Here we developed a rapid molecular diagnostic test to identify individuals of Cacopsylla pruni (Scopoli, 1763) (Hemiptera: Psyllidae), the main vector of the European stone fruit yellows phytoplasma. This psyllid encompasses two highly divergent genetic groups that are morphologically similar and that are characterized by genotyping several microsatellite markers, a costly and time-consuming protocol. With the aim of developing species-specific PCR primers, we sequenced the Internal Transcribed Spacer 2 (ITS2) on a collection of C . pruni samples from France and other European countries. ITS2 sequences showed that the two genetic groups represent two highly divergent clades. This enabled us to develop specific primers for the assignment of individuals to either genetic group in a single PCR, based on ITS2 amplicon size. All previously assigned individuals yielded bands of expected sizes, and the PCR proved efficient on a larger sample of 799 individuals. Because none appeared heterozygous at the ITS2 locus (i.e., none produced two bands), we inferred that the genetic groups of C . pruni , whose distribution is partly sympatric, constitute biological species that have not exchanged genes for an extended period of time. Other psyllid species (Cacopsylla, Psylla, Triozidae and Aphalaridae) failed to yield any amplicon. These primers are therefore unlikely to produce false positives and allow rapid assignment of C . pruni individuals to either cryptic species. PMID:23977301

SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees

PubMed Central

Mallo, Diego; De Oliveira Martins, Leonardo; Posada, David

2016-01-01

We present a fast and flexible software package—SimPhy—for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer—all three potentially leading to species tree/gene tree discordance—and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases. PMID:26526427

Investigation of the HLA component involved in rheumatoid arthritis (RA) by using the marker association-segregation [chi][sup 2] (MASC) method: Rejection of the unifying-shared-epitope hypothesis

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

Dizier, M.H.; Eliaou, J.F.; Babron, M.C.

In order to investigate the HLA component involved in rheumatoid arthritis (RA), the authors tested genetic models by the marker association-segregation [chi][sup 2] (MASC) method, using the HLA genotypic distribution observed in a sample of 97 RA patients. First they tested models assuming the involvement of a susceptibility gene linked to the DR locus. They showed that the present data are compatible with a simple model assuming the effect of a recessive allele of a biallelic locus linked to the DR locus and without any assumption of synergistic effect. Then they considered models assuming the direct involvement of the DRmore » allele products, and tested the unifying-shared-epitope hypothesis, which has been proposed. Under this hypothesis the DR alleles are assumed to be directly involved in the susceptibility to the disease because of the presence of similar or identical amino acid sequences in position 70-74 of the third hypervariable region of the DRBI molecules, shared by the RA-associated DR alleles DR4Dw4, DR4Dw14, and DR1. This hypothesis was strongly rejected with the present data. In the case of the direct involvement of the DR alleles, hypotheses more complex that the unifying-shared-epitope hypothesis would have to be considered. 28 refs., 2 tabs.« less

Determinants of Young Australians' Environmental Actions: The Role of Responsibility Attributions, Locus of Control, Knowledge and Attitudes

ERIC Educational Resources Information Center

Fielding, Kelly S.; Head, Brian W.

2012-01-01

The current study investigates determinants of young Australians' pro-environmental intentions and actions. Two samples of young people took part in the research: 12-17-year-olds (N = 1529) currently in secondary schooling and 18-24-year-olds (N = 2192) in post-secondary schooling or workforce. All participants completed an online "Youth and…

Phenotypic Variation for Diastatic power, ß-Amylase Activity, and ß-Amylase Thermostability vs. Allelic Variation at the Bmy1 Locus in a Sample of North American Barley Germplasm

USDA-ARS?s Scientific Manuscript database

Malting quality data including diastatic power, ß-amylase activity, and ß-amylase thermostability, were collected on malts from three barley (Hordeum vulgare L.) breeding program trials containing two growth habits and 165 lines grown in multiple environments. We attempted to identify causal polymor...

Admixture mapping in two Mexican samples identifies significant associations of locus ancestry with triglyceride levels in the BUD13/ZNF259/APOA5 region and fine mapping points to rs964184 as the main driver of the association signal.

PubMed

Parra, Esteban J; Mazurek, Andrew; Gignoux, Christopher R; Sockell, Alexandra; Agostino, Michael; Morris, Andrew P; Petty, Lauren E; Hanis, Craig L; Cox, Nancy J; Valladares-Salgado, Adan; Below, Jennifer E; Cruz, Miguel

2017-01-01

We carried out an admixture mapping study of lipid traits in two samples from Mexico City. Native American locus ancestry was significantly associated with triglyceride levels in a broad region of chromosome 11 overlapping the BUD13, ZNF259 and APOA5 genes. In our fine-mapping analysis of this region using dense genome-wide data, rs964184 is the only marker included in the 99% credible set of SNPs, providing strong support for rs964184 as the causal variant within this region. The frequency of the allele associated with increased triglyceride concentrations (rs964184-G) is between 30-40% higher in Native American populations from Mexico than in European populations. The evidence currently available for this variant indicates that it may be exerting its effect through three potential mechanisms: 1) modification of enhancer activity, 2) regulation of the expression of several genes in cis and/or trans, or 3) modification of the methylation patterns of the promoter of the APOA5 gene.

Admixture mapping in two Mexican samples identifies significant associations of locus ancestry with triglyceride levels in the BUD13/ZNF259/APOA5 region and fine mapping points to rs964184 as the main driver of the association signal

PubMed Central

Mazurek, Andrew; Sockell, Alexandra; Morris, Andrew P.; Petty, Lauren E.; Hanis, Craig L.; Cox, Nancy J.; Cruz, Miguel

2017-01-01

We carried out an admixture mapping study of lipid traits in two samples from Mexico City. Native American locus ancestry was significantly associated with triglyceride levels in a broad region of chromosome 11 overlapping the BUD13, ZNF259 and APOA5 genes. In our fine-mapping analysis of this region using dense genome-wide data, rs964184 is the only marker included in the 99% credible set of SNPs, providing strong support for rs964184 as the causal variant within this region. The frequency of the allele associated with increased triglyceride concentrations (rs964184-G) is between 30–40% higher in Native American populations from Mexico than in European populations. The evidence currently available for this variant indicates that it may be exerting its effect through three potential mechanisms: 1) modification of enhancer activity, 2) regulation of the expression of several genes in cis and/or trans, or 3) modification of the methylation patterns of the promoter of the APOA5 gene. PMID:28245265

Arousal and Expression of Anger: A Function of Locus of Control?

ERIC Educational Resources Information Center

Stockin, Bruce C.

Although psychologists have been investigating locus of control for more than two decades, few studies have examined how locus of control interacts with affective variables. To investigate the function of locus of control on arousal patterns and expressions of anger, 120 college students (60 internals, 60 externals, as measured by Rotter's (1966)…

A genome-wide approach to children's aggressive behavior: The EAGLE consortium.

PubMed

Pappa, Irene; St Pourcain, Beate; Benke, Kelly; Cavadino, Alana; Hakulinen, Christian; Nivard, Michel G; Nolte, Ilja M; Tiesler, Carla M T; Bakermans-Kranenburg, Marian J; Davies, Gareth E; Evans, David M; Geoffroy, Marie-Claude; Grallert, Harald; Groen-Blokhuis, Maria M; Hudziak, James J; Kemp, John P; Keltikangas-Järvinen, Liisa; McMahon, George; Mileva-Seitz, Viara R; Motazedi, Ehsan; Power, Christine; Raitakari, Olli T; Ring, Susan M; Rivadeneira, Fernando; Rodriguez, Alina; Scheet, Paul A; Seppälä, Ilkka; Snieder, Harold; Standl, Marie; Thiering, Elisabeth; Timpson, Nicholas J; Veenstra, René; Velders, Fleur P; Whitehouse, Andrew J O; Smith, George Davey; Heinrich, Joachim; Hypponen, Elina; Lehtimäki, Terho; Middeldorp, Christel M; Oldehinkel, Albertine J; Pennell, Craig E; Boomsma, Dorret I; Tiemeier, Henning

2016-07-01

Individual differences in aggressive behavior emerge in early childhood and predict persisting behavioral problems and disorders. Studies of antisocial and severe aggression in adulthood indicate substantial underlying biology. However, little attention has been given to genome-wide approaches of aggressive behavior in children. We analyzed data from nine population-based studies and assessed aggressive behavior using well-validated parent-reported questionnaires. This is the largest sample exploring children's aggressive behavior to date (N = 18,988), with measures in two developmental stages (N = 15,668 early childhood and N = 16,311 middle childhood/early adolescence). First, we estimated the additive genetic variance of children's aggressive behavior based on genome-wide SNP information, using genome-wide complex trait analysis (GCTA). Second, genetic associations within each study were assessed using a quasi-Poisson regression approach, capturing the highly right-skewed distribution of aggressive behavior. Third, we performed meta-analyses of genome-wide associations for both the total age-mixed sample and the two developmental stages. Finally, we performed a gene-based test using the summary statistics of the total sample. GCTA quantified variance tagged by common SNPs (10-54%). The meta-analysis of the total sample identified one region in chromosome 2 (2p12) at near genome-wide significance (top SNP rs11126630, P = 5.30 × 10(-8) ). The separate meta-analyses of the two developmental stages revealed suggestive evidence of association at the same locus. The gene-based analysis indicated association of variation within AVPR1A with aggressive behavior. We conclude that common variants at 2p12 show suggestive evidence for association with childhood aggression. Replication of these initial findings is needed, and further studies should clarify its biological meaning. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

A comparative study of entrepreneurs and managers: stress, burnout, locus of control, and social support.

PubMed

Rahim, M A

1995-01-01

This study investigated the relationships of job stress to job burnout, of locus of control and social support to stress and burnout, and the moderating effects of locus of control and social support on the stress-burnout relationship. These relationships were tested with questionnaire data collected from a random sample of entrepreneurs (N = 238) and managers (N = 288). Results showed that entrepreneurs reported that they had higher internal locus of control, received less social support, and had less job burnout than managers. Hierarchical regression analyses found support for eight of the ten main effects and one of the four moderating effects.

Adaptation at Specific Loci. II. Demographic and Biochemical Elements in the Maintenance of the Colias Pgi Polymorphism.

PubMed

Watt, W B

1983-04-01

Demographically oriented sampling in the wild and biochemical study of allozymes in the laboratory have been used to probe maintenance of the phosphoglucose isomerase polymorphism of Colias butterflies.-The several alleles at this locus show negative or no covariation among their frequencies in the wild. This rules out Wahlund effects as a cause of observations of heterozygote excess at this locus in broods that fly as single cohorts. Unusually heavy mortality among adults, due to drought stress or other causes, can preclude manifestation of differential survivorship among phosphoglucose isomerase genotypes. In broods composed of overlapping cohorts, heterozygote deficiency, apparently due to Wahlund effects in time as cohorts of different survivorship experience mix, can be found. Heterozygotes at this locus fly under a broader range of weather conditions than other genotypes.-Previously detected kinetic differentiation among the genotypes extends in greater magnitude to the glycolytic reaction direction, as well as to a broader range of test conditions than examined before. The heterozygote 3/4 is strikingly heterotic for several measures of kinetic functional effectiveness. Other heterozygotes are sometimes heterotic, more often intermediate (but not exactly so, nor additive in any sense) in properties between homozygotes.-Predictions are made from the biochemical analysis and from the insects' thermal ecology concerning distributions of the genotypes in the wild. Some agree with facts already established. Others are tested and confirmed from data already on hand. Still others are to be tested as reported in an accompanying paper.-All available evidence points to a combination of heterozygote advantage and fluctuating-environment selection as responsible for maintaining this polymorphism. There is considerable evidence for the operation of protein-structural constraint on the range of adaptations possible at this locus.

Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V.

PubMed

Achenbach, Ute; Paulo, Joao; Ilarionova, Evgenyia; Lübeck, Jens; Strahwald, Josef; Tacke, Eckhard; Hofferbert, Hans-Reinhard; Gebhardt, Christiane

2009-02-01

The damage caused by the parasitic root cyst nematode Globodera pallida is a major yield-limiting factor in potato cultivation . Breeding for resistance is facilitated by the PCR-based marker 'HC', which is diagnostic for an allele conferring high resistance against G. pallida pathotype Pa2/3 that has been introgressed from the wild potato species Solanum vernei into the Solanum tuberosum tetraploid breeding pool. The major quantitative trait locus (QTL) controlling this nematode resistance maps on potato chromosome V in a hot spot for resistance to various pathogens including nematodes and the oomycete Phytophthora infestans. An unstructured sample of 79 tetraploid, highly heterozygous varieties and breeding clones was selected based on presence (41 genotypes) or absence (38 genotypes) of the HC marker. Testing the clones for resistance to G. pallida confirmed the diagnostic power of the HC marker. The 79 individuals were genotyped for 100 single nucleotide polymorphisms (SNPs) at 10 loci distributed over 38 cM on chromosome V. Forty-five SNPs at six loci spanning 2 cM in the interval between markers GP21-GP179 were associated with resistance to G. pallida. Based on linkage disequilibrium (LD) between SNP markers, six LD groups comprising between 2 and 18 SNPs were identified. The LD groups indicated the existence of multiple alleles at a single resistance locus or at several, physically linked resistance loci. LD group C comprising 18 SNPs corresponded to the 'HC' marker. LD group E included 16 SNPs and showed an association peak, which positioned one nematode resistance locus physically close to the R1 gene family.

Adaptation at Specific Loci. II. Demographic and Biochemical Elements in the Maintenance of the Colias Pgi Polymorphism

PubMed Central

Watt, Ward B.

1983-01-01

Demographically oriented sampling in the wild and biochemical study of allozymes in the laboratory have been used to probe maintenance of the phosphoglucose isomerase polymorphism of Colias butterflies.—The several alleles at this locus show negative or no covariation among their frequencies in the wild. This rules out Wahlund effects as a cause of observations of heterozygote excess at this locus in broods that fly as single cohorts. Unusually heavy mortality among adults, due to drought stress or other causes, can preclude manifestation of differential survivorship among phosphoglucose isomerase genotypes. In broods composed of overlapping cohorts, heterozygote deficiency, apparently due to Wahlund effects in time as cohorts of different survivorship experience mix, can be found. Heterozygotes at this locus fly under a broader range of weather conditions than other genotypes.—Previously detected kinetic differentiation among the genotypes extends in greater magnitude to the glycolytic reaction direction, as well as to a broader range of test conditions than examined before. The heterozygote 3/4 is strikingly heterotic for several measures of kinetic functional effectiveness. Other heterozygotes are sometimes heterotic, more often intermediate (but not exactly so, nor additive in any sense) in properties between homozygotes.—Predictions are made from the biochemical analysis and from the insects' thermal ecology concerning distributions of the genotypes in the wild. Some agree with facts already established. Others are tested and confirmed from data already on hand. Still others are to be tested as reported in an accompanying paper.—All available evidence points to a combination of heterozygote advantage and fluctuating-environment selection as responsible for maintaining this polymorphism. There is considerable evidence for the operation of protein-structural constraint on the range of adaptations possible at this locus. PMID:17246121

Evidence that the APOE locus influences rate of disease progression in late onset familial Alzheimer`s disease but is not causative

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

Bennett, C.; Crawford, F.; Osborne, A.

1995-02-27

An association has been observed in several independent data sets between late onset Alzheimer`s Disease (AD) and the APOE locus on chromosome 19. We have examined the genotype in family history positive (FHP) and family history negative (FHN) cases and find a distortion of the APOE allele frequencies in accord with previous studies. However, when we examined the allele distribution of the at-risk siblings of the FHP group we found an excess of the {epsilon}4 allele which also differs significantly from historic controls but not from the affected siblings. The age distribution of the affected and unaffected siblings was similar,more » suggesting that the allelic frequency distortion in the unaffected siblings was not due to their being below the mean age of onset. Lod score linkage analysis, with age dependent onset and non-stringent specification of the genetic parameters, did not suggest linkage to the APOE locus. Furthermore, an analysis of variance of the age of disease free survival suggested that APOE genotype contributes a small fraction of the total variance indicating that the APOE locus is a poor predictor of disease free survival age within late onset families. One explanation for the age dependent association reported by other groups, and our results, is that the APOE locus enhances the rate of progression of the disease process in otherwise predisposed individuals and that variation at this locus is not able in and of itself to cause the disease. We suggest this hypothesis is compatible with the current literature regarding APOE and AD. 19 refs., 1 fig., 2 tabs.« less

Artemisinin resistance-associated polymorphisms at the K13-propeller locus are absent in Plasmodium falciparum isolates from Haiti.

PubMed

Carter, Tamar E; Boulter, Alexis; Existe, Alexandre; Romain, Jean R; St Victor, Jean Yves; Mulligan, Connie J; Okech, Bernard A

2015-03-01

Antimalarial drugs are a key tool in malaria elimination programs. With the emergence of artemisinin resistance in southeast Asia, an effort to identify molecular markers for surveillance of resistant malaria parasites is underway. Non-synonymous mutations in the kelch propeller domain (K13-propeller) in Plasmodium falciparum have been associated with artemisinin resistance in samples from southeast Asia, but additional studies are needed to characterize this locus in other P. falciparum populations with different levels of artemisinin use. Here, we sequenced the K13-propeller locus in 82 samples from Haiti, where limited government oversight of non-governmental organizations may have resulted in low-level use of artemisinin-based combination therapies. We detected a single-nucleotide polymorphism (SNP) at nucleotide 1,359 in a single isolate. Our results contribute to our understanding of the global genomic diversity of the K13-propeller locus in P. falciparum populations. © The American Society of Tropical Medicine and Hygiene.

Analysis of an "off-ladder" allele at the Penta D short tandem repeat locus.

PubMed

Yang, Y L; Wang, J G; Wang, D X; Zhang, W Y; Liu, X J; Cao, J; Yang, S L

2015-11-25

Kinship testing of a father and his son from Guangxi, China, the location of the Zhuang minority people, was performed using the PowerPlex® 18D System with a short tandem repeat typing kit. The results indicated that both the father and his son had an off-ladder allele at the Penta D locus, with a genetic size larger than that of the maximal standard allelic ladder. To further identify this locus, monogenic amplification, gene cloning, and genetic sequencing were performed. Sequencing analysis demonstrated that the fragment size of the Penta D-OL locus was 469 bp and the core sequence was [AAAGA]21, also called Penta D-21. The rare Penta D-21 allele was found to be distributed among the Zhuang population from the Guangxi Zhuang Autonomous Region of China; therefore, this study improved the range of DNA data available for this locus and enhanced our ability for individual identification of gene loci.

Cognitive abilities and genotype in a population-based sample of people with Prader-Willi syndrome.

PubMed

Whittington, J; Holland, A; Webb, T; Butler, J; Clarke, D; Boer, H

2004-02-01

Prader-Willi syndrome (PWS) is characterized by extreme floppiness at birth, impaired sexual development, short stature, severe over-eating, characteristic physical features and learning disabilities (LD). Impaired social cognition, literal mindedness and cognitive inflexibility are also present. The syndrome has two main genetic subtypes that both result in the failure of expression of maternally imprinted genes on chromosome 15 at the locus q11-13. Through multiple sources, we attempted to identify all people with PWS living in one health region in the UK. Additional people with PWS identified in other regions were also recruited to augment the study sample. A comparison group of people with LD as a result of aetiologies other than PWS was also identified. All people from these three groups, over age three, who gave their consent, were assessed using tests of ability and attainment. In addition, their main carers were interviewed using a semistructured interview. Blood samples for genetic diagnosis were obtained from all consenting participants. The IQ distribution of the population sample was approximately normal with a mean IQ 40 points below that of the general population. There were systematic differences between the two main genetic subtypes. Those with disomies differed in cognitive profiles from both those with deletions and the comparison LD group (the latter two groups were very similar) in terms of better verbal abilities and impaired coding ability. Some people with PWS deletions had strong visuospatial skills. We propose that the normal distribution of IQ, shifted downwards relative to that of the general population, is the result of a global effect on IQ of the PWS gene(s), and that the different cognitive profile seen in those with chromosome 15 maternal disomies is a specific effect of a gene, or genes, on chromosome 15 which is differentially either expressed or not expressed in those with disomies relative to those with deletions. One hypothesis is that these subtle cognitive differences are a manifestation of the genetic influences of gender-specific imprinted genes on cerebral lateralization. This requires further investigation.

Comparison of taxon-specific versus general locus sets for targeted sequence capture in plant phylogenomics.

PubMed

Chau, John H; Rahfeldt, Wolfgang A; Olmstead, Richard G

2018-03-01

Targeted sequence capture can be used to efficiently gather sequence data for large numbers of loci, such as single-copy nuclear loci. Most published studies in plants have used taxon-specific locus sets developed individually for a clade using multiple genomic and transcriptomic resources. General locus sets can also be developed from loci that have been identified as single-copy and have orthologs in large clades of plants. We identify and compare a taxon-specific locus set and three general locus sets (conserved ortholog set [COSII], shared single-copy nuclear [APVO SSC] genes, and pentatricopeptide repeat [PPR] genes) for targeted sequence capture in Buddleja (Scrophulariaceae) and outgroups. We evaluate their performance in terms of assembly success, sequence variability, and resolution and support of inferred phylogenetic trees. The taxon-specific locus set had the most target loci. Assembly success was high for all locus sets in Buddleja samples. For outgroups, general locus sets had greater assembly success. Taxon-specific and PPR loci had the highest average variability. The taxon-specific data set produced the best-supported tree, but all data sets showed improved resolution over previous non-sequence capture data sets. General locus sets can be a useful source of sequence capture targets, especially if multiple genomic resources are not available for a taxon.

Molecular typing of monophasic Salmonella 4,[5]:i:- strains isolated in Belgium (2008-2011).

PubMed

Boland, Cécile; Bertrand, Sophie; Mattheus, Wesley; Dierick, Katelijne; Wattiau, Pierre

2014-01-31

To assess the distribution of Salmonella 4,[5]:i:- subtypes in the Belgian food chain and compare it to the subtypes associated with human infections, a molecular assessment was initiated. Two hundred fifty-three Salmonella isolates serotyped as 4,[5]:i:- during the period 2008-2011 in Belgium and originating from animal productions, food or human clinical samples were analysed by a specific duplex PCR. One hundred ninety-four isolates (76.7%) fit the profile of a S. Typhimurium monophasic variant as defined by the European Food Safety Authority. The other isolates possessed but did not express the phase II flagellin gene (23.3%). Multiple Locus Variable Number of Tandem Repeats Analysis (MLVA) revealed many but closely related profiles in the fljB-negative S. Typhimurium monophasic variant isolates. Some MLVA types were associated with both human and animal isolates but no unique source of human contamination could be demonstrated. Copyright © 2013 Elsevier B.V. All rights reserved.

Population differentiation in the red-legged kittiwake (Rissa brevirostris) as revealed by mitochondrial DNA

USGS Publications Warehouse

Patirana, A.; Hatcher, S.A.; Friesen, Vicki L.

2002-01-01

Population decline in red-legged kittiwakes (Rissa brevirostris) over recent decades has necessitated the collection of information on the distribution of genetic variation within and among colonies for implementation of suitable management policies. Here we present a preliminary study of the extent of genetic structuring and gene flow among the three principal breeding locations of red-legged kittiwakes using the hypervariable Domain I of the mitochondrial control region. Genetic variation was high relative to other species of seabirds, and was similar among locations. Analysis of molecular variance indicated that population genetic structure was statistically significant, and nested clade analysis suggested that kittiwakes breeding on Bering Island maybe genetically isolated from those elsewhere. However, phylogeographic structure was weak. Although this analysis involved only a single locus and a small number of samples, it suggests that red-legged kittiwakes probably constitute a single evolutionary significant unit; the possibility that they constitute two management units requires further investigation.

Molecular investigation of mental retardation locus gene PRSS12 by linkage analysis

PubMed Central

Ali, Zafar; Babar, Masroor Ellahi; Ahmad, Jamil; Yousaf, Muhammad Zubair; Asif, Muhammad; Shah, Sajjad Ali

2011-01-01

The present study was carried out to determine the prevalence of families having mental retardation in Pakistani population. We enrolled seven mentally retarded (MR) families with two or more affected individuals. Family history was taken to minimize the chances of other abnormalities. Pedigrees were drawn using the Cyrillic software (version 2.1). The structure of pedigrees shows that all the marriages are consanguineous and the families have recessive mode of inheritance. All the families were studied by linkage analysis to mental retardation locus (MRT1)/gene PRSS12. Three STR markers (D4S191, D4S2392, and D4S3024) in vicinity of mental retardation (MR) locus (MRT1)/gene PRSS12 were amplified on all the sample of each family by PCR. The PCR products were then genotyped on non denaturing polyacrylamide gel electrophoresis (PAGE). The Haplotype were constructed to determine the pattern of inheritance and also to determine that a family was linked or unlinked to gene PRSS12. One out of the seven families was potentially linked to gene PRSS12, while the other six families remain unlinked. PMID:22090715

Molecular investigation of mental retardation locus gene PRSS12 by linkage analysis.

PubMed

Ali, Zafar; Babar, Masroor Ellahi; Ahmad, Jamil; Yousaf, Muhammad Zubair; Asif, Muhammad; Shah, Sajjad Ali

2011-05-01

The present study was carried out to determine the prevalence of families having mental retardation in Pakistani population. We enrolled seven mentally retarded (MR) families with two or more affected individuals. Family history was taken to minimize the chances of other abnormalities. Pedigrees were drawn using the Cyrillic software (version 2.1). The structure of pedigrees shows that all the marriages are consanguineous and the families have recessive mode of inheritance. All the families were studied by linkage analysis to mental retardation locus (MRT1)/gene PRSS12. Three STR markers (D4S191, D4S2392, and D4S3024) in vicinity of mental retardation (MR) locus (MRT1)/gene PRSS12 were amplified on all the sample of each family by PCR. The PCR products were then genotyped on non denaturing polyacrylamide gel electrophoresis (PAGE). The Haplotype were constructed to determine the pattern of inheritance and also to determine that a family was linked or unlinked to gene PRSS12. One out of the seven families was potentially linked to gene PRSS12, while the other six families remain unlinked.

Epiregulin (EREG) and human V-ATPase (TCIRG1): genetic variation, ethnicity and pulmonary tuberculosis susceptibility in Guinea-Bissau and The Gambia

PubMed Central

White, Marquitta J.; Tacconelli, Alessandra; Chen, Jane S.; Wejse, Christian; Hill, Philip C.; Gomez, Victor F; Velez-Edwards, Digna R.; Østergaard, Lars J.; Hu, Ting; Moore, Jason H.; Novelli, Giuseppe; Scott, William K.; Williams, Scott M.; Sirugo, Giorgio

2017-01-01

We analyzed two West African samples (Guinea-Bissau: n = 289 cases, 322 controls; The Gambia: n = 240 cases, 248 controls) to evaluate single nucleotide polymorphisms (SNPs) in Epiregulin (EREG) and V-ATPase (T cell immune regulator 1, TCIRG1) using single and multi-locus analyses to determine whether previously described associations with pulmonary tuberculosis (PTB) in Vietnamese and Italians would replicate in African populations. We did not detect any significant single locus or haplotype associations in either sample. We also performed exploratory pairwise interaction analyses using Visualization of Statistical Epistasis Networks (ViSEN), a novel method to detect only interactions among multiple variables, to elucidate possible interaction effects between SNPs and demographic factors. Although we found no strong evidence of marginal effects, there were several significant pairwise interactions that were identified in either the Guinea-Bissau or The Gambia samples, two of which replicated across populations. Our results indicate that the effects of EREG and TCIRG1 variants on PTB susceptibility, to the extent that they exist, are dependent on gene-gene interactions in West African populations as detected with ViSEN. In addition, epistatic effects are likely to be influenced by inter- and intra-population differences in genetic or environmental context and/or the mycobacterial lineages causing disease. PMID:24898387

Geographic distribution of haplotype diversity at the bovine casein locus

PubMed Central

Jann, Oliver C; Ibeagha-Awemu, Eveline M; Özbeyaz, Ceyhan; Zaragoza, Pilar; Williams, John L; Ajmone-Marsan, Paolo; Lenstra, Johannes A; Moazami-Goudarzi, Katy; Erhardt, Georg

2004-01-01

The genetic diversity of the casein locus in cattle was studied on the basis of haplotype analysis. Consideration of recently described genetic variants of the casein genes which to date have not been the subject of diversity studies, allowed the identification of new haplotypes. Genotyping of 30 cattle breeds from four continents revealed a geographically associated distribution of haplotypes, mainly defined by frequencies of alleles at CSN1S1 and CSN3. The genetic diversity within taurine breeds in Europe was found to decrease significantly from the south to the north and from the east to the west. Such geographic patterns of cattle genetic variation at the casein locus may be a result of the domestication process of modern cattle as well as geographically differentiated natural or artificial selection. The comparison of African Bos taurus and Bos indicus breeds allowed the identification of several Bos indicus specific haplotypes (CSN1S1*C-CSN2*A2-CSN3*AI/CSN3*H) that are not found in pure taurine breeds. The occurrence of such haplotypes in southern European breeds also suggests that an introgression of indicine genes into taurine breeds could have contributed to the distribution of the genetic variation observed. PMID:15040901

Operationa1 Logistics 2010.

DTIC Science & Technology

1997-04-02

movements control center (MCC) which is co-located with a material management center (MMC) forming a distribution management center (DMC). The MMC...missions by a section in Support Operations called the Distribution Management Center (DMC)29. The DMC executes the distribution management (also...restructured organizations are the formula for making theater distribution a reality and the locus of these changes is the Distribution Management Center

Fifty-three polymorphic microsatellite loci in the chestnut blight fungus, Cryphonectria parasitica

Treesearch

T.L. Kubisiak; C. Dutech; M.G. Milgroom

2006-01-01

We report on 53 microsatellite loci for use in population genetic or linkage mapping studies in Cryphonectria parasitica . In 40 isolates collected from throughout the Northern Hemisphere, the number of alleles per locus ranged from two to 14 (mean 5.17) with gene diversity values ranging from 0.049 to 0.859 (mean 0.437). Samples from Asia were more...

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...

Fractional parentage analysis and a scale-free reproductive network of brown trout.

PubMed

Koyano, Hitoshi; Serbezov, Dimitar; Kishino, Hirohisa; Schweder, Tore

2013-11-07

In this study, we developed a method of fractional parentage analysis using microsatellite markers. We propose a method for calculating parentage probability, which considers missing data and genotyping errors due to null alleles and other causes, by regarding observed alleles as realizations of random variables which take values in the set of alleles at the locus and developing a method for simultaneously estimating the true and null allele frequencies of all alleles at each locus. We then applied our proposed method to a large sample collected from a wild population of brown trout (Salmo trutta). On analyzing the data using our method, we found that the reproductive success of brown trout obeyed a power law, indicating that when the parent-offspring relationship is regarded as a link, the reproductive system of brown trout is a scale-free network. Characteristics of the reproductive network of brown trout include individuals with large bodies as hubs in the network and different power exponents of degree distributions between males and females. © 2013 Elsevier Ltd. All rights reserved.

Recombination and selection in the major histocompatibility complex of the endangered forest musk deer (Moschus berezovskii).

PubMed

Cai, Ruibo; Shafer, Aaron B A; Laguardia, Alice; Lin, Zhenzhen; Liu, Shuqiang; Hu, Defu

2015-11-25

The forest musk deer (Moschus berezovskii) is a high elevation species distributed across western China and northern Vietnam. Once abundant, habitat loss and poaching has led to a dramatic decrease in population numbers prompting the IUCN to list the species as endangered. Here, we characterized the genetic diversity of a Major Histocompatibility Complex (MHC) locus and teased apart driving factors shaping its variation. Seven DRB exon 2 alleles were identified among a group of randomly sampled forest musk deer from a captive population in the Sichuan province of China. Compared to other endangered or captive ungulates, forest musk deer have relatively low levels of MHC genetic diversity. Non-synonymous substitutions primarily occurred in the putative peptide-binding region (PBR), with analyses suggesting that recombination and selection has shaped the genetic diversity across the locus. Specifically, inter-allelic recombination generated novel allelic combinations, with evidence for both positive selection acting on the PBR and negative selection on the non-PBR. An improved understanding of functional genetic variability of the MHC will facilitate better design and management of captive breeding programs for this endangered species.

An omnibus permutation test on ensembles of two-locus analyses can detect pure epistasis and genetic heterogeneity in genome-wide association studies.

PubMed

Setsirichok, Damrongrit; Tienboon, Phuwadej; Jaroonruang, Nattapong; Kittichaijaroen, Somkit; Wongseree, Waranyu; Piroonratana, Theera; Usavanarong, Touchpong; Limwongse, Chanin; Aporntewan, Chatchawit; Phadoongsidhi, Marong; Chaiyaratana, Nachol

2013-01-01

This article presents the ability of an omnibus permutation test on ensembles of two-locus analyses (2LOmb) to detect pure epistasis in the presence of genetic heterogeneity. The performance of 2LOmb is evaluated in various simulation scenarios covering two independent causes of complex disease where each cause is governed by a purely epistatic interaction. Different scenarios are set up by varying the number of available single nucleotide polymorphisms (SNPs) in data, number of causative SNPs and ratio of case samples from two affected groups. The simulation results indicate that 2LOmb outperforms multifactor dimensionality reduction (MDR) and random forest (RF) techniques in terms of a low number of output SNPs and a high number of correctly-identified causative SNPs. Moreover, 2LOmb is capable of identifying the number of independent interactions in tractable computational time and can be used in genome-wide association studies. 2LOmb is subsequently applied to a type 1 diabetes mellitus (T1D) data set, which is collected from a UK population by the Wellcome Trust Case Control Consortium (WTCCC). After screening for SNPs that locate within or near genes and exhibit no marginal single-locus effects, the T1D data set is reduced to 95,991 SNPs from 12,146 genes. The 2LOmb search in the reduced T1D data set reveals that 12 SNPs, which can be divided into two independent sets, are associated with the disease. The first SNP set consists of three SNPs from MUC21 (mucin 21, cell surface associated), three SNPs from MUC22 (mucin 22), two SNPs from PSORS1C1 (psoriasis susceptibility 1 candidate 1) and one SNP from TCF19 (transcription factor 19). A four-locus interaction between these four genes is also detected. The second SNP set consists of three SNPs from ATAD1 (ATPase family, AAA domain containing 1). Overall, the findings indicate the detection of pure epistasis in the presence of genetic heterogeneity and provide an alternative explanation for the aetiology of T1D in the UK population.

Locus of Control, Self-esteem, Stimulus Appraisal, and Depressive Symptoms in Children

ERIC Educational Resources Information Center

Moyal, Barbara R.

1977-01-01

Variables of self-esteem, locus of control, stimulus appraisal, and depressive symptoms, which are related to depression in adults, were investigated in a sample of nonreferred Grade 5 and Grade 6 children. Grade and sex effects were not significant. All other intervariable correlations were significant. (Author)

Knowledge-Driven Analysis Identifies a Gene–Gene Interaction Affecting High-Density Lipoprotein Cholesterol Levels in Multi-Ethnic Populations

PubMed Central

Ma, Li; Brautbar, Ariel; Boerwinkle, Eric; Sing, Charles F.

2012-01-01

Total cholesterol, low-density lipoprotein cholesterol, triglyceride, and high-density lipoprotein cholesterol (HDL-C) levels are among the most important risk factors for coronary artery disease. We tested for gene–gene interactions affecting the level of these four lipids based on prior knowledge of established genome-wide association study (GWAS) hits, protein–protein interactions, and pathway information. Using genotype data from 9,713 European Americans from the Atherosclerosis Risk in Communities (ARIC) study, we identified an interaction between HMGCR and a locus near LIPC in their effect on HDL-C levels (Bonferroni corrected P c = 0.002). Using an adaptive locus-based validation procedure, we successfully validated this gene–gene interaction in the European American cohorts from the Framingham Heart Study (P c = 0.002) and the Multi-Ethnic Study of Atherosclerosis (MESA; P c = 0.006). The interaction between these two loci is also significant in the African American sample from ARIC (P c = 0.004) and in the Hispanic American sample from MESA (P c = 0.04). Both HMGCR and LIPC are involved in the metabolism of lipids, and genome-wide association studies have previously identified LIPC as associated with levels of HDL-C. However, the effect on HDL-C of the novel gene–gene interaction reported here is twice as pronounced as that predicted by the sum of the marginal effects of the two loci. In conclusion, based on a knowledge-driven analysis of epistasis, together with a new locus-based validation method, we successfully identified and validated an interaction affecting a complex trait in multi-ethnic populations. PMID:22654671

Evaluation of two multi-locus sequence typing schemes for commensal Escherichia coli from dairy cattle in Washington State.

PubMed

Ahmed, Sara; Besser, Thomas E; Call, Douglas R; Weissman, Scott J; Jones, Lisa P; Davis, Margaret A

2016-05-01

Multi-locus sequence typing (MLST) is a useful system for phylogenetic and epidemiological studies of multidrug-resistant Escherichiacoli. Most studies utilize a seven-locus MLST, but an alternate two-locus typing method (fumC and fimH; CH typing) has been proposed that may offer a similar degree of discrimination at lower cost. Herein, we compare CH typing to the standard seven-locus method for typing commensal E. coli isolates from dairy cattle. In addition, we evaluated alternative combinations of eight loci to identify combinations that maximize discrimination and congruence with standard seven-locus MLST among commensal E. coli while minimizing the cost. We also compared both methods when used for typing uropathogenic E. coli (UPEC). CH typing was less discriminatory for commensal E. coli than the standard seven-locus method (Simpson's Index of Diversity=0.933 [0.902-0.964] and 0.97 [0.96-0.979], respectively). Combining fimH with housekeeping gene loci improved discriminatory power for commensal E. coli from cattle but resulted in poor congruence with MLST. We found that a four-locus typing method including the housekeeping genes adk, purA, gyrB and recA could be used to minimize cost without sacrificing discriminatory power or congruence with Achtman seven-locus MLST when typing commensal E. coli. Copyright © 2016 Elsevier B.V. All rights reserved.

Detection and evaluation of DNA methylation markers found at SCGN and KLF14 loci to estimate human age.

PubMed

Alghanim, Hussain; Antunes, Joana; Silva, Deborah Soares Bispo Santos; Alho, Clarice Sampaio; Balamurugan, Kuppareddi; McCord, Bruce

2017-11-01

Recent developments in the analysis of epigenetic DNA methylation patterns have demonstrated that certain genetic loci show a linear correlation with chronological age. It is the goal of this study to identify a new set of epigenetic methylation markers for the forensic estimation of human age. A total number of 27 CpG sites at three genetic loci, SCGN, DLX5 and KLF14, were examined to evaluate the correlation of their methylation status with age. These sites were evaluated using 72 blood samples and 91 saliva samples collected from volunteers with ages ranging from 5 to 73 years. DNA was bisulfite modified followed by PCR amplification and pyrosequencing to determine the level of DNA methylation at each CpG site. In this study, certain CpG sites in SCGN and KLF14 loci showed methylation levels that were correlated with chronological age, however, the tested CpG sites in DLX5 did not show a correlation with age. Using a 52-saliva sample training set, two age-predictor models were developed by means of a multivariate linear regression analysis for age prediction. The two models performed similarly with a single-locus model explaining 85% of the age variance at a mean absolute deviation of 5.8 years and a dual-locus model explaining 84% of the age variance with a mean absolute deviation of 6.2 years. In the validation set, the mean absolute deviation was measured to be 8.0 years and 7.1 years for the single- and dual-locus model, respectively. Another age predictor model was also developed using a 40-blood sample training set that accounted for 71% of the age variance. This model gave a mean absolute deviation of 6.6 years for the training set and 10.3years for the validation set. The results indicate that specific CpGs in SCGN and KLF14 can be used as potential epigenetic markers to estimate age using saliva and blood specimens. These epigenetic markers could provide important information in cases where the determination of a suspect's age is critical in developing investigative leads. Copyright © 2017. Published by Elsevier B.V.

Molecular and genetic characterization of the S locus in Hordeum bulbosum L., a wild self-incompatible species related to cultivated barley.

PubMed

Kakeda, Katsuyuki; Ibuki, Toshiro; Suzuki, Junko; Tadano, Hidetaka; Kurita, Yuko; Hanai, Yosuke; Kowyama, Yasuo

2008-12-01

Gametophytic self-incompatibility (GSI) in the grasses is controlled by a distinct two-locus genetic system governed by the multiallelic loci S and Z. We have employed diploid Hordeum bulbosum as a model species for identifying the self-incompatibility (SI) genes and for elucidating the molecular mechanisms of the two-locus SI system in the grasses. In this study, we attempted to identify S haplotype-specific cDNAs expressed in pistils and anthers at the flowering stage in H. bulbosum, using the AFLP-based mRNA fingerprinting (AMF, also called cDNA-AFLP) technique. We used the AMF-derived DNA clones as markers for fine mapping of the S locus, and found that the locus resided in a chromosomal region displaying remarkable suppression of recombination, encompassing a large physical region. Furthermore, we identified three AMF-derived markers displaying complete linkage to the S locus, although they showed no significant homology with genes of known functions. Two of these markers showed expression patterns that were specific to the reproductive organs (pistil or anther), suggesting that they could be potential candidates for the S gene.

Integrating genome-wide genetic variations and monocyte expression data reveals trans-regulated gene modules in humans.

PubMed

Rotival, Maxime; Zeller, Tanja; Wild, Philipp S; Maouche, Seraya; Szymczak, Silke; Schillert, Arne; Castagné, Raphaele; Deiseroth, Arne; Proust, Carole; Brocheton, Jessy; Godefroy, Tiphaine; Perret, Claire; Germain, Marine; Eleftheriadis, Medea; Sinning, Christoph R; Schnabel, Renate B; Lubos, Edith; Lackner, Karl J; Rossmann, Heidi; Münzel, Thomas; Rendon, Augusto; Erdmann, Jeanette; Deloukas, Panos; Hengstenberg, Christian; Diemert, Patrick; Montalescot, Gilles; Ouwehand, Willem H; Samani, Nilesh J; Schunkert, Heribert; Tregouet, David-Alexandre; Ziegler, Andreas; Goodall, Alison H; Cambien, François; Tiret, Laurence; Blankenberg, Stefan

2011-12-01

One major expectation from the transcriptome in humans is to characterize the biological basis of associations identified by genome-wide association studies. So far, few cis expression quantitative trait loci (eQTLs) have been reliably related to disease susceptibility. Trans-regulating mechanisms may play a more prominent role in disease susceptibility. We analyzed 12,808 genes detected in at least 5% of circulating monocyte samples from a population-based sample of 1,490 European unrelated subjects. We applied a method of extraction of expression patterns-independent component analysis-to identify sets of co-regulated genes. These patterns were then related to 675,350 SNPs to identify major trans-acting regulators. We detected three genomic regions significantly associated with co-regulated gene modules. Association of these loci with multiple expression traits was replicated in Cardiogenics, an independent study in which expression profiles of monocytes were available in 758 subjects. The locus 12q13 (lead SNP rs11171739), previously identified as a type 1 diabetes locus, was associated with a pattern including two cis eQTLs, RPS26 and SUOX, and 5 trans eQTLs, one of which (MADCAM1) is a potential candidate for mediating T1D susceptibility. The locus 12q24 (lead SNP rs653178), which has demonstrated extensive disease pleiotropy, including type 1 diabetes, hypertension, and celiac disease, was associated to a pattern strongly correlating to blood pressure level. The strongest trans eQTL in this pattern was CRIP1, a known marker of cellular proliferation in cancer. The locus 12q15 (lead SNP rs11177644) was associated with a pattern driven by two cis eQTLs, LYZ and YEATS4, and including 34 trans eQTLs, several of them tumor-related genes. This study shows that a method exploiting the structure of co-expressions among genes can help identify genomic regions involved in trans regulation of sets of genes and can provide clues for understanding the mechanisms linking genome-wide association loci to disease.

External locus of control contributes to racial disparities in memory and reasoning training gains in ACTIVE

PubMed Central

Zahodne, Laura B.; Meyer, Oanh L.; Choi, Eunhee; Thomas, Michael L.; Willis, Sherry L.; Marsiske, Michael; Gross, Alden L.; Rebok, George W.; Parisi, Jeanine M.

2015-01-01

Racial disparities in cognitive outcomes may be partly explained by differences in locus of control. African Americans report more external locus of control than non-Hispanic Whites, and external locus of control is associated with poorer health and cognition. The aims of this study were to compare cognitive training gains between African American and non-Hispanic White participants in the Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE) study and determine whether racial differences in training gains are mediated by locus of control. The sample comprised 2,062 (26% African American) adults aged 65 and older who participated in memory, reasoning, or speed training. Latent growth curve models evaluated predictors of 10-year cognitive trajectories separately by training group. Multiple group modeling examined associations between training gains and locus of control across racial groups. Compared to non-Hispanic Whites, African Americans evidenced less improvement in memory and reasoning performance after training. These effects were partially mediated by locus of control, controlling for age, sex, education, health, depression, testing site, and initial cognitive ability. African Americans reported more external locus of control, which was associated with smaller training gains. External locus of control also had a stronger negative association with reasoning training gain for African Americans than for Whites. No racial difference in training gain was identified for speed training. Future intervention research with African Americans should test whether explicitly targeting external locus of control leads to greater cognitive improvement following cognitive training. PMID:26237116

Orosomucoid typing of apes (family Pongidae) by isoelectric focusing: Among primates do only humans have two functional orosomucoid loci

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

Yuasa, I.; Umetsu, K.; Udono, T.

1991-12-01

It has been demonstrated that human orosomucoid (ORM) is controlled by more than one functional loci, while Macaca ORM is controlled by one locus. To examine the time when the ORM gene was duplicated in the evolution of primates, plasma samples from 118 apes (family Pongidae) belonging to 4 genera and 12 species were investigated for ORM polymorphism using isoelectric focusing followed by immunoprinting. The band patterns of ORM in the subfamily Ponginae showed quantitatively different products as in humans. A pedigree study of common chimpanzees supported the two-locus model for ORM. Gibbons (subfamily Hylobatinae) displayed highly variable band patterns,more » but the number of loci was not determined unequivocally. Thus, this study shows that duplication of the ORM gene in primates occurred either before or after the divergence of hylobatinae and Ponginae, consistent with a previous prediction from the molecular evolutionary rate of ORM.« less

New development and validation of 50 SSR markers in breadfruit (Artocarpus altilis, Moraceae) by next-generation sequencing1

PubMed Central

De Bellis, Fabien; Malapa, Roger; Kagy, Valérie; Lebegin, Stéphane; Billot, Claire; Labouisse, Jean-Pierre

2016-01-01

Premise of the study: Using next-generation sequencing technology, new microsatellite loci were characterized in Artocarpus altilis (Moraceae) and two congeners to increase the number of available markers for genotyping breadfruit cultivars. Methods and Results: A total of 47,607 simple sequence repeat loci were obtained by sequencing a library of breadfruit genomic DNA with an Illumina MiSeq system. Among them, 50 single-locus markers were selected and assessed using 41 samples (39 A. altilis, one A. camansi, and one A. heterophyllus). All loci were polymorphic in A. altilis, 44 in A. camansi, and 21 in A. heterophyllus. The number of alleles per locus ranged from two to 19. Conclusions: The new markers will be useful for assessing the identity and genetic diversity of breadfruit cultivars on a small geographical scale, gaining a better understanding of farmer management practices, and will help to optimize breadfruit genebank management. PMID:27610273

SE33 locus as a reliable genetic marker for forensic DNA analysis systems

PubMed

Bhinder, Munir Ahmad; Zahoor, Muhammad Yasir; Sadia, Haleema; Qasim, Muhammad; Perveen, Rukhsana; Anjum, Ghulam Murtaza; Iqbal, Muhammad; Ullah, Najeeb; Shehzad, Wasim; Tariq, Muhammad; Waryah, Ali Muhammad

2018-06-14

Background/aim: Genetic variation, an authentic tool of individual discrimination, is being used for forensic investigations worldwide. A missing result for even one out of 13-17 markers leads to an inconclusive report. Additional reliable markers are required to compensate such deficiencies. The SE33 locus has high genetic variability in different populations and is being used in forensic investigation systems in some countries. The purpose of the study was to assess the viability of use of the SE33 locus as a supportive marker for forensic DNA profiling. Materials and methods: Amplification of the SE33 locus was performed using the PowerPlex ES Monoplex System SE33 (Promega). After genotyping 204 Pakistani individuals, different genetic and forensic parameters for the SE33 locus were studied. Results: Genotyping of the SE33 locus revealed a total of 43 alleles including 3 novel alleles. Significant values of different forensic and genetic parameters including power of discrimination, power of exclusion, and polymorphism information content were observed. Conclusions: Addition of the SE33 locus in forensic DNA profiling may help to produce conclusive reports where results are inconclusive due to degraded evidence samples. The SE33 locus can confidently be used for Pakistani and neighboring populations having common ancestors from Iran to Central Asia, the Middle East, India and Turkey.

Partial isodisomy for maternal chromosome 7 and short stature in an individual with a mutation at the COL1A2 locus.

PubMed

Spotila, L D; Sereda, L; Prockop, D J

1992-12-01

Uniparental disomy for chromosome 7 has been described previously in two individuals with cystic fibrosis. Here, we describe a third case that was discovered because the proband was homozygous for a mutation in the COL1A2 gene for type I procollagen, although his mother was heterozygous and his father did not have the mutation. Phenotypically, the proband was similar to the two previously reported cases with uniparental disomy for chromosome 7, in that he was short in stature and growth retarded. Paternity was assessed with five polymorphic markers. Chromosome 7 inheritance in the proband was analyzed using 12 polymorphic markers distributed along the entire chromosome. Similar analysis of the proband's two brothers established the phase of the alleles at the various loci, assuming minimal recombination. The proband inherited only maternal alleles at five loci and was homozygous at all loci examined, except one. He was heterozygous for an RFLP at the IGBP-1 locus at 7p13-p12. The results suggest that the isodisomy was not complete because of a recombination event involving the proximal short arms of two maternal chromosomes. In addition, the phenotype of proportional dwarfism in the proband suggests imprinting of one or more growth-related genes on chromosome 7.

The mutY gene: a mutator locus in Escherichia coli that generates G.C----T.A transversions.

PubMed Central

Nghiem, Y; Cabrera, M; Cupples, C G; Miller, J H

1988-01-01

We have used a strain with an altered lacZ gene, which reverts to wild type via only certain transversions, to detect transversion-specific mutators in Escherichia coli. Detection relied on a papillation technique that uses a combination of beta-galactosides to reveal blue Lac+ papillae. One class of mutators is specific for the G.C----T.A transversion as determined by the reversion pattern of a set of lacZ mutations and by the distribution of forward nonsense mutations in the lacI gene. The locus responsible for the mutator phenotype is designated mutY and maps near 64 min on the genetic map of E. coli. The mutY locus may act in a similar but reciprocal fashion to the previously characterized mutT locus, which results in A.T----C.G transversions. Images PMID:3128795

Molecular Typing of Mycobacterium Tuberculosis Complex by 24-Locus Based MIRU-VNTR Typing in Conjunction with Spoligotyping to Assess Genetic Diversity of Strains Circulating in Morocco

PubMed Central

Bouklata, Nada; Supply, Philip; Jaouhari, Sanae; Charof, Reda; Seghrouchni, Fouad; Sadki, Khalid; El Achhab, Youness; Nejjari, Chakib; Filali-Maltouf, Abdelkarim

2015-01-01

Background Standard 24-locus Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-VNTR) typing allows to get an improved resolution power for tracing TB transmission and predicting different strain (sub) lineages in a community. Methodology During 2010–2012, a total of 168 Mycobacterium tuberculosis Complex (MTBC) isolates were collected by cluster sampling from 10 different Moroccan cities, and centralized by the National Reference Laboratory of Tuberculosis over the study period. All isolates were genotyped using spoligotyping, and a subset of 75 was genotyped using 24-locus based MIRU-VNTR typing, followed by first line drug susceptibility testing. Corresponding strain lineages were predicted using MIRU-VNTRplus database. Principal Findings Spoligotyping resulted in 137 isolates in 18 clusters (2–50 isolates per cluster: clustering rate of 81.54%) corresponding to a SIT number in the SITVIT database, while 31(18.45%) patterns were unique of which 10 were labelled as “unknown” according to the same database. The most prevalent spoligotype family was LAM; (n = 81 or 48.24% of isolates, dominated by SIT42, n = 49), followed by Haarlem (23.80%), T superfamily (15.47%), >Beijing (2.97%), > U clade (2.38%) and S clade (1.19%). Subsequent 24-Locus MIRU-VNTR typing identified 64 unique types and 11 isolates in 5 clusters (2 to 3isolates per cluster), substantially reducing clusters defined by spoligotyping only. The single cluster of three isolates corresponded to two previously treated MDR-TB cases and one new MDR-TB case known to be contact a same index case and belonging to a same family, albeit residing in 3 different administrative regions. MIRU-VNTR loci 4052, 802, 2996, 2163b, 3690, 1955, 424, 2531, 2401 and 960 were highly discriminative in our setting (HGDI >0.6). Conclusions 24-locus MIRU-VNTR typing can substantially improve the resolution of large clusters initially defined by spoligotyping alone and predominating in Morocco, and could therefore be used to better study tuberculosis transmission in a population-based, multi-year sample context. PMID:26285026

Genetic demographic networks: Mathematical model and applications.

PubMed

Kimmel, Marek; Wojdyła, Tomasz

2016-10-01

Recent improvement in the quality of genetic data obtained from extinct human populations and their ancestors encourages searching for answers to basic questions regarding human population history. The most common and successful are model-based approaches, in which genetic data are compared to the data obtained from the assumed demography model. Using such approach, it is possible to either validate or adjust assumed demography. Model fit to data can be obtained based on reverse-time coalescent simulations or forward-time simulations. In this paper we introduce a computational method based on mathematical equation that allows obtaining joint distributions of pairs of individuals under a specified demography model, each of them characterized by a genetic variant at a chosen locus. The two individuals are randomly sampled from either the same or two different populations. The model assumes three types of demographic events (split, merge and migration). Populations evolve according to the time-continuous Moran model with drift and Markov-process mutation. This latter process is described by the Lyapunov-type equation introduced by O'Brien and generalized in our previous works. Application of this equation constitutes an original contribution. In the result section of the paper we present sample applications of our model to both simulated and literature-based demographies. Among other we include a study of the Slavs-Balts-Finns genetic relationship, in which we model split and migrations between the Balts and Slavs. We also include another example that involves the migration rates between farmers and hunters-gatherers, based on modern and ancient DNA samples. This latter process was previously studied using coalescent simulations. Our results are in general agreement with the previous method, which provides validation of our approach. Although our model is not an alternative to simulation methods in the practical sense, it provides an algorithm to compute pairwise distributions of alleles, in the case of haploid non-recombining loci such as mitochondrial and Y-chromosome loci in humans. Copyright © 2016 Elsevier Inc. All rights reserved.

Identification and characterization of pin and thrum alleles of two genes that co-segregate with the Primula S locus.

PubMed

Li, Jinhong; Webster, Margaret; Furuya, Masaki; Gilmartin, Philip M

2007-07-01

The study of heteromorphy in Primula over the past 140 years has established the reproductive significance of this breeding system. Plants produce either thrum or pin flowers that demonstrate reciprocal herkogamy. Thrums have short styles and produce large pollen from anthers at the mouth of the flower; pins have long styles and produce small pollen from anthers located within the corolla tube. The control of heteromorphy is orchestrated by the S locus with dominant (S) and recessive (s) alleles that comprise a co-adapted linkage group of genes. Thrum plants are heterozygous (Ss) and pin plants are homozygous (ss). Reciprocal crosses between the two forms are required for fertilization; within-morph crosses are impeded by a sporophytic self-incompatibility system. Rare recombination events within the S locus produce self-fertile homostyles. As a first step towards identifying genes located at the S locus, we used fluorescent differential display to screen for differential gene expression in pin and thrum flowers. Rather than only detecting differentially regulated genes, we identified two S locus linked genes by virtue of allelic variation between pin and thrum transcripts. Analysis of pin and thrum plants together with homostyle recombinant reveals that one gene flanks the locus, whereas the other shows complete linkage. One gene is related to Arabidopsis flower-timing genes Col9 and Col10; the other encodes a small predicted membrane protein of unknown function. Notwithstanding the diallelic behaviour of the Primula S locus, analysis of pin and thrum plants reveal three alleles for each gene: two pin and one thrum.

Influence of ghrelin gene polymorphisms on hypertension and atherosclerotic disease.

PubMed

Berthold, Heiner K; Giannakidou, Eleni; Krone, Wilhelm; Trégouët, David-Alexandre; Gouni-Berthold, Ioanna

2010-02-01

Ghrelin is involved in several metabolic and cardiovascular processes. Recent evidence suggests its involvement in blood pressure regulation and hypertension. The aim of the study was to determine associations of single-nucleotide polymorphisms (SNPs) and haplotypes of the ghrelin gene (GHRL) with hypertension and atherosclerotic disease. Six GHRL SNPs (rs27647, rs26802, rs34911341, rs696217, rs4684677 and a -473G/A (with no assigned rsID)) were investigated in a sample of 1143 hypertensive subjects and 1489 controls of Caucasian origin. Both single-locus and haplotype association analyses were performed. In single-locus analyses, only the non-synonymous rs34911341 was associated with hypertension (odds ratio (OR)=1.95 (95% confidence interval (CI): 1.26-3.02), P=0.003). Six common haplotypes with frequency >1% were inferred from the studied GHRL SNPs, and their frequency distribution was significantly different between hypertensive subjects and controls (chi(2)=12.96 with 5 d.f. (degree of freedom), P=0.024). The effect of rs26802 was found to be significantly (P=0.017) modulated by other GHRL SNPs, as its C allele conferred either an increased risk (OR=1.30 (1.08-1.57), P=0.005) or a decreased risk (OR=0.50 (0.23-1.06), P=0.07) of hypertension according to the two different haplotypes on which it can be found. No association of GHRL SNPs or haplotypes with atherosclerotic disease was observed. In conclusion, we observed statistical evidence for association between GHRL SNPs and risk of hypertension.

Race Differences in Self-Perception and Locus of Control during Adolescence and Early Adulthood.

ERIC Educational Resources Information Center

Tashakkori, Abbas; Thompson, Vaida D.

Data from a longitudinal sample of 14,721 White (7,193 male, 7,528 female) and 5,197 Black (2,400 male, 2,797 female) respondents tested first between ages 16 and 19 and in two follow-ups were explored in relation to Black-White, male-female differences in self-esteem and causal orientations. On general self-esteem scores, Blacks rated themselves…

Selective DNA Pooling for Determination of Linkage between a Molecular Marker and a Quantitative Trait Locus

PubMed Central

Darvasi, A.; Soller, M.

1994-01-01

Selective genotyping is a method to reduce costs in marker-quantitative trait locus (QTL) linkage determination by genotyping only those individuals with extreme, and hence most informative, quantitative trait values. The DNA pooling strategy (termed: ``selective DNA pooling'') takes this one step further by pooling DNA from the selected individuals at each of the two phenotypic extremes, and basing the test for linkage on marker allele frequencies as estimated from the pooled samples only. This can reduce genotyping costs of marker-QTL linkage determination by up to two orders of magnitude. Theoretical analysis of selective DNA pooling shows that for experiments involving backcross, F(2) and half-sib designs, the power of selective DNA pooling for detecting genes with large effect, can be the same as that obtained by individual selective genotyping. Power for detecting genes with small effect, however, was found to decrease strongly with increase in the technical error of estimating allele frequencies in the pooled samples. The effect of technical error, however, can be markedly reduced by replication of technical procedures. It is also shown that a proportion selected of 0.1 at each tail will be appropriate for a wide range of experimental conditions. PMID:7896115

Ancient Himalayan wolf (Canis lupus chanco) lineage in Upper Mustang of the Annapurna Conservation Area, Nepal

PubMed Central

Chetri, Madhu; Jhala, Yadvendradev V.; Jnawali, Shant R.; Subedi, Naresh; Dhakal, Maheshwar; Yumnam, Bibek

2016-01-01

Abstract The taxonomic status of the wolf (Canis lupus) in Nepal’s Trans-Himalaya is poorly understood. Recent genetic studies have revealed the existence of three lineages of wolves in the Indian sub-continent. Of these, the Himalayan wolf, Canis lupus chanco, has been reported to be the most ancient lineage historically distributed within the Nepal Himalaya. These wolves residing in the Trans-Himalayan region have been suggested to be smaller and very different from the European wolf. During October 2011, six fecal samples suspected to have originated from wolves were collected from Upper Mustang in the Annapurna Conservation Area of Nepal. DNA extraction and amplification of the mitochondrial (mt) control region (CR) locus yielded sequences from five out of six samples. One sample matched domestic dog sequences in GenBank, while the remaining four samples were aligned within the monophyletic and ancient Himalayan wolf clade. These four sequences which matched each other, were new and represented a novel Himalayan wolf haplotype. This result confirms that the endangered ancient Himalayan wolf is extant in Nepal. Detailed genomic study covering Nepal’s entire Himalayan landscape is recommended in order to understand their distribution, taxonomy and, genetic relatedness with other wolves potentially sharing the same landscape. PMID:27199590

Genetic architecture of epigenetic and neuronal ageing rates in human brain regions

PubMed Central

Lu, Ake T.; Hannon, Eilis; Levine, Morgan E.; Crimmins, Eileen M.; Lunnon, Katie; Mill, Jonathan; Geschwind, Daniel H.; Horvath, Steve

2017-01-01

Identifying genes regulating the pace of epigenetic ageing represents a new frontier in genome-wide association studies (GWASs). Here using 1,796 brain samples from 1,163 individuals, we carry out a GWAS of two DNA methylation-based biomarkers of brain age: the epigenetic ageing rate and estimated proportion of neurons. Locus 17q11.2 is significantly associated (P=4.5 × 10−9) with the ageing rate across five brain regions and harbours a cis-expression quantitative trait locus for EFCAB5 (P=3.4 × 10−20). Locus 1p36.12 is significantly associated (P=2.2 × 10−8) with epigenetic ageing of the prefrontal cortex, independent of the proportion of neurons. Our GWAS of the proportion of neurons identified two genome-wide significant loci (10q26 and 12p13.31) and resulted in a gene set that overlaps significantly with sets found by GWAS of age-related macular degeneration (P=1.4 × 10−12), ulcerative colitis (P<1.0 × 10−20), type 2 diabetes (P=2.8 × 10−13), hip/waist circumference in men (P=1.1 × 10−9), schizophrenia (P=1.6 × 10−9), cognitive decline (P=5.3 × 10−4) and Parkinson's disease (P=8.6 × 10−3). PMID:28516910

Validation of a pXO2-A PCR Assay To Explore Diversity among Italian Isolates of Bacillus anthracis Strains Closely Related to the Live, Attenuated Carbosap Vaccine

PubMed Central

Muscillo, M.; La Rosa, G.; Sali, M.; De Carolis, E.; Adone, R.; Ciuchini, F.; Fasanella, A.

2005-01-01

Several circulating Bacillus anthracis strains isolated in Italy and belonging to the A1.a cluster, genotype 3 (A1.a-3) are genotypically indistinguishable from Carbosap, a live attenuated vaccine strain, containing both pXO1 and pXO2 plasmids. The genotype was assessed by using eight-locus multilocus variable-number tandem repeat analysis. We describe here the use of a ninth locus able to explore variability among strains that have the same genotype. It is important to be able to genotype the wild isolate of B. anthracis strains from outbreaks of anthrax in areas where Carbosap vaccination of cattle and sheep is common practice. A total of 27 representative field strains isolated in Italy and four vaccinal strains, namely, Carbosap, Sterne, Pasteur I, and Pasteur II, were characterized by a ninth marker, called pXO2-A. Twenty-three field strains were genotype 3 and therefore identical to Carbosap. The marker was in the pXO2 plasmid and is based on the polymorphism of the already-known VX2-3 locus. Detection was obtained by PCR with fluorescence-labeled forward primers in order to produce appropriate fragments for capillary electrophoresis with an ABI 310 genetic analyzer. Genetic relationships showed heterogeneity in all of the examined samples. Interestingly, with respect to genotype 3, samples grouped into eight different subtypes, A to H, and the subtype G, had only two samples indistinguishable from Carbosap. The results of the present study confirm the validity of a hierarchical progressive protocol for discrimination among closely related isolates. PMID:16145138

Diversifying Selection Underlies the Origin of Allozyme Polymorphism at the Phosphoglucose Isomerase Locus in Tigriopus californicus

PubMed Central

Schoville, Sean D.; Flowers, Jonathan M.; Burton, Ronald S.

2012-01-01

The marine copepod Tigriopus californicus lives in intertidal rock pools along the Pacific coast, where it exhibits strong, temporally stable population genetic structure. Previous allozyme surveys have found high frequency private alleles among neighboring subpopulations, indicating that there is limited genetic exchange between populations. Here we evaluate the factors responsible for the diversification and maintenance of alleles at the phosphoglucose isomerase (Pgi) locus by evaluating patterns of nucleotide variation underlying previously identified allozyme polymorphism. Copepods were sampled from eleven sites throughout California and Baja California, revealing deep genetic structure among populations as well as genetic variability within populations. Evidence of recombination is limited to the sample from Pescadero and there is no support for linkage disequilibrium across the Pgi locus. Neutrality tests and codon-based models of substitution suggest the action of natural selection due to elevated non-synonymous substitutions at a small number of sites in Pgi. Two sites are identified as the charge-changing residues underlying allozyme polymorphisms in T. californicus. A reanalysis of allozyme variation at several focal populations, spanning a period of 26 years and over 200 generations, shows that Pgi alleles are maintained without notable frequency changes. Our data suggest that diversifying selection accounted for the origin of Pgi allozymes, while McDonald-Kreitman tests and the temporal stability of private allozyme alleles suggests that balancing selection may be involved in the maintenance of amino acid polymorphisms within populations. PMID:22768211

Analysis of a library of macaque nuclear mitochondrial sequences confirms macaque origin of divergent sequences from old oral polio vaccine samples.

PubMed

Vartanian, Jean-Pierre; Wain-Hobson, Simon

2002-05-28

Nuclear mtDNA sequences (numts) are a widespread family of paralogs evolving as pseudogenes in chromosomal DNA [Zhang, D. E. & Hewitt, G. M. (1996) TREE 11, 247-251 and Bensasson, D., Zhang, D., Hartl, D. L. & Hewitt, G. M. (2001) TREE 16, 314-321]. When trying to identify the species origin of an unknown DNA sample by way of an mtDNA locus, PCR may amplify both mtDNA and numts. Indeed, occasionally numts dominate confounding attempts at species identification [Bensasson, D., Zhang, D. X. & Hewitt, G. M. (2000) Mol. Biol. Evol. 17, 406-415; Wallace, D. C., et al. (1997) Proc. Natl. Acad. Sci. USA 94, 14900-14905]. Rhesus and cynomolgus macaque mtDNA haplotypes were identified in a study of oral polio vaccine samples dating from the late 1950s [Blancou, P., et al. (2001) Nature (London) 410, 1045-1046]. They were accompanied by a number of putative numts. To confirm that these putative numts were of macaque origin, a library of numts corresponding to a small segment of 12S rDNA locus has been made by using DNA from a Chinese rhesus macaque. A broad distribution was found with up to 30% sequence variation. Phylogenetic analysis showed that the evolutionary trajectories of numts and bona fide mtDNA haplotypes do not overlap with the signal exception of the host species; mtDNA fragments are continually crossing over into the germ line. In the case of divergent mtDNA sequences from old oral polio vaccine samples [Blancou, P., et al. (2001) Nature (London) 410, 1045-1046], all were closely related to numts in the Chinese macaque library.

Relationships between locus of control and paranormal beliefs.

PubMed

Newby, Robert W; Davis, Jessica Boyette

2004-06-01

The present study investigated the associations between scores on paranormal beliefs, locus of control, and certain psychological processes such as affect and cognitions as measured by the Linguistic Inquiry and Word Count. Analysis yielded significant correlations between scores on Locus of Control and two subscales of Tobacyk's (1988) Revised Paranormal Beliefs Scale, New Age Philosophy and Traditional Paranormal Beliefs. A step-wise multiple regression analysis indicated that Locus of Control was significantly related to New Age Philosophy. Other correlations were found between Tobacyk's subscales, Locus of Control, and three processes measured by the Linguistic Inquiry and Word Count.

The relationship between personality and attainment in 16-19-year-old students in a sixth form college: II: Self-perception, gender and attainment.

PubMed

Summerfield, M; Youngman, M

1999-06-01

A related paper (Summerfield & Youngman, 1999) has described the development of a scale, the Student Self-Perception Scale (SSPS) designed to explore the relationship between academic self-concept, attainment and personality in sixth form college students. The study aimed to identify groups of students exhibiting varying patterns of relationship using a range of measures including the SSPS. Issues of gender and also examined. The samples comprised a pilot sample of 152 students (aged 16-17 years from two sixth form colleges) and a main sample of 364 students (mean age, 16 yrs 10 mths range 16:0 to 18:6 years, from one sixth form college). The main sample included similar numbers of male and female students (46% male, 54% female) and ethnic minority students comprised 14% of this sample. Data comprised responses to two personality measures (the SSPS, Summerfield, 1995, and the Nowicki-Strickland Locus of Control Scale, Nowicki & Strickland, 1973), various student and tutor estimates of success, and performance data from college records. Students were classified using relocation cluster analysis and cluster differences verified using discriminant function analysis. Thirty outcome models were tested using covariance regression analysis. Eight distinct and interpretable groups, consistent with other research, were identified but the hypothesis of a positive, linear relationship between mastery and academic attainment was not sustained without qualification. Previous attainment was the major determinant of final performance. Gender variations were detected on the personality measures, particularly Confidence of outcomes, Prediction discrepancy, Passivity, Mastery, Dependency and Locus of control, and these were implicated in the cluster characteristics. The results suggest that a non-linear methodology may be required to isolate relationships between self-concept, personality and attainment, especially where gender effects may exist.

Study of design and control of remote manipulators. Modeling manipulator arms with distributed flexibility for design and control

NASA Technical Reports Server (NTRS)

Book, W. J.

1974-01-01

The interactions of control system and distributed flexible structural dynamics is explored for mechanical arms. A modeling process using 4 x 4 transfer matrices is described which permits the closed loop response of many current arm configurations to be evaluated. Root locus, frequency response, modal shapes, and time impulse response have all been obtained from the digital computer implementation of this model, which is oriented to arm design and allows for easy variation of the arm configuration through data cards. The model corresponds with experimentally observed natural frequencies with an average error of less than 5% in the first three flexible modes in the seven cases considered. The model was used to explore the limits imposed by structural flexibility on a nondimensionalized two link arm with one and two joints for planar motion.

External locus of control contributes to racial disparities in memory and reasoning training gains in ACTIVE.

PubMed

Zahodne, Laura B; Meyer, Oanh L; Choi, Eunhee; Thomas, Michael L; Willis, Sherry L; Marsiske, Michael; Gross, Alden L; Rebok, George W; Parisi, Jeanine M

2015-09-01

Racial disparities in cognitive outcomes may be partly explained by differences in locus of control. African Americans report more external locus of control than non-Hispanic Whites, and external locus of control is associated with poorer health and cognition. The aims of this study were to compare cognitive training gains between African American and non-Hispanic White participants in the Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE) study and determine whether racial differences in training gains are mediated by locus of control. The sample comprised 2,062 (26% African American) adults aged 65 and older who participated in memory, reasoning, or speed training. Latent growth curve models evaluated predictors of 10-year cognitive trajectories separately by training group. Multiple group modeling examined associations between training gains and locus of control across racial groups. Compared to non-Hispanic Whites, African Americans evidenced less improvement in memory and reasoning performance after training. These effects were partially mediated by locus of control, controlling for age, sex, education, health, depression, testing site, and initial cognitive ability. African Americans reported more external locus of control, which was associated with smaller training gains. External locus of control also had a stronger negative association with reasoning training gain for African Americans than for Whites. No racial difference in training gain was identified for speed training. Future intervention research with African Americans should test whether explicitly targeting external locus of control leads to greater cognitive improvement following cognitive training. (c) 2015 APA, all rights reserved).

Thorough Investigation of a Canine Autoinflammatory Disease (AID) Confirms One Main Risk Locus and Suggests a Modifier Locus for Amyloidosis

PubMed Central

Olsson, Mia; Tintle, Linda; Kierczak, Marcin; Perloski, Michele; Tonomura, Noriko; Lundquist, Andrew; Murén, Eva; Fels, Max; Tengvall, Katarina; Pielberg, Gerli; Dufaure de Citres, Caroline; Dorso, Laetitia; Abadie, Jérôme; Hanson, Jeanette; Thomas, Anne; Leegwater, Peter; Hedhammar, Åke; Lindblad-Toh, Kerstin; Meadows, Jennifer R. S.

2013-01-01

Autoinflammatory disease (AID) manifests from the dysregulation of the innate immune system and is characterised by systemic and persistent inflammation. Clinical heterogeneity leads to patients presenting with one or a spectrum of phenotypic signs, leading to difficult diagnoses in the absence of a clear genetic cause. We used separate genome-wide SNP analyses to investigate five signs of AID (recurrent fever, arthritis, breed specific secondary dermatitis, otitis and systemic reactive amyloidosis) in a canine comparative model, the pure bred Chinese Shar-Pei. Analysis of 255 DNA samples revealed a shared locus on chromosome 13 spanning two peaks of association. A three-marker haplotype based on the most significant SNP (p<2.6×10−8) from each analysis showed that one haplotypic pair (H13-11) was present in the majority of AID individuals, implicating this as a shared risk factor for all phenotypes. We also noted that a genetic signature (F ST) distinguishing the phenotypic extremes of the breed specific Chinese Shar-Pei thick and wrinkled skin, flanked the chromosome 13 AID locus; suggesting that breed development and differentiation has played a parallel role in the genetics of breed fitness. Intriguingly, a potential modifier locus for amyloidosis was revealed on chromosome 14, and an investigation of candidate genes from both this and the chromosome 13 regions revealed significant (p<0.05) renal differential expression in four genes previously implicated in kidney or immune health (AOAH, ELMO1, HAS2 and IL6). These results illustrate that phenotypic heterogeneity need not be a reflection of genetic heterogeneity, and that genetic modifiers of disease could be masked if syndromes were not first considered as individual clinical signs and then as a sum of their component parts. PMID:24130694

How does locus of control and inflated sense of responsibility relate to obsessive-compulsive symptoms in Turkish adolescents?

PubMed

Altin, Müjgan; Karanci, A Nuray

2008-12-01

This study aimed to examine the effects of responsibility attitudes, locus of control and their interactions on the general obsessive-compulsive (OC) symptomatology and the dimensions of OC symptoms in a sample of Turkish adolescents (n=385), their ages varied from 16 to 20 with a mean of 17.23 (S.D.=.68). The results of the present study revealed a significantly positive relationship between responsibility attitudes and general OC symptomatology. However, locus of control did not appear as a significant predictor of general OC symptomatology. Furthermore, results revealed that there was a significant interaction effect of responsibility attitudes with locus of control on OC symptomatology. That is, an inflated sense of responsibility and the presence of an external locus of control produced the highest level of OC symptoms. Related to the dimensions of OC symptoms, responsibility was a weak predictor of obsessive thinking symptoms, and a moderate predictor of cleanliness and checking symptoms. Locus of control and its interaction with responsibility attitudes only significantly predicted obsessional thinking symptoms.

Use of multiple-locus variable-number tandem repeat analysis to evaluate Escherichia coli O157 subtype distribution and transmission dynamics following natural exposure on a closed beef feedlot facility.

PubMed

Williams, Michele L; Pearl, David L; Bishop, Katherine E; Lejeune, Jeffrey T

2013-10-01

To better understand the epizootiology of Escherichia coli O157:H7 among cattle, all E. coli O157 isolates recovered on a research feedlot during a single feeding period were characterized by multiple-locus variable-number tandem repeat analysis (MLVA). Three distinct MLVA subtypes (A, B, C), accounting for 24%, 15%, and 64% of total isolates, respectively, were identified. Subtypes A and B were isolated at the initiation of sampling, but their prevalence waned and subtype C, first isolated on the third sampling date, became the predominant subtype on the feedlot. Supershedding events, however, occurred with equal frequency for all three MLVA-types. Using a multilevel logistic regression model, we investigated whether the odds of shedding subtype C relative to subtypes A or B were associated with time, diet, or the presence of a penmate shedding high numbers of subtype C. Only time and exposure to an animal shedding MLVA-type C at 10³ colony-forming units or greater in the pen at the time of sampling were significantly associated with increased shedding of subtype C. High-level shedding of those E. coli O157 subtypes better suited for survival in the environment and/or in the host appear to play a significant role in the development of predominant E. coli O157 subtypes. Supershedding events alone are neither required nor sufficient to drive the epidemiology of specific E. coli O157 subtypes. Additional factors are necessary to direct successful on-farm transmission of E. coli O157.

Identification of a Major Locus Contributing to Erythrocyte 2,3-Diphosphoglycerate Variability in Hooded (Long-Evans) Rats

PubMed Central

Noble, N. A.; Brewer, G. J.

1977-01-01

The erythrocyte glycolytic intermediate 2,3-diphosphoglycerate (DPG) and adenosine triphosphate (ATP) play an important role in oxygen transport and delivery by binding to hemoglobin (Hb) and reducing its affinity for oxygen. Considerable quantitative variability in the levels of DPG and ATP exists in human populations and in a population of hooded (Long-Evans) rats we have studied. This paper presents the results of studies on the genetic component of DPG-level variation in an outbred population of hooded rats. Beginning with about 100 rats, a two-way selection experiment was initiated. Pairs of rats with the highest DPG levels were mated to produce a High-DPG rat strain and animals with the lowest DPG levels were mated to produce a Low-DPG strain. Mean DPG levels responded rapidly to selection and, from generation 3 on, the differences between strain means were highly significant. Ten High-DPG strain rats were intercrossed with 10 Low-DPG strain rats of generation 10 to produce an F1 generation in which the DPG levels were almost as high as those of High-DPG animals. This indicates partial dominance of High-DPG alleles. The F2 DPG-level distribution showed two distinct subpopulations. The high DPG subpopulation contained three times as many animals as the low DPG subpopulation. From these results and the statistical analyses performed, it was concluded that the DPG differences between strains were due to an allelic difference at one major locus, the allele carried by the High-DPG strain showing partial dominance over the allele carried by the Low-DPG strain. It appears that this locus may also effect ATP levels to a large extent and is polymorphic in hooded rat populations. Identification of this locus gives us a useful tool for studies of the physiological effects of DPG variability, as well as providing an example of a major gene effect in a quantitatively varying trait. PMID:863239

Cognitive Dysfunction, Locus of Control and Treatment Outcome among Chronic Alcoholics.

ERIC Educational Resources Information Center

Abbott, Max W.

While alcoholism is no longer regarded as a unitary disorder, conventional measures of congition and personality have yet to be shown capable of consistently predicting clinical outcomes. To investigate cognitive dysfunction and locus of control as predictors of post treatment outcome in a large sample of alcoholics, 106 alcoholics (74 men, 32…

Parental Academic Socialization: Effects of Home-Based Parental Involvement on Locus of Control across U.S. Ethnic Groups

ERIC Educational Resources Information Center

Suizzo, Marie-Anne; Soon, Kokyung

2006-01-01

This study investigates the relations between three academic socialisation processes and late adolescents' internal locus of control. A sample of 249 college students from four ethnic groups completed three measures. Three factors explained 46.44% of the variance in academic socialisation, and the following differences were found: emotional…

Rangewide Genetic Variation in Coast Redwood Populations at a Chloroplast Microsatellite Locus

Treesearch

Chris Brinegar

2012-01-01

Old growth and second growth populations of coast redwood (Sequoia sempervirens) were sampled at 10 locations throughout its range and analyzed at a highly variable chloroplast microsatellite locus. Very low FST values indicated that there was no significant genetic differentiation between adjacent old growth and second growth populations at each location. Genetic...

Exercise Locus of Control, Behavior, and Intention among Mexican American Youth

ERIC Educational Resources Information Center

Guinn, Bobby; Vincent, Vern; Dugas, Donna; Semper, Tom; Jorgensen, Layne; Nelson, Larry

2006-01-01

Mexican American youth have higher physical inactivity rates than their Black or non-Hispanic White counterparts. The purpose of this study was to examine the relationships among exercise locus of control, age, present exercise level, weight status, and gender with intention to exercise in a sample of Mexican American youth. The study sample…

Students' Commitment, Engagement and Locus of Control as Predictor of Academic Achievement at Higher Education Level

ERIC Educational Resources Information Center

Sarwar, Muhammad; Ashrafi, Ghulam Muhammad

2014-01-01

The purpose of this study was to analyze Students' Commitment, Engagement and Locus of Control as predictors of Academic Achievement at Higher Education Level. We used analytical model and conclusive research approach to conduct study and survey method for data collection. We selected 369 students using multistage sampling technique from three…

Probability distribution of haplotype frequencies under the two-locus Wright-Fisher model by diffusion approximation.

PubMed

Boitard, Simon; Loisel, Patrice

2007-05-01

The probability distribution of haplotype frequencies in a population, and the way it is influenced by genetical forces such as recombination, selection, random drift ...is a question of fundamental interest in population genetics. For large populations, the distribution of haplotype frequencies for two linked loci under the classical Wright-Fisher model is almost impossible to compute because of numerical reasons. However the Wright-Fisher process can in such cases be approximated by a diffusion process and the transition density can then be deduced from the Kolmogorov equations. As no exact solution has been found for these equations, we developed a numerical method based on finite differences to solve them. It applies to transient states and models including selection or mutations. We show by several tests that this method is accurate for computing the conditional joint density of haplotype frequencies given that no haplotype has been lost. We also prove that it is far less time consuming than other methods such as Monte Carlo simulations.

Contribution of GLC3A locus to Primary Congenital Glaucoma in Pakistani population.

PubMed

Bashir, Rasheeda; Sanai, Mahrukh; Azeem, Adnan; Altaf, Imran; Saleem, Faiza; Naz, Sadaf

2014-01-01

To check the contribution of GLC3A locus to primary congenital glaucoma in the Pakistani population. We enrolled twenty-nine sporadic cases and three families with multiple individuals affected with recessive primary congenital glaucoma in the year 2013. It was a genetic linkage study accomplished jointly in Department of Biotechnology of Lahore College for Women University and School of Biological Sciences, University of the Punjab, Lahore. Samples from all affected individuals were checked for homozygosity for alleles of microsatellite markers spanning CYP1B1 at GLC3A locus. Genotyping was performed with fluorescently labeled primers by capillary electrophoresis. For familial cases, linkage was evaluated by checking the co-segregation of the phenotype with the genotypes. Two-point LOD score was calculated for each microsatellite marker with MLINK. Our study revealed that GLCA3 may contribute to glaucoma in 17% of the sporadic cases and patients in 2 of the 3 families. This data suggests that the GLC3A may make an important contribution to autosomal recessive primary congenital glaucoma in the Pakistani population. Genotyping and Sequencing of more families will be helpful to identify the common mutations in CYP1B1 in future.

Modifier gene study of meconium ileus in cystic fibrosis: statistical considerations and gene mapping results

PubMed Central

Dorfman, Ruslan; Li, Weili; Sun, Lei; Lin, Fan; Wang, Yongqian; Sandford, Andrew; Paré, Peter D.; McKay, Karen; Kayserova, Hana; Piskackova, Tereza; Macek, Milan; Czerska, Kamila; Sands, Dorota; Tiddens, Harm; Margarit, Sonia; Repetto, Gabriela; Sontag, Marci K.; Accurso, Frank J.; Blackman, Scott; Cutting, Garry R.; Tsui, Lap-Chee; Corey, Mary; Durie, Peter; Zielenski, Julian; Strug, Lisa J.

2010-01-01

Cystic fibrosis (CF) is a monogenic disease due to mutations in the CFTR gene. Yet, variability in CF disease presentation is presumed to be affected by modifier genes, such as those recently demonstrated for the pulmonary aspect. Here, we conduct a modifier gene study for meconium ileus (MI), an intestinal obstruction that occurs in 16–20% of CF newborns, providing linkage and association results from large family and case–control samples. Linkage analysis of modifier traits is different than linkage analysis of primary traits on which a sample was ascertained. Here, we articulate a source of confounding unique to modifier gene studies and provide an example of how one might overcome the confounding in the context of linkage studies. Our linkage analysis provided evidence of a MI locus on chromosome 12p13.3, which was segregating in up to 80% of MI families with at least one affected offspring (HLOD = 2.9). Fine mapping of the 12p13.3 region in a large case–control sample of pancreatic insufficient Canadian CF patients with and without MI pointed to the involvement of ADIPOR2 in MI (p = 0.002). This marker was substantially out of Hardy–Weinberg equilibrium in the cases only, and provided evidence of a cohort effect. The association with rs9300298 in the ADIPOR2 gene at the 12p13.3 locus was replicated in an independent sample of CF families. A protective locus, using the phenotype of no-MI, mapped to 4q13.3 (HLOD = 3.19), with substantial heterogeneity. A candidate gene in the region, SLC4A4, provided preliminary evidence of association (p = 0.002), warranting further follow-up studies. Our linkage approach was used to direct our fine-mapping studies, which uncovered two potential modifier genes worthy of follow-up. PMID:19662435

Association of gene polymorphisms in ABO blood group chromosomal regions and menstrual disorders

PubMed Central

SU, YONG; KONG, GUI-LIAN; SU, YA-LI; ZHOU, YAN; LV, LI-FANG; WANG, QIONG; HUANG, BAO-PING; ZHENG, RUI-ZHI; LI, QUAN-ZHONG; YUAN, HUI-JUAN; ZHAO, ZHI-GANG

2015-01-01

This study aimed to investigate whether single nucleotide polymorphisms (SNPs) located near the gene of the ABO blood group play an important role in the genetic aetiology of menstrual disorders (MDs). Polymerase chain reaction-ligase detection reaction technology was used to detect eight SNPs near the ABO gene location on the chromosomes in 250 cases of MD and 250 cases of normal menstruation. The differences in the distribution of each genotype, as well as the allele frequency in the normal and control groups, were analysed using Pearson's χ2 test to search for disease-associated loci. SHEsis software was used to analyse the linkage disequilibrium and haplotype frequencies and to inspect the correlation between haplotypes and the disease. Compared with the control group, the experimental group exhibited statistically significant differences in the genotype distribution frequencies of the rs657152 locus of the ABO blood group gene and the rs17250673 locus of the tumour necrosis factor cofactor 2 (TRAF2) gene, which is located downstream of the ABO gene. The allele distribution frequencies of rs657152 and rs495828 loci in the ABO blood group gene exhibited significant differences between the groups. Dominant and recessive genetic model analysis of each locus revealed that the experimental group exhibited statistically significant differences from the control group in the genotype distribution frequencies of rs657152 and rs495828 loci, respectively. These results indicate that the ABO blood group gene and TRAF2 gene may be a cause of MDs. PMID:26136981

Autoradiographic analysis of the in vivo distribution of 3H-imipramine and 3H-desipramine in brain: Comparison to in vitro binding patterns

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

Duncan, G.E.; Paul, I.A.; Fassberg, J.B.

1991-03-01

Using high resolution autoradiographic techniques, the distribution of radioactivity in forebrain and brainstem was assessed after 4 injection of 3H-impramine or 3H-desipramine. Results were compared with regional binding of the drugs to brain sections in vitro. Similar topographic binding of 3H-imipramine and 3H-desipramine was observed in vitro among brain regions, except in the paraventricular nucleus of the hypothalamus and locus coeruleus, where binding was greater for 3H-desipramine. For both 3H-desipramine and 3H-imipramine, some brain regions that exhibited high binding in vitro also showed high accumulation after in vivo injection. However, certain regions that contained high densities of binding sites formore » the antidepressant drugs as measured by in vitro binding showed very low accumulation of radioactivity after in vivo treatment. Such regions included the dentate gyrus of the hippocampus, layer 1 of piriform cortex, caudate-putamen, pontine and midbrain central gray, and cerebellar granular layer. Compared to in vitro binding of the drugs, the distribution of imipramine and desipramine in vivo appears more anatomically selective. For imipramine, primary sites of action in vivo, as indicated by the topographic distribution in brain, appear to be the locus coeruleus, hippocampus, lateral septal nucleus, and amygdala. For desipramine, the greatest accumulation in vivo was found in the locus coeruleus, paraventricular nucleus of the hypothalamus, and anterior thalamic nuclei.« less

The relationship between the INTERMED patient complexity instrument and Level of Care Utilisation System (LOCUS).

PubMed

Thurber, Steven; Wilson, Ann; Realmuto, George; Specker, Sheila

2018-03-01

To investigate the concurrent and criterion validity of two independently developed measurement instruments, INTERMED and LOCUS, designed to improve the treatment and clinical management of patients with complex symptom manifestations. Participants (N = 66) were selected from hospital records based on the complexity of presenting symptoms, with tripartite diagnoses across biological, psychiatric and addiction domains. Biopsychosocial information from hospital records were submitted to INTERMED and LOCUS grids. In addition, Global Assessment of Functioning (GAF) ratings were gathered for statistical analyses. The product moment correlation between INTERMED and LOCUS was 0.609 (p = .01). Inverse zero-order correlations for INTERMED and LOCUS total score and GAF were obtained. However, only the beta weight for LOCUS and GAF was significant. An exploratory principal components analysis further illuminated areas of convergence between the instruments. INTERMED and LOCUS demonstrated shared variance. INTERMED appeared more sensitive to complex medical conditions and severe physiological reactions, whereas LOCUS findings are more strongly related to psychiatric symptoms. Implications are discussed.

Low genetic diversity of Pneumocystis jirovecii among Cuban population based on two-locus mitochondrial typing.

PubMed

de Armas, Yaxsier; Friaza, Vicente; Capó, Virginia; Durand-Joly, Isabelle; Govín, Anamays; de la Horra, Carmen; Dei-Cas, Eduardo; Calderón, Enrique J

2012-05-01

Genotypes of two different loci of the Pneumocystis jirovecii mitochondrial gene were studied in specimens from a total of 75 Pneumocystis pneumonia patients in Spain, France and Cuba. A new genotype of the mitochondrial small subunit rRNA gene of P. jirovecii (160A/196T) was identified, which was revealed to be the most common in these three countries, especially in Cuba where its proportion reached 93.8%. Our data imply that the new genotype might be circulating worldwide and also suggests that the distribution of P. jirovecii genotypes could be narrower in islands such as Cuba.

A Third Locus for Autosomal Dominant Cerebellar Ataxia Type 1 Maps to Chromosome 14q24.3-qter: Evidence for the Existence of a Fourth Locus

PubMed Central

Stevanin, Giovanni; Le Guern, Eric; Ravisé, Nicole; Chneiweiss, Hervé; Dürr, Alexandra; Cancel, Géraldine; Vignal, Alain; Boch, Anne-Laure; Ruberg, Merle; Penet, Christiane; Pothin, Yolaine; Lagroua, Isabelle; Haguenau, Michel; Rancurel, Gérald; Weissenbach, Jean; Agid, Yves; Brice, Alexis

1994-01-01

The autosomal dominant cerebellar ataxias (ADCA) type I are a group of neurological disorders that are clinically and genetically heterogeneous. Two genes implicated in the disease, SCA1 (spinal cerebellar ataxia 1) and SCA2, are already localized. We have mapped a third locus to chromosome 14q24.3-qter, by linkage analysis in a non-SCA1/non-SCA2 family and have confirmed its existence in a second such family. We suggest designating this new locus “SCA3.” Combined analysis of the two families restricted the SCA3 locus to a 15-cM interval between markers D14S67 and D14S81. The gene for Machado-Joseph disease (MJD), a clinically different form of ADCA type I, has been recently assigned to chromosome 14q24.3-q32. Although the SCA3 locus is within the MJD region, linkage analyses cannot yet demonstrate whether they result from mutations of the same gene. Linkage to all three loci (SCA1, SCA2, and SCA3) was excluded in another family, which indicates the existence of a fourth ADCA type I locus. PMID:8279460

Short hypervariable microhaplotypes: A novel set of very short high discriminating power loci without stutter artefacts.

PubMed

van der Gaag, Kristiaan J; de Leeuw, Rick H; Laros, Jeroen F J; den Dunnen, Johan T; de Knijff, Peter

2018-07-01

Since two decades, short tandem repeats (STRs) are the preferred markers for human identification, routinely analysed by fragment length analysis. Here we present a novel set of short hypervariable autosomal microhaplotypes (MH) that have four or more SNPs in a span of less than 70 nucleotides (nt). These MHs display a discriminating power approaching that of STRs and provide a powerful alternative for the analysis;1;is of forensic samples that are problematic when the STR fragment size range exceeds the integrity range of severely degraded DNA or when multiple donors contribute to an evidentiary stain and STR stutter artefacts complicate profile interpretation. MH typing was developed using the power of massively parallel sequencing (MPS) enabling new powerful, fast and efficient SNP-based approaches. MH candidates were obtained from queries in data of the 1000 Genomes, and Genome of the Netherlands (GoNL) projects. Wet-lab analysis of 276 globally dispersed samples and 97 samples of nine large CEPH families assisted locus selection and corroboration of informative value. We infer that MHs represent an alternative marker type with good discriminating power per locus (allowing the use of a limited number of loci), small amplicon sizes and absence of stutter artefacts that can be especially helpful when unbalanced mixed samples are submitted for human identification. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Fine-scale mapping of the 4q24 locus identifies two independent loci associated with breast cancer risk.

PubMed

Guo, Xingyi; Long, Jirong; Zeng, Chenjie; Michailidou, Kyriaki; Ghoussaini, Maya; Bolla, Manjeet K; Wang, Qin; Milne, Roger L; Shu, Xiao-Ou; Cai, Qiuyin; Beesley, Jonathan; Kar, Siddhartha P; Andrulis, Irene L; Anton-Culver, Hoda; Arndt, Volker; Beckmann, Matthias W; Beeghly-Fadiel, Alicia; Benitez, Javier; Blot, William; Bogdanova, Natalia; Bojesen, Stig E; Brauch, Hiltrud; Brenner, Hermann; Brinton, Louise; Broeks, Annegien; Brüning, Thomas; Burwinkel, Barbara; Cai, Hui; Canisius, Sander; Chang-Claude, Jenny; Choi, Ji-Yeob; Couch, Fergus J; Cox, Angela; Cross, Simon S; Czene, Kamila; Darabi, Hatef; Devilee, Peter; Droit, Arnaud; Dörk, Thilo; Fasching, Peter A; Fletcher, Olivia; Flyger, Henrik; Fostira, Florentia; Gaborieau, Valerie; García-Closas, Montserrat; Giles, Graham G; Grip, Mervi; Guénel, Pascal; Haiman, Christopher A; Hamann, Ute; Hartman, Mikael; Hollestelle, Antoinette; Hopper, John L; Hsiung, Chia-Ni; Ito, Hidemi; Jakubowska, Anna; Johnson, Nichola; Kabisch, Maria; Kang, Daehee; Khan, Sofia; Knight, Julia A; Kosma, Veli-Matti; Lambrechts, Diether; Le Marchand, Loic; Li, Jingmei; Lindblom, Annika; Lophatananon, Artitaya; Lubinski, Jan; Mannermaa, Arto; Manoukian, Siranoush; Margolin, Sara; Marme, Frederik; Matsuo, Keitaro; McLean, Catriona A; Meindl, Alfons; Muir, Kenneth; Neuhausen, Susan L; Nevanlinna, Heli; Nord, Silje; Olson, Janet E; Orr, Nick; Peterlongo, Paolo; Putti, Thomas Choudary; Rudolph, Anja; Sangrajrang, Suleeporn; Sawyer, Elinor J; Schmidt, Marjanka K; Schmutzler, Rita K; Shen, Chen-Yang; Shi, Jiajun; Shrubsole, Martha J; Southey, Melissa C; Swerdlow, Anthony; Teo, Soo Hwang; Thienpont, Bernard; Toland, Amanda Ewart; Tollenaar, Robert A E M; Tomlinson, Ian P M; Truong, Thérèse; Tseng, Chiu-Chen; van den Ouweland, Ans; Wen, Wanqing; Winqvist, Robert; Wu, Anna; Yip, Cheng Har; Zamora, M Pilar; Zheng, Ying; Hall, Per; Pharoah, Paul D P; Simard, Jacques; Chenevix-Trench, Georgia; Dunning, Alison M; Easton, Douglas F; Zheng, Wei

2015-11-01

A recent association study identified a common variant (rs9790517) at 4q24 to be associated with breast cancer risk. Independent association signals and potential functional variants in this locus have not been explored. We conducted a fine-mapping analysis in 55,540 breast cancer cases and 51,168 controls from the Breast Cancer Association Consortium. Conditional analyses identified two independent association signals among women of European ancestry, represented by rs9790517 [conditional P = 2.51 × 10(-4); OR, 1.04; 95% confidence interval (CI), 1.02-1.07] and rs77928427 (P = 1.86 × 10(-4); OR, 1.04; 95% CI, 1.02-1.07). Functional annotation using data from the Encyclopedia of DNA Elements (ENCODE) project revealed two putative functional variants, rs62331150 and rs73838678 in linkage disequilibrium (LD) with rs9790517 (r(2) ≥ 0.90) residing in the active promoter or enhancer, respectively, of the nearest gene, TET2. Both variants are located in DNase I hypersensitivity and transcription factor-binding sites. Using data from both The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), we showed that rs62331150 was associated with level of expression of TET2 in breast normal and tumor tissue. Our study identified two independent association signals at 4q24 in relation to breast cancer risk and suggested that observed association in this locus may be mediated through the regulation of TET2. Fine-mapping study with large sample size warranted for identification of independent loci for breast cancer risk. ©2015 American Association for Cancer Research.

Fine-scale mapping of the 4q24 locus identifies two independent loci associated with breast cancer risk

PubMed Central

Guo, Xingyi; Long, Jirong; Zeng, Chenjie; Michailidou, Kyriaki; Ghoussaini, Maya; Bolla, Manjeet K.; Wang, Qin; Milne, Roger L.; Shu, Xiao-Ou; Cai, Qiuyin; Beesley, Jonathan; Kar, Siddhartha P.; Andrulis, Irene L.; Anton-Culver, Hoda; Arndt, Volker; Beckmann, Matthias W.; Beeghly-Fadiel, Alicia; Benitez, Javier; Blot, William; Bogdanova, Natalia; Bojesen, Stig E.; Brauch, Hiltrud; Brenner, Hermann; Brinton, Louise; Broeks, Annegien; Brüning, Thomas; Burwinkel, Barbara; Cai, Hui; Canisius, Sander; Chang-Claude, Jenny; Choi, Ji-Yeob; Couch, Fergus J.; Cox, Angela; Cross, Simon S.; Czene, Kamila; Darabi, Hatef; Devilee, Peter; Droit, Arnaud; Dörk, Thilo; Fasching, Peter A.; Fletcher, Olivia; Flyger, Henrik; Fostira, Florentia; Gaborieau, Valerie; García-Closas, Montserrat; Giles, Graham G.; Grip, Mervi; Guénel, Pascal; Haiman, Christopher A.; Hamann, Ute; Hartman, Mikael; Hollestelle, Antoinette; Hopper, John L.; Hsiung, Chia-Ni; Ito, Hidemi; Jakubowska, Anna; Johnson, Nichola; Kabisch, Maria; Kang, Daehee; Khan, Sofia; Knight, Julia A.; Kosma, Veli-Matti; Lambrechts, Diether; Marchand, Loic Le; Li, Jingmei; Lindblom, Annika; Lophatananon, Artitaya; Lubinski, Jan; Mannermaa, Arto; Manoukian, Siranoush; Margolin, Sara; Marme, Frederik; Matsuo, Keitaro; McLean, Catriona A.; Meindl, Alfons; Muir, Kenneth; Neuhausen, Susan L.; Nevanlinna, Heli; Nord, Silje; Olson, Janet E.; Orr, Nick; Peterlongo, Paolo; Putti, Thomas Choudary; Rudolph, Anja; Sangrajrang, Suleeporn; Sawyer, Elinor J.; Schmidt, Marjanka K.; Schmutzler, Rita K.; Shen, Chen-Yang; Shi, Jiajun; Shrubsole, Martha J; Southey, Melissa C.; Swerdlow, Anthony; Teo, Soo Hwang; Thienpont, Bernard; Toland, Amanda Ewart; Tollenaar, Robert A.E.M.; Tomlinson, Ian P.M.; Truong, Thérèse; Tseng, Chiu-chen; van den Ouweland, Ans; Wen, Wanqing; Winqvist, Robert; Wu, Anna; Yip, Cheng Har; Zamora, M. Pilar; Zheng, Ying; Hall, Per; Pharoah, Paul D.P.; Simard, Jacques; Chenevix-Trench, Georgia; Dunning, Alison M.; Easton, Douglas F.; Zheng, Wei

2015-01-01

Background A recent association study identified a common variant (rs9790517) at 4q24 to be associated with breast cancer risk. Independent association signals and potential functional variants in this locus have not been explored. Methods We conducted a fine-mapping analysis in 55,540 breast cancer cases and 51,168 controls from the Breast Cancer Association Consortium. Results Conditional analyses identified two independent association signals among women of European ancestry, represented by rs9790517 (conditional p = 2.51 × 10−4; OR = 1.04; 95% CI 1.02–1.07) and rs77928427 (p = 1.86 × 10−4; OR = 1.04; 95% CI 1.02–1.07). Functional annotation using data from the Encyclopedia of DNA Elements (ENCODE) project revealed two putative functional variants, rs62331150 and rs73838678 in linkage disequilibrium (LD) with rs9790517 (r2 ≥ 0.90) residing in the active promoter or enhancer, respectively, of the nearest gene, TET2. Both variants are located in DNase I hypersensitivity and transcription factor binding sites. Using data from both The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), we showed that rs62331150 was associated with level of expression of TET2 in breast normal and tumor tissue. Conclusion Our study identified two independent association signals at 4q24 in relation to breast cancer risk and suggested that observed association in this locus may be mediated through the regulation of TET2. Impact Fine-mapping study with large sample size warranted for identification of independent loci for breast cancer risk. PMID:26354892

A multiple-locus variable-number tandem repeat analysis (MLVA) of Listeria monocytogenes isolated from Norwegian salmon-processing factories and from listeriosis patients.

PubMed

Lunestad, B T; Truong, T T T; Lindstedt, B-A

2013-10-01

The objective of this study was to characterize Listeria monocytogenes isolated from farmed Atlantic salmon (Salmo salar) and the processing environment in three different Norwegian factories, and compare these to clinical isolates by multiple-locus variable-number tandem repeat analysis (MLVA). The 65 L. monocytogenes isolates obtained gave 15 distinct MLVA profiles. There was great heterogeneity in the distribution of MLVA profiles in factories and within each factory. Nine of the 15 MLVA profiles found in the fish-associated isolates were found to match human profiles. The MLVA profile 07-07-09-10-06 was the most common strain in Norwegian listeriosis patients. L. monocytogenes with this profile has previously been associated with at least two known listeriosis outbreaks in Norway, neither determined to be due to fish consumption. However, since this profile was also found in fish and in the processing environment, fish should be considered as a possible food vehicle during sporadic cases and outbreaks of listeriosis.

Health-related locus of control and health behaviour among university students in North Rhine Westphalia, Germany.

PubMed

Helmer, Stefanie M; Krämer, Alexander; Mikolajczyk, Rafael T

2012-12-29

Health control beliefs were postulated to be associated with health behaviour. However, the results of studies assessing these associations suggest that they might not be universal. Among young adults associations have been reported, but the evidence is limited. The objective of this analysis was to re-examine these associations in a sample of university students in Germany. Data from a multicentre cross-sectional study among university students in North Rhine-Westphalia, Germany was used (N=3,306). The Multidimensional Health Locus of Control Scale with three dimensions (one internal and two external) and six aspects of health behaviour (smoking habits, alcohol use, drug consumption, being over-/ or underweight, physical activity, and importance of healthy nutrition) were evaluated. Students with stronger internal locus of control paid more attention to healthy nutrition and displayed a higher level of physical activity. Individuals with a stronger belief in health professionals were less likely to use drugs and paid more attention to healthy nutrition. Furthermore, higher scores in the second external locus of control dimension (beliefs in luck or chance) were associated with a higher likelihood of current smoking, lower physical activity and less attention to healthy nutrition. Students engaged more strongly in unhealthy behaviour if they believed that luck determines health. In contrast, believing in having control over one's own health was associated with more healthy behaviour. These findings support the need to consider health control beliefs while designing preventive strategies in this specific population.

Health-related locus of control and health behaviour among university students in North Rhine Westphalia, Germany

PubMed Central

2012-01-01

Background Health control beliefs were postulated to be associated with health behaviour. However, the results of studies assessing these associations suggest that they might not be universal. Among young adults associations have been reported, but the evidence is limited. The objective of this analysis was to re-examine these associations in a sample of university students in Germany. Findings Data from a multicentre cross-sectional study among university students in North Rhine-Westphalia, Germany was used (N=3,306). The Multidimensional Health Locus of Control Scale with three dimensions (one internal and two external) and six aspects of health behaviour (smoking habits, alcohol use, drug consumption, being over-/ or underweight, physical activity, and importance of healthy nutrition) were evaluated. Students with stronger internal locus of control paid more attention to healthy nutrition and displayed a higher level of physical activity. Individuals with a stronger belief in health professionals were less likely to use drugs and paid more attention to healthy nutrition. Furthermore, higher scores in the second external locus of control dimension (beliefs in luck or chance) were associated with a higher likelihood of current smoking, lower physical activity and less attention to healthy nutrition. Conclusions Students engaged more strongly in unhealthy behaviour if they believed that luck determines health. In contrast, believing in having control over one’s own health was associated with more healthy behaviour. These findings support the need to consider health control beliefs while designing preventive strategies in this specific population. PMID:23273039

The Effect of Locus of Control on Message Acceptance and Recall.

ERIC Educational Resources Information Center

Cole, Catherine A.; Singh, Surendra

Locus of control is a personality trait that influences human behavior in many situations. Internal-external control reactions to a persuasive message and the recall of the message were examined in two studies. In the first study, 35 undergraduate students' locus of control was measured using Duttweiler's Internal Control Measure. On the basis of…

Parental Efficacy and the Development of Social Competence in Young Children.

ERIC Educational Resources Information Center

Swick, Kevin J.; Hassell, Tammy

This study examined the relation of two aspects of parental efficacy (locus of control and interpersonal support) to the social competence of 62 children aged 2 to 5 years in a preschool setting. The following assessment instruments were used: Schaefer's (1979) Locus of Control Inventory to measure parental locus of control; Paul's Home Support…

Social capital, political trust, and health locus of control: a population-based study.

PubMed

Lindström, Martin

2011-02-01

To investigate the association between political trust in the Riksdag and lack of belief in the possibility to influence one's own health (external locus of control), taking horizontal trust into account. The 2008 public health survey in Skåne is a cross-sectional postal questionnaire study with a 55% participation rate. A random sample of 28,198 persons aged 18-80 years participated. Logistic regression models were used to investigate the associations between political trust in the Riksdag (an aspect of vertical trust) and lack of belief in the possibility to influence one's own health (external locus of control). The multiple regression analyses included age, country of birth, education, and horizontal trust in other people. A 33.7% of all men and 31.8% of all women lack internal locus of control. Low (external) health locus of control is more common in higher age groups, among people born outside Sweden, with lower education, low horizontal trust, low political trust, and no opinion concerning political trust. Respondents with not particularly strong political trust, no political trust at all and no opinion have significantly higher odds ratios of external locus of control throughout the multiple regression analyses. Low political trust in the Riksdag seems to be independently associated with external health locus of control.

Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

PubMed Central

Wang, Xianshu; McGuffog, Lesley; Lee, Andrew; Olswold, Curtis; Kuchenbaecker, Karoline B.; Soucy, Penny; Fredericksen, Zachary; Barrowdale, Daniel; Dennis, Joe; Gaudet, Mia M.; Dicks, Ed; Kosel, Matthew; Healey, Sue; Sinilnikova, Olga M.; Lee, Adam; Bacot, François; Vincent, Daniel; Hogervorst, Frans B. L.; Peock, Susan; Stoppa-Lyonnet, Dominique; Jakubowska, Anna; Investigators, kConFab; Radice, Paolo; Schmutzler, Rita Katharina; Domchek, Susan M.; Piedmonte, Marion; Singer, Christian F.; Friedman, Eitan; Thomassen, Mads; Hansen, Thomas V. O.; Neuhausen, Susan L.; Szabo, Csilla I.; Blanco, Ignacio; Greene, Mark H.; Karlan, Beth Y.; Garber, Judy; Phelan, Catherine M.; Weitzel, Jeffrey N.; Montagna, Marco; Olah, Edith; Andrulis, Irene L.; Godwin, Andrew K.; Yannoukakos, Drakoulis; Goldgar, David E.; Caldes, Trinidad; Nevanlinna, Heli; Osorio, Ana; Terry, Mary Beth; Daly, Mary B.; van Rensburg, Elizabeth J.; Hamann, Ute; Ramus, Susan J.; Ewart Toland, Amanda; Caligo, Maria A.; Olopade, Olufunmilayo I.; Tung, Nadine; Claes, Kathleen; Beattie, Mary S.; Southey, Melissa C.; Imyanitov, Evgeny N.; Tischkowitz, Marc; Janavicius, Ramunas; John, Esther M.; Kwong, Ava; Diez, Orland; Balmaña, Judith; Barkardottir, Rosa B.; Arun, Banu K.; Rennert, Gad; Teo, Soo-Hwang; Ganz, Patricia A.; Campbell, Ian; van der Hout, Annemarie H.; van Deurzen, Carolien H. M.; Seynaeve, Caroline; Gómez Garcia, Encarna B.; van Leeuwen, Flora E.; Meijers-Heijboer, Hanne E. J.; Gille, Johannes J. P.; Ausems, Margreet G. E. M.; Blok, Marinus J.; Ligtenberg, Marjolijn J. L.; Rookus, Matti A.; Devilee, Peter; Verhoef, Senno; van Os, Theo A. M.; Wijnen, Juul T.; Frost, Debra; Ellis, Steve; Fineberg, Elena; Platte, Radka; Evans, D. Gareth; Izatt, Louise; Eeles, Rosalind A.; Adlard, Julian; Eccles, Diana M.; Cook, Jackie; Brewer, Carole; Douglas, Fiona; Hodgson, Shirley; Morrison, Patrick J.; Side, Lucy E.; Donaldson, Alan; Houghton, Catherine; Rogers, Mark T.; Dorkins, Huw; Eason, Jacqueline; Gregory, Helen; McCann, Emma; Murray, Alex; Calender, Alain; Hardouin, Agnès; Berthet, Pascaline; Delnatte, Capucine; Nogues, Catherine; Lasset, Christine; Houdayer, Claude; Leroux, Dominique; Rouleau, Etienne; Prieur, Fabienne; Damiola, Francesca; Sobol, Hagay; Coupier, Isabelle; Venat-Bouvet, Laurence; Castera, Laurent; Gauthier-Villars, Marion; Léoné, Mélanie; Pujol, Pascal; Mazoyer, Sylvie; Bignon, Yves-Jean; Złowocka-Perłowska, Elżbieta; Gronwald, Jacek; Lubinski, Jan; Durda, Katarzyna; Jaworska, Katarzyna; Huzarski, Tomasz; Spurdle, Amanda B.; Viel, Alessandra; Peissel, Bernard; Bonanni, Bernardo; Melloni, Giulia; Ottini, Laura; Papi, Laura; Varesco, Liliana; Tibiletti, Maria Grazia; Peterlongo, Paolo; Volorio, Sara; Manoukian, Siranoush; Pensotti, Valeria; Arnold, Norbert; Engel, Christoph; Deissler, Helmut; Gadzicki, Dorothea; Gehrig, Andrea; Kast, Karin; Rhiem, Kerstin; Meindl, Alfons; Niederacher, Dieter; Ditsch, Nina; Plendl, Hansjoerg; Preisler-Adams, Sabine; Engert, Stefanie; Sutter, Christian; Varon-Mateeva, Raymonda; Wappenschmidt, Barbara; Weber, Bernhard H. F.; Arver, Brita; Stenmark-Askmalm, Marie; Loman, Niklas; Rosenquist, Richard; Einbeigi, Zakaria; Nathanson, Katherine L.; Rebbeck, Timothy R.; Blank, Stephanie V.; Cohn, David E.; Rodriguez, Gustavo C.; Small, Laurie; Friedlander, Michael; Bae-Jump, Victoria L.; Fink-Retter, Anneliese; Rappaport, Christine; Gschwantler-Kaulich, Daphne; Pfeiler, Georg; Tea, Muy-Kheng; Lindor, Noralane M.; Kaufman, Bella; Shimon Paluch, Shani; Laitman, Yael; Skytte, Anne-Bine; Gerdes, Anne-Marie; Pedersen, Inge Sokilde; Moeller, Sanne Traasdahl; Kruse, Torben A.; Jensen, Uffe Birk; Vijai, Joseph; Sarrel, Kara; Robson, Mark; Kauff, Noah; Mulligan, Anna Marie; Glendon, Gord; Ozcelik, Hilmi; Ejlertsen, Bent; Nielsen, Finn C.; Jønson, Lars; Andersen, Mette K.; Ding, Yuan Chun; Steele, Linda; Foretova, Lenka; Teulé, Alex; Lazaro, Conxi; Brunet, Joan; Pujana, Miquel Angel; Mai, Phuong L.; Loud, Jennifer T.; Walsh, Christine; Lester, Jenny; Orsulic, Sandra; Narod, Steven A.; Herzog, Josef; Sand, Sharon R.; Tognazzo, Silvia; Agata, Simona; Vaszko, Tibor; Weaver, Joellen; Stavropoulou, Alexandra V.; Buys, Saundra S.; Romero, Atocha; de la Hoya, Miguel; Aittomäki, Kristiina; Muranen, Taru A.; Duran, Mercedes; Chung, Wendy K.; Lasa, Adriana; Dorfling, Cecilia M.; Miron, Alexander; Benitez, Javier; Senter, Leigha; Huo, Dezheng; Chan, Salina B.; Sokolenko, Anna P.; Chiquette, Jocelyne; Tihomirova, Laima; Friebel, Tara M.; Agnarsson, Bjarni A.; Lu, Karen H.; Lejbkowicz, Flavio; James, Paul A.; Hall, Per; Dunning, Alison M.; Tessier, Daniel; Cunningham, Julie; Slager, Susan L.; Wang, Chen; Hart, Steven; Stevens, Kristen; Simard, Jacques; Pastinen, Tomi; Pankratz, Vernon S.; Offit, Kenneth; Antoniou, Antonis C.

2013-01-01

BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7×10−8, HR = 1.14, 95% CI: 1.09–1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4×10−8, HR = 1.27, 95% CI: 1.17–1.38) and 4q32.3 (rs4691139, P = 3.4×10−8, HR = 1.20, 95% CI: 1.17–1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific association. The 17q21.31 locus was also associated with ovarian cancer risk in 8,211 BRCA2 carriers (P = 2×10−4). These loci may lead to an improved understanding of the etiology of breast and ovarian tumors in BRCA1 carriers. Based on the joint distribution of the known BRCA1 breast cancer risk-modifying loci, we estimated that the breast cancer lifetime risks for the 5% of BRCA1 carriers at lowest risk are 28%–50% compared to 81%–100% for the 5% at highest risk. Similarly, based on the known ovarian cancer risk-modifying loci, the 5% of BRCA1 carriers at lowest risk have an estimated lifetime risk of developing ovarian cancer of 28% or lower, whereas the 5% at highest risk will have a risk of 63% or higher. Such differences in risk may have important implications for risk prediction and clinical management for BRCA1 carriers. PMID:23544013

Work-family conflict, locus of control, and women's well-being: tests of alternative pathways.

PubMed

Noor, Noraini M

2002-10-01

The author tested for the 3 possible pathways (i.e., direct, moderator, and mediator effects) in which locus of control can influence the relationship between work-family conflict and well-being. The author predicted that work-family conflict would be negatively correlated with well-being. In a sample of 310 Malaysian employed women with families, work-family conflict was a significant predictor of both job satisfaction and distress--negatively related to job satisfaction and positively related to symptoms of distress. More important, the results provided support for the effects of all 3 pathways of control on the relationship between work-family conflict and well-being, depending on the outcome measure: For job satisfaction, locus of control had direct effects, acted as a partial mediator, and played a significant moderating role. In contrast, only the direct effect of locus of control predicted distress. The author discusses those findings with reference to the literature on work-family conflict, locus of control, and the issue of stress-distress specificity.

The Relationship between Critical Thinking Disposition and Locus of Control in Pre-Service Teachers

ERIC Educational Resources Information Center

Oguz, Aytunga; Sariçam, Hakan

2016-01-01

The aim of the current research study was to examine the link between critical thinking dispositions and locus of control in pre-service teachers. The participants of this study were selected via easily accessible sampling technique. The participants consist of 347 pre-service teachers (203 female, 144 male) in Kütahya, Turkey. The Rotter…

Parenting Styles Influence on Locus of Control, Self-Efficacy and Academic Adjustment in College Students

ERIC Educational Resources Information Center

Mills, Kimberly Tracey

2010-01-01

The purpose of this study was to investigate the relationship between perceived parenting style, locus of control, self-efficacy, and student outcome (i.e. academic performance, GPA) in a sample of college students. The relationship among gender and ethnicity were also examined across these variables. There were 100 participants in this study,…

spads 1.0: a toolbox to perform spatial analyses on DNA sequence data sets.

PubMed

Dellicour, Simon; Mardulyn, Patrick

2014-05-01

SPADS 1.0 (for 'Spatial and Population Analysis of DNA Sequences') is a population genetic toolbox for characterizing genetic variability within and among populations from DNA sequences. In view of the drastic increase in genetic information available through sequencing methods, spads was specifically designed to deal with multilocus data sets of DNA sequences. It computes several summary statistics from populations or groups of populations, performs input file conversions for other population genetic programs and implements locus-by-locus and multilocus versions of two clustering algorithms to study the genetic structure of populations. The toolbox also includes two MATLAB and r functions, GDISPAL and GDIVPAL, to display differentiation and diversity patterns across landscapes. These functions aim to generate interpolating surfaces based on multilocus distance and diversity indices. In the case of multiple loci, such surfaces can represent a useful alternative to multiple pie charts maps traditionally used in phylogeography to represent the spatial distribution of genetic diversity. These coloured surfaces can also be used to compare different data sets or different diversity and/or distance measures estimated on the same data set. © 2013 John Wiley & Sons Ltd.

Self-Esteem, Locus of Control, and First-Time NCLEX-RN Passage of BSN Students at Historically Black Colleges and Universities.

PubMed

Chavis, Pamella Ivey

Relationships between self-esteem, locus of control (LOC), and first-time passage of National Council Licensure Examination for Registered Nurses (NCLEX-RN®) were examined at baccalaureate nursing programs at two historically black colleges and universities. Shortages continue to exceed demands for RNs prepared at the baccalaureate level. Inconsistent pass rates on the NCLEX-RN for graduates of historically black colleges and universities impede the supply of RNs. Surveys and archival data were used to examine characteristics of the sample and explore relationships among variables. All participants (N = 90) reported high self-esteem and internal LOC. Models suggested that all those with high self-esteem and internal LOC would pass the NCLEX-RN; only 85 percent passed the first time. Statistical analysis revealed a lack of statistical significance between self-esteem, LOC, and first-time passage. Variables not included in the study may have affected first-time passage.

Physical properties of VNTR data, and their impact on a test of allelic independence

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

Devlin, B.; Risch, N.

1993-08-01

In this article the authors describe the physical properties of VNTR data, as well as their effects on the two-dimensional distribution of fragment pairs. Tests of independence of alleles at a locus may confound those physical properties with allele independence. A recently proposed test by Geisser and Johnson is an example. The authors show that alleles can be strictly independent, yet the proposed test suggests large violations of allele independence because it is sensitive to well-known electrophoretic phenomena. 7 refs., 4 tabs.

Polymorphism in the two-locus Levene model with nonepistatic directional selection.

PubMed

Bürger, Reinhard

2009-11-01

For the Levene model with soft selection in two demes, the maintenance of polymorphism at two diallelic loci is studied. Selection is nonepistatic and dominance is intermediate. Thus, there is directional selection in every deme and at every locus. We assume that selection is in opposite directions in the two demes because otherwise no polymorphism is possible. If at one locus there is no dominance, then a complete analysis of the dynamical and equilibrium properties is performed. In particular, a simple necessary and sufficient condition for the existence of an internal equilibrium and sufficient conditions for global asymptotic stability are obtained. These results are extended to deme-independent degree of dominance at one locus. A perturbation analysis establishes structural stability within the full parameter space. In the absence of genotype-environment interaction, which requires deme-independent dominance at both loci, nongeneric equilibrium behavior occurs, and the introduction of arbitrarily small genotype-environment interaction changes the equilibrium structure and may destroy stable polymorphism. The volume of the parameter space for which a (stable) two-locus polymorphism is maintained is computed numerically. It is investigated how this volume depends on the strength of selection and on the dominance relations. If the favorable allele is (partially) dominant in its deme, more than 20% of all parameter combinations lead to a globally asymptotically stable, fully polymorphic equilibrium.

Detection of a molecular deletion at the DXS732 locus in a patient with X-linked hypohidrotic ectodermal dysplasia (EDA), with the identification of a unique junctional fragment

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

Zonana, J.; Gault, J.; Jones, M.

1993-01-01

X-linked hypohidrotic ectodermal dysplasia (EDA) has been localized to the Xq12-q13.1. A panel of genomic DNA samples from 80 unrelated males with EDA has been screened for deletions at seven genetic loci within the Xq12-13 region. A single individual was identified with a deletion at the DXS732 locus by hybridization with the mouse genomic probe pcos169E/4. This highly conserved DNA probe is from locus DXCrc169, which is tightly linked to the Ta locus, the putative mouse homologue of EDA. The proband had the classical phenotype of EDA, with no other phenotypic abnormalities, and a normal cytogenetic analysis. A human genomicmore » DNA clone, homologous to pcos169E/4, was isolated from a human X-chromosome cosmid library. On hybridization with the cosmid, the proband was found to be only partially deleted at the DXS732 locus, with a unique junctional fragment identified in the proband and in three of his maternal relatives. This is the first determination of carrier status for EDA in females, by direct mutation analysis. Failure to detect deletion of the other loci tested in the proband suggests that the DXS732 locus is the closest known locus to the EDA gene. Since the DXS732 locus contains a highly conserved sequence, it must be considered to be a candidate locus for the EDA gene itself. 18 refs., 3 figs., 1 tab.« less

HLA-E coding and 3' untranslated region variability determined by next-generation sequencing in two West-African population samples.

PubMed

Castelli, Erick C; Mendes-Junior, Celso T; Sabbagh, Audrey; Porto, Iane O P; Garcia, André; Ramalho, Jaqueline; Lima, Thálitta H A; Massaro, Juliana D; Dias, Fabrício C; Collares, Cristhianna V A; Jamonneau, Vincent; Bucheton, Bruno; Camara, Mamadou; Donadi, Eduardo A

2015-12-01

HLA-E is a non-classical Human Leucocyte Antigen class I gene with immunomodulatory properties. Whereas HLA-E expression usually occurs at low levels, it is widely distributed amongst human tissues, has the ability to bind self and non-self antigens and to interact with NK cells and T lymphocytes, being important for immunosurveillance and also for fighting against infections. HLA-E is usually the most conserved locus among all class I genes. However, most of the previous studies evaluating HLA-E variability sequenced only a few exons or genotyped known polymorphisms. Here we report a strategy to evaluate HLA-E variability by next-generation sequencing (NGS) that might be used to other HLA loci and present the HLA-E haplotype diversity considering the segment encoding the entire HLA-E mRNA (including 5'UTR, introns and the 3'UTR) in two African population samples, Susu from Guinea-Conakry and Lobi from Burkina Faso. Our results indicate that (a) the HLA-E gene is indeed conserved, encoding mainly two different protein molecules; (b) Africans do present several unknown HLA-E alleles presenting synonymous mutations; (c) the HLA-E 3'UTR is quite polymorphic and (d) haplotypes in the HLA-E 3'UTR are in close association with HLA-E coding alleles. NGS has proved to be an important tool on data generation for future studies evaluating variability in non-classical MHC genes. Copyright © 2015 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Genetic analysis and fine mapping of a rice brown planthopper (Nilaparvata lugens Stål) resistance gene bph19(t).

PubMed

Chen, J W; Wang, L; Pang, X F; Pan, Q H

2006-04-01

Genetic analysis and fine mapping of a resistance gene against brown planthopper (BPH) biotype 2 in rice was performed using two F(2) populations derived from two crosses between a resistant indica cultivar (cv.), AS20-1, and two susceptible japonica cvs., Aichi Asahi and Lijiangxintuanheigu. Insect resistance was evaluated using F(1) plants and the two F(2) populations. The results showed that a single recessive gene, tentatively designated as bph19(t), conditioned the resistance in AS20-1. A linkage analysis, mainly employing microsatellite markers, was carried out in the two F(2) populations through bulked segregant analysis and recessive class analysis (RCA), in combination with bioinformatics analysis (BIA). The resistance gene locus bph19(t) was finely mapped to a region of about 1.0 cM on the short arm of chromosome 3, flanked by markers RM6308 and RM3134, where one known marker RM1022, and four new markers, b1, b2, b3 and b4, developed in the present study were co-segregating with the locus. To physically map this locus, the bph19(t)-linked markers were landed on bacterial artificial chromosome or P1 artificial chromosome clones of the reference cv., Nipponbare, released by the International Rice Genome Sequencing Project. Sequence information of these clones was used to construct a physical map of the bph19(t) locus, in silico, by BIA. The bph19(t) locus was physically defined to an interval of about 60 kb. The detailed genetic and physical maps of the bph19(t) locus will facilitate marker-assisted gene pyramiding and cloning.

An Investigation of Preservice Teachers' Perceptions of Locus of Control, Self-Regulation, and Motivation in Online Learning

ERIC Educational Resources Information Center

Min, Sung-Ho

2012-01-01

This study examined how students' perceptions of locus of control, self-regulation, and motivation were related in an online learning environment. The participants were 73 preservice teachers enrolled in two online technology courses. Near the end of their online course, the participants completed "Brown's Locus of Control…

Locus of Control, Interest in Schooling and Science Achievement of Some Deaf and Typical Secondary School Students in Nigeria

ERIC Educational Resources Information Center

Olatoye, R. Ademola; Aanu, E. Mosunmola

2010-01-01

This study compared locus of control, interest in school and science achievement of typical and deaf secondary school students. The study also investigated influence of students' locus of control and interest in school on general science achievement. Seventy two (72) deaf and 235 typical children were purposively selected from eight secondary…

Complex Copy Number Variation of AMY1 does not Associate with Obesity in two East Asian Cohorts.

PubMed

Yong, Rita Y Y; Mustaffa, Su'Aidah B; Wasan, Pavandip S; Sheng, Liang; Marshall, Christian R; Scherer, Stephen W; Teo, Yik-Ying; Yap, Eric P H

2016-07-01

The human amylase gene locus at chromosome 1p21.1 is structurally complex. This region contains two pancreatic amylase genes, AMY2B, AMY2A, and a salivary gene AMY1. The AMY1 gene harbors extensive copy number variation (CNV), and recent studies have implicated this variation in adaptation to starch-rich diets and in association to obesity for European and Asian populations. In this study, we showed that by combining quantitative PCR and digital PCR, coupled with careful experimental design and calibration, we can improve the resolution of genotyping CNV with high copy numbers (CNs). In two East Asian populations of Chinese and Malay ethnicity studied, we observed a unique non-normal distribution of AMY1 diploid CN genotypes with even:odd CNs ratio of 4.5 (3.3-4.7), and an association between the common AMY2A CN = 2 genotype and odd CNs of AMY1, that could be explained by the underlying haplotypic structure. In two further case-control cohorts (n = 932 and 145, for Chinese and Malays, respectively), we did not observe the previously reported association between AMY1 and obesity or body mass index. Improved methods for accurately genotyping multiallelic CNV loci and understanding the haplotype complexity at the AMY1 locus are necessary for population genetics and association studies. © 2016 WILEY PERIODICALS, INC.

Partial isodisomy for maternal chromosome 7 and short stature in an individual with a mutation at the COL1A2 locus.

PubMed Central

Spotila, L D; Sereda, L; Prockop, D J

1992-01-01

Uniparental disomy for chromosome 7 has been described previously in two individuals with cystic fibrosis. Here, we describe a third case that was discovered because the proband was homozygous for a mutation in the COL1A2 gene for type I procollagen, although his mother was heterozygous and his father did not have the mutation. Phenotypically, the proband was similar to the two previously reported cases with uniparental disomy for chromosome 7, in that he was short in stature and growth retarded. Paternity was assessed with five polymorphic markers. Chromosome 7 inheritance in the proband was analyzed using 12 polymorphic markers distributed along the entire chromosome. Similar analysis of the proband's two brothers established the phase of the alleles at the various loci, assuming minimal recombination. The proband inherited only maternal alleles at five loci and was homozygous at all loci examined, except one. He was heterozygous for an RFLP at the IGBP-1 locus at 7p13-p12. The results suggest that the isodisomy was not complete because of a recombination event involving the proximal short arms of two maternal chromosomes. In addition, the phenotype of proportional dwarfism in the proband suggests imprinting of one or more growth-related genes on chromosome 7. Images Figure 1 Figure 3 Figure 4 Figure 5 PMID:1463018

A locus problem solved by using a mechanism with three dyads and two leading elements

NASA Astrophysics Data System (ADS)

Popescu, I.; Sass, L.; Romanescu, A. E.

2016-11-01

In Geometry there are many types of loci, solved by means of classic geometrical considerations and yielding lines and arcs of circles or conics. Yet more complicated locus can be solved by means of the Theory of Mechanisms. Our research starts from a locus and provides a solution based on the Theory of Mechanisms, finding the equivalent mechanism. The structural and cinematic analysis of the mechanism is made, determining the trajectory of a point representing the locus which presents interest. The mechanism has three dyads and two leading elements, for which the movements were correlated by means of a coefficient q. For various values of q different loci were obtained, similar for close values of q but different for significantly different values of q.

Selective sweep at the Drosophila melanogaster Suppressor of Hairless locus and its association with the In(2L)t inversion polymorphism.

PubMed Central

Depaulis, F; Brazier, L; Veuille, M

1999-01-01

The hitchhiking model of population genetics predicts that an allele favored by Darwinian selection can replace haplotypes from the same locus previously established at a neutral mutation-drift equilibrium. This process, known as "selective sweep," was studied by comparing molecular variation between the polymorphic In(2L)t inversion and the standard chromosome. Sequence variation was recorded at the Suppressor of Hairless (Su[H]) gene in an African population of Drosophila melanogaster. We found 47 nucleotide polymorphisms among 20 sequences of 1.2 kb. Neutrality tests were nonsignificant at the nucleotide level. However, these sites were strongly associated, because 290 out of 741 observed pairwise combinations between them were in significant linkage disequilibrium. We found only seven haplotypes, two occurring in the 9 In(2L)t chromosomes, and five in the 11 standard chromosomes, with no shared haplotype. Two haplotypes, one in each chromosome arrangement, made up two-thirds of the sample. This low haplotype diversity departed from neutrality in a haplotype test. This pattern supports a selective sweep hypothesis for the Su(H) chromosome region. PMID:10388820

Immunoglobulin λ Gene Rearrangement Can Precede κ Gene Rearrangement

DOE PAGES

Berg, Jörg; Mcdowell, Mindy; Jäck, Hans-Martin; ...

1990-01-01

Imore » mmunoglobulin genes are generated during differentiation of B lymphocytes by joining gene segments. A mouse pre-B cell contains a functional immunoglobulin heavy-chain gene, but no light-chain gene. Although there is only one heavy-chain locus, there are two lightchain loci: κ and λ .t has been reported that κ loci in the germ-line configuration are never (in man) or very rarely (in the mouse) present in cells with functionally rearranged λ -chain genes. Two explanations have been proposed to explain this: (a) the ordered rearrangement theory, which postulates that light-chain gene rearrangement in the pre-B cell is first attempted at the κ locus, and that only upon failure to produce a functional κ chain is there an attempt to rearrange the λ locus; and (b) the stochastic theory, which postulates that rearrangement at the λ locus proceeds at a rate that is intrinsically much slower than that at the κ locus. We show here that λ -chain genes are generated whether or not the κ locus has lost its germ-line arrangement, a result that is compatible only with the stochastic theory.« less

Assessing disease-modifying effects of norepinephrine in Down syndrome and Alzheimer's disease.

PubMed

Ponnusamy, Ravikumar; McNerney, M Windy; Moghadam, Shahrzad; Salehi, Ahmad

2017-11-08

Building upon the knowledge that a number of important brain circuits undergo significant degeneration in Alzheimer's disease, numerous recent studies suggest that the norepinephrine-ergic system in the brainstem undergoes significant alterations early in the course of both Alzheimer's disease and Down syndrome. Massive projections from locus coeruleus neurons to almost the entire brain, extensive innervation of brain capillaries, and widespread distribution of noradrenergic receptors enable the norepinephrine-ergic system to play a crucial role in neural processes, including cognitive function. These anatomical and functional characteristics support the role of the norepinephrine-ergic system as an important target for developing new therapies for cognitive dysfunction. Careful neuropathological examinations using postmortem samples from individuals with Alzheimer's disease have implicated the role of the norepinephrine-ergic system in the etiopathogenesis of Alzheimer's disease. Furthermore, numerous studies have supported the existence of a strong interaction between norepinephrine-ergic and neuroimmune systems. We explore the interaction between the two systems that could play a role in the disease-modifying effects of norepinephrine in Alzheimer's disease and Down syndrome. Copyright © 2017. Published by Elsevier B.V.

Identification of Cryptosporidium Species and Genotypes in Scottish Raw and Drinking Waters during a One-Year Monitoring Period▿

PubMed Central

Nichols, R. A. B.; Connelly, L.; Sullivan, C. B.; Smith, H. V.

2010-01-01

We analyzed 1,042 Cryptosporidium oocyst-positive slides (456 from raw waters and 586 from drinking waters) of which 55.7% contained 1 or 2 oocysts, to determine species/genotypes present in Scottish waters. Two nested PCR-restriction fragment length polymorphism (RFLP) assays targeting different loci (1 and 2) of the hypervariable region of the 18S rRNA gene were used for species identification, and 62.4% of samples were amplified with at least one of the PCR assays. More samples (577 slides; 48.7% from raw water and 51.3% from drinking water) were amplified at locus 1 than at locus 2 (419 slides; 50.1% from raw water and 49.9% from drinking water). PCR at loci 1 and 2 amplified 45.4% and 31.7% of samples containing 1 or 2 oocysts, respectively. We detected both human-infectious and non-human-infectious species/genotype oocysts in Scottish raw and drinking waters. Cryptosporidium andersoni, Cryptosporidium parvum, and the Cryptosporidium cervine genotype (now Cryptosporidium ubiquitum) were most commonly detected in both raw and drinking waters, with C. ubiquitum being most common in drinking waters (12.5%) followed by C. parvum (4.2%) and C. andersoni (4.0%). Numerous samples (16.6% total; 18.9% from drinking water) contained mixtures of two or more species/genotypes, and we describe strategies for unraveling their identity. Repetitive analysis for discriminating mixtures proved useful, but both template concentration and PCR assay influenced outcomes. Five novel Cryptosporidium spp. (SW1 to SW5) were identified by RFLP/sequencing, and Cryptosporidium sp. SW1 was the fourth most common contaminant of Scottish drinking water (3%). PMID:20639357

Genetic linkage analysis using pooled DNA and infrared detection of tailed STRP primer patterns

NASA Astrophysics Data System (ADS)

Oetting, William S.; Wildenberg, Scott C.; King, Richard A.

1996-04-01

The mapping of a disease locus to a specific chromosomal region is an important step in the eventual isolation and analysis of a disease causing gene. Conventional mapping methods analyze large multiplex families and/or smaller nuclear families to find linkage between the disease and a chromosome marker that maps to a known chromosomal region. This analysis is time consuming and tedious, typically requiring the determination of 30,000 genotypes or more. For appropriate populations, we have instead utilized pooled DNA samples for gene mapping which greatly reduces the amount of time necessary for an initial chromosomal screen. This technique assumes a common founder for the disease locus of interest and searches for a region of a chromosome shared between affected individuals. Our analysis involves the PCR amplification of short tandem repeat polymorphisms (STRP) to detect these shared regions. In order to reduce the cost of genotyping, we have designed unlabeled tailed PCR primers which, when combined with a labeled universal primer, provides for an alternative to synthesizing custom labeled primers. The STRP pattern is visualized with an infrared fluorescence based automated DNA sequencer and the patterns quantitated by densitometric analysis of the allele pattern. Differences in the distribution of alleles between pools of affected and unaffected individuals, including a reduction in the number of alleles in the affected pool, indicate the sharing of a region of a chromosome. We have found this method effective for markers 10 - 15 cM away from the disease locus for a recessive genetic disease.

Patterns of MHC-DRB1 polymorphism in a post-glacial island canid, the Newfoundland red fox (Vulpes vulpes deletrix), suggest balancing selection at species and population timescales.

PubMed

Marshall, H Dawn; Langille, Barbara L; Hann, Crystal A; Whitney, Hugh G

2016-05-01

As the only native insular Newfoundland canid between the extinction of the wolf in the 1930s and the recent arrival of coyotes, the red fox (Vulpes vulpes deletrix Bangs 1898) poses interesting questions about genetic distinctiveness and the post-glacial colonization history of the island's depauperate mammalian fauna. Here, we characterized genetic variability at the major histocompatibility complex (MHC) class II DR β1 domain (DRB1) locus in 28 red foxes from six sampling localities island-wide and compared it with mitochondrial control region (CR) diversity and DRB1 diversity in other canids. Our goals were to describe novel DRB1 alleles in a new canid population and to make inferences about the role of selection in maintaining their diversity. As in numerous studies of vertebrates, we found an order-of-magnitude higher nucleotide diversity at the DRB1 locus compared with the CR and significantly positive nonsynonymous-to-synonymous substitution ratios, indicative of selection in the distant past. Although the evidence is weaker, the Ewens-Watterson test of neutrality and the geographical distribution of variation compared with the CR suggest a role for selection over the evolutionary timescale of populations. We report the first genetic data from the DRB1 locus in the red fox and establish baseline information regarding immunogenetic variation in this island canid population which should inform continued investigations of population demography, adaptive genetic diversity, and wildlife disease in red foxes and related species.

Genetic data and de novo mutation rates in father-son pairs of 23 Y-STR loci in Southern Brazil population.

PubMed

Da Fré, Nicole Nascimento; Rodenbusch, Rodrigo; Gastaldo, André Zoratto; Hanson, Erin; Ballantyne, Jack; Alho, Clarice Sampaio

2015-11-01

We evaluated haplotype and allele frequencies, as well as statistical forensic parameters, for 23 Y-chromosome short tandem repeats (STRs) loci of the PowerPlex®Y23 system (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, Y-GATA-H4, DYS481, DYS533, DYS549, DYS570, DYS576, DYS643) in a sample of 150 apparently healthy males, resident in South Brazil. A total of 150 different haplotypes were identified. The highest gene diversity (GD) was observed for the single locus marker DYS570 (GD = 0.7888) and for a two-locus system DYS385 (GD = 0.9009). We also examined 150 father-son pairs by the same system, and a total of 13 mutations were identified in the 3450 father-son allelic transfers, with an overall mutation rate across the 23 loci of 3.768 × 10(-3) (95% CI: 3.542 × 10(-3) to 3.944 × 10(-3)). In all cases there was only one locus mutated with gain/loss of repeats in the son (5 one-repeat gains, and 7 one-repeat and 1 two-repeat losses); we observed no instances of mutations involving a non-integral number of repeats.

Waardenberg syndrome (WS) type I is caused by defects at multiple loci, one of which is near ALPP on chromosome 2: First report of the WS consortium

PubMed Central

Farrer, Lindsay A.; Grundfast, Kenneth M.; Amos, Jean; Arnos, Kathleen S.; Asher, James H.; Beighton, Peter; Diehl, Scott R.; Fex, Jörgen; Foy, Carole; Friedman, Thomas B.; Greenberg, Jacquie; Hoth, Christopher; Marazita, Mary; Milunsky, Aubrey; Morell, Robert; Nance, Walter; Newton, Valerie; Ramesar, Rajkumar; Agustin, Theresa B. San; Skare, James; Stevens, Cathy A.; Wagner, Ronald G.; Wilcox, Edward R.; Winship, Ingrid; Read, Andrew P.

1992-01-01

Previous studies have localized the gene for Waardenburg syndrome (WS) type I to the distal portion of chromosome 2q, near the ALPP locus. We pooled linkage data obtained from 41 WS type I and 3 WS type II families which were typed for six polymorphic loci on chromosome 2q in order to refine the location of the WS locus (WS1) and evaluate the extent of genetic heterogeneity. In the course of this work, we developed diagnostic criteria for genetic and phenotypic studies. Our findings, based on two-locus and multilocus analysis using a linkage map established from reference pedigrees, suggest that there are two or more mutations causing WS, one of which (i.e., WS1) is located on chromosome 2q, between the ALPP and FN1 loci, at distances of 7.8 cM and 11.2 cM for each marker, respectively. The results also indicate that WS1 is responsible for the illness in approximately 45% of all families in this sample. However, the odds favoring this position over a location between ALPP and SAG are only 2:1 when alternate assumptions about the proportion of linked families are considered. We conclude that a more saturated map of this region of chromosome 2q, including highly polymorphic markers, will be needed to accurately distinguish linked families and, ultimately, isolate the mutant gene. PMID:1349198

A PCR marker linked to a THCA synthase polymorphism is a reliable tool to discriminate potentially THC-rich plants of Cannabis sativa L.

PubMed

Staginnus, Christina; Zörntlein, Siegfried; de Meijer, Etienne

2014-07-01

Neither absolute THC content nor morphology allows the unequivocal discrimination of fiber cultivars and drug strains of Cannabis sativa L. unequivocally. However, the CBD/THC ratio remains constant throughout the plant's life cycle, is independent of environmental factors, and considered to be controlled by a single locus (B) with two codominant alleles (B(T) and B(D)). The homozygous B(T)/B(T) genotype underlies the THC-predominant phenotype, B(D)/B(D) is CBD predominant, and an intermediate phenotype is induced by the heterozygous state (B(T)/B(D)). Using PCR-based markers in two segregating populations, we proved that the THCA synthase gene represents the postulated B locus and that specific sequence polymorphisms are absolutely linked either to the THC-predominant or the THC-intermediate chemotype. The absolute linkage provides an excellent reliability of the marker signal in forensic casework. For validation, the species-specific marker system was applied to a large number of casework samples and fiber hemp cultivars. © 2014 American Academy of Forensic Sciences.

Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system.

PubMed

Hanson, Sara J; Byrne, Kevin P; Wolfe, Kenneth H

2014-11-11

Saccharomyces cerevisiae has a complex system for switching the mating type of haploid cells, requiring the genome to have three mating-type (MAT)-like loci and a mechanism for silencing two of them. How this system originated is unknown, because the three-locus system is present throughout the family Saccharomycetaceae, whereas species in the sister Candida clade have only one locus and do not switch. Here we show that yeasts in a third clade, the methylotrophs, have a simpler two-locus switching system based on reversible inversion of a section of chromosome with MATa genes at one end and MATalpha genes at the other end. In Hansenula polymorpha the 19-kb invertible region lies beside a centromere so that, depending on the orientation, either MATa or MATalpha is silenced by centromeric chromatin. In Pichia pastoris, the orientation of a 138-kb invertible region puts either MATa or MATalpha beside a telomere and represses transcription of MATa2 or MATalpha2. Both species are homothallic, and inversion of their MAT regions can be induced by crossing two strains of the same mating type. The three-locus system of S. cerevisiae, which uses a nonconservative mechanism to replace DNA at MAT, likely evolved from a conservative two-locus system that swapped genes between expression and nonexpression sites by inversion. The increasing complexity of the switching apparatus, with three loci, donor bias, and cell lineage tracking, can be explained by continuous selection to increase sporulation ability in young colonies. Our results provide an evolutionary context for the diversity of switching and silencing mechanisms.

Evolution of hierarchical cytoplasmic inheritance in the plasmodial slime mold Physarum polycephalum.

PubMed

Iwanaga, Akiko; Sasaki, Akira

2004-04-01

A striking linear dominance relationship for uniparental mitochondrial transmission is known between many mating types of plasmodial slime mold Physarum polycephalum. We herein examine how such hierarchical cytoplasmic inheritance evolves in isogamous organisms with many self-incompatible mating types. We assume that a nuclear locus determines the mating type of gametes and that another nuclear locus controls the digestion of mitochondria DNAs (mtDNAs) of the recipient gamete after fusion. We then examine the coupled genetic dynamics for the evolution of self-incompatible mating types and biased mitochondrial transmission between them. In Physarum, a multiallelic nuclear locus matA controls both the mating type of the gametes and the selective elimination of the mtDNA in the zygotes. We theoretically examine two potential mechanisms that might be responsible for the preferential digestion of mitochondria in the zygote. In the first model, the preferential digestion of mitochondria is assumed to be the outcome of differential expression levels of a suppressor gene carried by each gamete (suppression-power model). In the second model (site-specific nuclease model), the digestion of mtDNAs is assumed to be due to their cleavage by a site-specific nuclease that cuts the mtDNA at unmethylated recognition sites. Also assumed is that the mtDNAs are methylated at the same recognition site prior to the fusion, thereby being protected against the nuclease of the same gamete, and that the suppressor alleles convey information for the recognition sequences of nuclease and methylase. In both models, we found that a linear dominance hierarchy evolves as a consequence of the buildup of a strong linkage disequilibrium between the mating-type locus and the suppressor locus, though it fails to evolve if the recombination rate between the two loci is larger than a threshold. This threshold recombination rate depends on the number of mating types and the degree of fitness reduction in the heteroplasmic zygotes. If the recombination rate is above the threshold, suppressor alleles are equally distributed in each mating type at evolutionary equilibrium. Based on the theoretical results of the site-specific nuclease model, we propose that a nested subsequence structure in the recognition sequence should underlie the linear dominance hierarchy of mitochondrial transmission.

Genetic distance of Malaysian mousedeer based on mitochondrial DNA cytochrome oxidase I (COI) and D-loop region sequences

NASA Astrophysics Data System (ADS)

Bakar, Mohamad-Azam Akmal Abu; Rovie-Ryan, Jeffrine Japning; Ampeng, Ahmad; Yaakop, Salmah; Nor, Shukor Md; Md-Zain, Badrul Munir

2018-04-01

Mousedeer is one of the primitive mammals that can be found mainly in Southeast-Asia region. There are two species of mousedeer in Malaysia which are Tragulus kanchil and Tragulus napu. Both species can be distinguish by size, coat coloration, and throat pattern but clear diagnosis still cannot be found. The objective of the study is to show the genetic distance relationship between T. kanchil and T. napu and their population based on mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) and D-loop region. There are 42 sample of mousedeer were used in this study collected by PERHILITAN from different locality. Another 29 D-loop sequence were retrieved from Genbank for comparative analysis. All sample were amplified using universal primer and species-specific primer for COI and D-loop genes via PCR process. The amplified sequences were analyzed to determine genetic distance of T. kanchil and T. napu. From the analysis, the average genetic distance between T. kanchil and T. napu based on locus COI and D-loop were 0.145 and 0.128 respectively. The genetic distance between populations of T. kanchil based on locus COI was between 0.003-0.013. For locus D-loop, genetic distance analysis showed distance in relationship between west-coast populations to east-coast population of T. kanchil. COI and D-loop mtDNA region provided a clear picture on the relationship within the mousedeer species. Last but not least, conservation effort toward protecting this species can be done by study the molecular genetics and prevent the extinction of this species.

Genomic Analysis of the Appearance of Ovarian Mast Cells in Neonatal MRL/MpJ Mice

PubMed Central

Nakamura, Teppei; Sakata, Yuko; Otsuka-Kanazawa, Saori; Ichii, Osamu; Chihara, Masataka; Nagasaki, Ken-ichi; Namiki, Yuka; Kon, Yasuhiro

2014-01-01

In MRL/MpJ mice, ovarian mast cells (OMCs) are more abundant than in other mouse strains, and tend to distribute beneath the ovarian surface epithelium at birth. This study investigated the factors regulating the appearance of neonatal OMCs in progeny of the cross between MRL/MpJ and C57BL/6N strains. F1 neonates had less than half the number of OMCs than MRL/MpJ. Interestingly, MRLB6F1 had more neonatal OMCs than B6MRLF1, although they were distributed over comparable areas. Furthermore, in MRL/MpJ fetuses for which parturition was delayed until embryonic day 21.5, the number of OMCs was significantly higher than in age-matched controls at postnatal day 2. These results suggest that the number of OMCs was influenced by the environmental factors during pregnancy. Quantitative trait locus analysis using N2 backcross progeny revealed two significant loci on chromosome 8: D8Mit343–D8Mit312 for the number of OMCs and D8Mit86–D8Mit89 for their distribution, designated as mast cell in the ovary of MRL/MpJ 1 (mcom1) and mcom2, respectively. Among MC migration-associated genes, ovarian expression of chemokine (C-C motif) ligand 17 at mcom1 locus was significantly higher in MRL/MpJ than in C57BL/6N, and positively correlated with the expression of OMC marker genes. These results indicate that the appearance of neonatal OMCs in MRL/MpJ is controlled by environmental factors and filial genetic factors, and that the abundance and distribution of OMCs are regulated by independent filial genetic elements. PMID:24956472

Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species.

PubMed

Chen, Shilin; Yao, Hui; Han, Jianping; Liu, Chang; Song, Jingyuan; Shi, Linchun; Zhu, Yingjie; Ma, Xinye; Gao, Ting; Pang, Xiaohui; Luo, Kun; Li, Ying; Li, Xiwen; Jia, Xiaocheng; Lin, Yulin; Leon, Christine

2010-01-07

The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL+matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over. Here, we compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species. Our ranking criteria included PCR amplification efficiency, differential intra- and inter-specific divergences, and the DNA barcoding gap. Our data suggest that the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications. Furthermore, we tested the discrimination ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the ITS2 was 92.7% at the species level. The ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species. We also propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa.

Linkage Disequilibrium Under Recurrent Bottlenecks

PubMed Central

Schaper, E.; Eriksson, A.; Rafajlovic, M.; Sagitov, S.; Mehlig, B.

2012-01-01

To model deviations from selectively neutral genetic variation caused by different forms of selection, it is necessary to first understand patterns of neutral variation. Best understood is neutral genetic variation at a single locus. But, as is well known, additional insights can be gained by investigating multiple loci. The resulting patterns reflect the degree of association (linkage) between loci and provide information about the underlying multilocus gene genealogies. The statistical properties of two-locus gene genealogies have been intensively studied for populations of constant size, as well as for simple demographic histories such as exponential population growth and single bottlenecks. By contrast, the combined effect of recombination and sustained demographic fluctuations is poorly understood. Addressing this issue, we study a two-locus Wright–Fisher model of a population subject to recurrent bottlenecks. We derive coalescent approximations for the covariance of the times to the most recent common ancestor at two loci in samples of two chromosomes. This covariance reflects the degree of association and thus linkage disequilibrium between these loci. We find, first, that an effective population-size approximation describes the numerically observed association between two loci provided that recombination occurs either much faster or much more slowly than the population-size fluctuations. Second, when recombination occurs frequently between but rarely within bottlenecks, we observe that the association of gene histories becomes independent of physical distance over a certain range of distances. Third, we show that in this case, a commonly used measure of linkage disequilibrium, σd2 (closely related to r^2), fails to capture the long-range association between two loci. The reason is that constituent terms, each reflecting the long-range association, cancel. Fourth, we analyze a limiting case in which the long-range association can be described in terms of a Xi coalescent allowing for simultaneous multiple mergers of ancestral lines. PMID:22048021

[Genetic diversity of microsatellite loci in captive Amur tigers].

PubMed

Zhang, Yu-Gaung; Li, Di-Qiang; Xiao, Qi-Ming; Rao, Li-Qun; Zhang, Xue-Wen

2004-09-01

The tiger is one of the most threatened wildlife species since the abundance and distribution of tiger have decreased dramatically in the last century. The wild Amur tiger (Panthera tigris altaica) only distributed in northeast China, the far east area of Russia and the north Korea and its size of wild population is about 450 in the world and 20 in China. Several hundred captive populations of Amur tigers are the main source to protect gene library of tiger and the source of recovering the wild populations. The Breeding Center for Felidae at Hengdaohezi and Haoerbin Tiger Park in Heilongjiang Province is the biggest captive breeding base in China. How to make clear the genetic pedigree and establish reasonable breeding system is the urgent issues. So we use the microsatellite DNA markers and non-invasive technology to research on the genetic diversity of captive Amur tiger in this study. Ten microsatellite loci (Fca005, Fca075, Fca094, Fca152, Fca161, Fca294, Pti002, Pti003, Pti007 and Pti010), highly variable nuclear markers, were studied their genetic diversity in 113 captive Amur tigers. The PCR amplified products of microsatellite loci were detected by non-denatured polyacrylamide gel electrophoresis. Allele numbers, allelic frequency, gene heterozygosity(H(e)), polymorphism information content(PIC) and effective number of allele(N(e)) were calculated. 41 alleles were found and their size were ranged from 110bp to 250bp in ten microsatellite loci, Fca152 had 6 alleles, Fca075, Fca094 and Fca294 had 5 alleles, Fca005 and Pti002 had 4 alleles and the others had 3 alleles in all tiger samples, respectively. The allelic frequencies were from 0.009 to 0.767; The He ranged from 0.385 to 0.707, and Fca294 and Pti010 locus had the highest and lowest value; the PIC were from 0.353 to 0.658, Fca294 and Pti010 locus had the highest and lowest value; and N(e) were from 1.626 to 3.409, Fca294 and Pti010 locus had the highest and lowest value, which showed the ten microsatellie loci had high or medium polymorphism in these Amur tigers and had high genetic diversity. At the same time, we only found even bases variability which showed the even bases repeat sequence (CA/GT) maybe the basic unit for length variability of microsatellite in all loci. In this study, the samples were made up of 75 hair specimens, 23 blood specimens and 15 tissue specimens, we obtained the genome DNA from hairs using the non-invasive DNA technology and demonstrated that DNA derived from hair samples is as good as that obtained from blood samples for the analysis of microsatellite polymorphism. These results imply that microsatellite DNA markers and non-invasive DNA technology can help study the genetic diversity of Amur tiger. This method could be used in the captive management of other endangered species.

Global genetic architecture of an erythroid quantitative trait locus, HMIP-2.

PubMed

Menzel, Stephan; Rooks, Helen; Zelenika, Diana; Mtatiro, Siana N; Gnanakulasekaran, Akshala; Drasar, Emma; Cox, Sharon; Liu, Li; Masood, Mariam; Silver, Nicholas; Garner, Chad; Vasavda, Nisha; Howard, Jo; Makani, Julie; Adekile, Adekunle; Pace, Betty; Spector, Tim; Farrall, Martin; Lathrop, Mark; Thein, Swee Lay

2014-11-01

HMIP-2 is a human quantitative trait locus affecting peripheral numbers, size and hemoglobin composition of red blood cells, with a marked effect on the persistence of the fetal form of hemoglobin, HbF, in adults. The locus consists of multiple common variants in an enhancer region for MYB (chr 6q23.3), which encodes the hematopoietic transcription factor cMYB. Studying a European population cohort and four African-descended groups of patients with sickle cell anemia, we found that all share a set of two spatially separate HbF-promoting alleles at HMIP-2, termed "A" and "B." These typically occurred together ("A-B") on European chromosomes, but existed on separate homologous chromosomes in Africans. Using haplotype signatures for "A" and "B," we interrogated public population datasets. Haplotypes carrying only "A" or "B" were typical for populations in Sub-Saharan Africa. The "A-B" combination was frequent in European, Asian, and Amerindian populations. Both alleles were infrequent in tropical regions, possibly undergoing negative selection by geographical factors, as has been reported for malaria with other hematological traits. We propose that the ascertainment of worldwide distribution patterns for common, HbF-promoting alleles can aid their further genetic characterization, including the investigation of gene-environment interaction during human migration and adaptation. © 2014 The Authors. Annals of Human Genetics published by University College London (UCL) and John Wiley & Sons Ltd.

[Locus HS.633957 expression in human gastrointestinal tract and tumors].

PubMed

Polev, D E; Krukovskaia, L L; Kozlov, A P

2011-01-01

Human locus HS.633957 corresponds to its namesake cluster in the UniGene database http:/www.ncbi.nlm.nih.gov/unigene. It is located on chromosome 7 and is 3.7 tpn in size. It does not seem to encode proteins nor has its function been identified. According to bioinformation evidence, its expression is tumor-specific. PCR assay on kDNA samples from different intact human tissues detected its slight expression in liver, heart, embryonal brain and kidney as well as in a wide spectrum of tumors. This work features locus Hs.633957 expression in different parts of human gastrointestinal tract and tumors.

Frame of Reference Model of Self-Concept and Locus of Control: A Cross Gender Study in the United Arab Emirates.

ERIC Educational Resources Information Center

Abu-Hilal, Maher M.

A study tested predictions for I/E (internal external) frame of reference model and extended this model to include locus of control. A sample of upper elementary (n=181) and junior high (n=191) students in the United Arab Emirates participated in the study. Structural equation modeling (SEM) analyses provided support to the external comparison…

The Interrelationship of Social Anxiety with Anxiety, Depression, Locus of Control, Ways of Coping and Ego Strength amongst University Students

ERIC Educational Resources Information Center

Shepherd, Robin-Marie; Edelman, Robert J.

2009-01-01

This is the first study to investigate the interrelationship of social anxiety with the variables anxiety, depression, locus of control, ego strength and ways of coping in a sample of university students. There were high scores of social anxiety which were related to high scores on measures of anxiety and depression, low ego strength, external…

Modeling Turnover Intentions and Their Antecedents Using the Locus of Control as a Moderator: A Case of Customer Service Employees

ERIC Educational Resources Information Center

Chiu, Chou-Kang; Lin, Chieh-Peng; Tsai, Yuan Hui; Hsiao, Ching-Yun

2005-01-01

The psychological model of organizational commitment (OC) has been extensively investigated in U.S. workers (Near, 1989), but less frequently applied in cross-personality studies. The investigation proposes a model of turnover intentions (TI) that uses locus of control (LOC) as a moderator. A causal model and a firm-specific sample were used to…

Population-specific variation in haplotype composition and heterozygosity at the POLB locus.

PubMed

Yamtich, Jennifer; Speed, William C; Straka, Eva; Kidd, Judith R; Sweasy, Joann B; Kidd, Kenneth K

2009-05-01

DNA polymerase beta plays a central role in base excision repair (BER), which removes large numbers of endogenous DNA lesions from each cell on a daily basis. Little is currently known about germline polymorphisms within the POLB locus, making it difficult to study the association of variants at this locus with human diseases such as cancer. Yet, approximately thirty percent of human tumor types show variants of DNA polymerase beta. We have assessed the global frequency distributions of coding and common non-coding SNPs in and flanking the POLB gene for a total of 14 sites typed in approximately 2400 individuals from anthropologically defined human populations worldwide. We have found a marked difference between haplotype frequencies in African populations and in non-African populations.

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

Mao, Peiyuan; Urry, C. Megan

We investigate a sample of 622 blazars with measured fluxes at 12 wavebands across the radio-to-gamma-ray spectrum but without spectroscopic or photometric redshifts. This sample includes hundreds of sources with newly analyzed X-ray spectra reported here. From the synchrotron peak frequencies, estimated by fitting the broadband spectral energy distributions (SEDs), we find that the fraction of high-synchrotron-peaked blazars in these 622 sources is roughly the same as in larger samples of blazars that do have redshifts. We characterize the no-redshift blazars using their infrared colors, which lie in the distinct locus called the WISE blazar strip, then estimate their redshiftsmore » using a KNN regression based on the redshifts of the closest blazars in the WISE color–color plot. Finally, using randomly drawn values from plausible redshift distributions, we simulate the SEDs of these blazars and compare them to known blazar SEDs. Based on all these considerations, we conclude that blazars without redshift estimates are unlikely to be high-luminosity, high-synchrotron-peaked objects, which had been suggested in order to explain the “blazar sequence”—an observed trend of SED shape with luminosity—as a selection effect. Instead, the observed properties of no-redshift blazars are compatible with a causal connection between jet power and electron cooling, i.e., a true blazar sequence.« less

The stability of locus equation slopes across stop consonant voicing/aspiration

NASA Astrophysics Data System (ADS)

Sussman, Harvey M.; Modarresi, Golnaz

2004-05-01

The consistency of locus equation slopes as phonetic descriptors of stop place in CV sequences across voiced and voiceless aspirated stops was explored in the speech of five male speakers of American English and two male speakers of Persian. Using traditional locus equation measurement sites for F2 onsets, voiceless labial and coronal stops had significantly lower locus equation slopes relative to their voiced counterparts, whereas velars failed to show voicing differences. When locus equations were derived using F2 onsets for voiced stops that were measured closer to the stop release burst, comparable to the protocol for measuring voiceless aspirated stops, no significant effects of voicing/aspiration on locus equation slopes were observed. This methodological factor, rather than an underlying phonetic-based explanation, provides a reasonable account for the observed flatter locus equation slopes of voiceless labial and coronal stops relative to voiced cognates reported in previous studies [Molis et al., J. Acoust. Soc. Am. 95, 2925 (1994); O. Engstrand and B. Lindblom, PHONUM 4, 101-104]. [Work supported by NIH.

Molecular epidemiological characteristics of Salmonella enterica serovars Enteritidis, Typhimurium and Livingstone strains isolated in a Tunisian university hospital.

PubMed

Ktari, Sonia; Ksibi, Boutheina; Gharsallah, Houda; Mnif, Basma; Maalej, Sonda; Rhimi, Fouzia; Hammami, Adnene

2016-03-01

Enteritidis, Typhimurium and Livingstone are the main Salmonella enterica serovars recovered in Tunisia. Here, we aimed to assess the genetic diversity of fifty-seven Salmonella enterica strains from different sampling periods, origins and settings using pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST) and multi-locus variable-number tandem repeat analysis (MLVA). Salmonella Enteritidis, isolated from human and food sources from two regions in Sfax in 2007, were grouped into one cluster using PFGE. However, using MLVA these strains were divided into two clusters. Salmonella Typhimurium strains, recovered in 2012 and represent sporadic cases of human clinical isolates, were included in one PFGE cluster. Nevertheless, the MLVA technique, divided Salmonella Typhimurium isolates into six clusters with diversity index reaching (DI = 0.757). For Salmonella Livingstone which was responsible of two nosocomial outbreaks during 2000-2003, the PFGE and MLVA methods showed that these strains were genetically closely related. Salmonella Enteritidis and Salmonella Livingstone populations showed a single ST lineage ST11 and ST543 respectively. For Salmonella Typhimurium, two MLST sequence types ST19 and ST328 were defined. Salmonella Enteritidis and Salmonella Typhimurium strains were clearly differentiated by MLVA which was not the case using PFGE. © 2015 APMIS. Published by John Wiley & Sons Ltd.

High-resolution mapping of the S-locus in Turnera leads to the discovery of three genes tightly associated with the S-alleles.

PubMed

Labonne, Jonathan J D; Goultiaeva, Alina; Shore, Joel S

2009-06-01

While the breeding system known as distyly has been used as a model system in genetics, and evolutionary biology for over a century, the genes determining this system remain unknown. To positionally clone genes determining distyly, a high-resolution map of the S-locus region of Turnera has been constructed using segregation data from 2,013 backcross progeny. We discovered three putative genes tightly linked with the S-locus. An N-acetyltransferase (TkNACE) flanks the S-locus at 0.35 cM while a sulfotransferase (TkST1) and a non-LTR retroelement (TsRETRO) show complete linkage to the S-locus. An assay of population samples of six species revealed that TsRETRO, initially discovered in diploid Turnera subulata, is also associated with the S-allele in tetraploid T. subulata and diploid Turnera scabra. The sulfotransferase gene shows some level of differential expression in long versus short styles, indicating it might be involved in some aspect of distyly. The complete linkage of TkST1 and TsRETRO to the S-locus suggests that both genes may reside within, or in the immediate vicinity of the S-locus. Chromosome walking has been initiated using one of the genes discovered in the present study to identify the genes determining distyly.

Locus of control, quality of life, anxiety, and depression among Malaysian breast cancer patients: The mediating role of uncertainty.

PubMed

Pahlevan Sharif, Saeed

2017-04-01

The main objective of this study was to investigate the mediating role of uncertainty in the relationship between locus of control with quality of life, anxiety, and depression. A descriptive and correlational survey was conducted in a private hospital in Kuala Lumpur, Malaysia. A convenience sample of 118 Malaysian breast cancer patients voluntarily participated in the study and responded to a set of questionnaires including: socio-demographic questionnaire, the short form of Locus of Control Scale, the Functional Assessment of Cancer Therapy-Breast (FACT-B), the Hospital Anxiety and Depression Scale (HADS), and the Short-Form Mishel Uncertainty in Illness Scale (SF-MUIS). The results revealed that breast cancer patients with higher internal locus of control and lower external locus of control experience a higher quality of life, lower anxiety, and lower depression. Also, uncertainty mediated the relationship between locus of control with quality of life and depression (quasi-significant). The findings indicated the need for early, targeted psychological interventions seeking to gradually shift cancer patients' locus of control from external to internal in order to improve their quality of life and reduce their depression and anxiety. Moreover, health care providers by providing relevant information to cancer patients, especially for externally oriented patients, can reduce their uncertainty which in turn would improve their quality of life. Copyright © 2017 Elsevier Ltd. All rights reserved.

Use of swabs for sampling epithelial cells for molecular genetics analyses in Enteroctopus

USGS Publications Warehouse

Hollenback, Nathan; Scheel, David; Gravley, Megan C.; Sage, George K.; Toussaint, Rebecca K.; Talbot, Sandra L.

2017-01-01

We evaluated the efficacy of using swabs to collect cells from the epidermis of octopus as a non-invasive DNA source for classical genetic studies, and demonstrated value of the technique by incorporating it into an effort to determine, within a day, the lineage of captured, live Enteroctopus (E. dofleini or a cryptic lineage). The cryptic lineage was targeted for captive behavioral and morphological studies, while once genetically identified, the non-target lineage could be more rapidly released back to the wild. We used commercially available sterile foamtipped swabs and a high-salt preservation buffer to collect and store paired swab and muscle (arm tip) tissue sampled from live Enteroctopus collected from Prince William Sound, Alaska. We performed a one-day extraction of DNA from epithelial swab samples and amplification of two diagnostic microsatellite loci to determine the lineage of each of the 21 individuals. Following this rapid lineage assessment, which allowed us to release non-target individuals within a day of laboratory work, we compared paired swab and muscle tissue samples from each individual to assess quantity of DNA yields and consistency of genotyping results, followed by assessment of locus-by-locus reliability of DNA extracts from swabs. Epithelial swabs yielded, on average, lower quantities of DNA (170.32 ± 74.72 (SD) ng/μL) relative to DNA obtained from tissues collected using invasive or destructive techniques (310.95 ± 147.37 (SD) ng/μL. We observed some decrease in yields of DNA from extractions of swab samples conducted 19 and 31 months after initial extractions when samples were stored at room temperature in lysis buffer. All extractions yielded quantities of DNA sufficient to amplify and score all loci, which included fragment data from 10 microsatellite loci (nine polymorphic loci and monomorphic locus EdoμA106), and nucleotide sequence data from a 528 base pair portion of the nuclear octopine dehydrogenase gene. All results from genotyping and sequencing using paired swab and muscle tissue extracts were concordant, and experimental reliability levels for multilocus genotypes generated from swab samples exceeded 97%. This technique is useful for studies in which invasive sampling is not optimal, and in remote field situations since samples can be stored at ambient temperatures for at least 31 months. The use of epithelial swabs is thus a noninvasive technique appropriate for sampling genetic material from live octopuses for use in classical genetic studies as well as supporting experimental and behavioral studies.

Inheritance of Adrenal Phenylethanolamine N-Methyltransferase Activity in the Rat

PubMed Central

Stolk, Jon M.; Vantini, Guido; Guchhait, Ras B.; Hurst, Jeffrey H.; Perry, Bruce D.; U'Prichard, David C.; Elston, Robert C.

1984-01-01

Phenylethanolamine N-methyltransferase (PNMT) is the enzyme that catalyzes the S-adenosyl-l-methionine-dependent methylation of (-)norepinephrine to (-)epinephrine in the adrenal medulla. Adrenal PNMT activity is markedly different in two highly inbred rat strains; enzyme activity in the F344 strain is more than fivefold greater than that in the Buf strain. Initial characterization of the enzyme in the two inbred strains reveals evidence for catalytic and structural differences, as reflected in dissimilar Km values for the cosubstrate (S-adenosyl-l-methionine) and prominent differences in thermal inactivation curves. To assess adrenal PNMT activity in an F344 x Buf pedigree, we employed a statistical procedure to test for one- and two-locus hypotheses in the presence of within-class correlations due to cage or litter effects. The PNMT data in the pedigree are best accounted for by segregation at a simple major locus superimposed upon a polygenic background; data obtained from the biochemical studies suggest that the major locus is a structural gene locus. PMID:6149973

Giardia duodenalis and Cryptosporidium occurrence in Australian sea lions (Neophoca cinerea) exposed to varied levels of human interaction

PubMed Central

Delport, Tiffany C.; Asher, Amy J.; Beaumont, Linda J.; Webster, Koa N.; Harcourt, Robert G.; Power, Michelle L.

2014-01-01

Giardia and Cryptosporidium are amongst the most common protozoan parasites identified as causing enteric disease in pinnipeds. A number of Giardia assemblages and Cryptosporidium species and genotypes are common in humans and terrestrial mammals and have also been identified in marine mammals. To investigate the occurrence of these parasites in an endangered marine mammal, the Australian sea lion (Neophoca cinerea), genomic DNA was extracted from faecal samples collected from wild populations (n = 271) in Southern and Western Australia and three Australian captive populations (n = 19). These were screened using PCR targeting the 18S rRNA of Giardia and Cryptosporidium. Giardia duodenalis was detected in 28 wild sea lions and in seven captive individuals. Successful sequencing of the 18S rRNA gene assigned 27 Giardia isolates to assemblage B and one to assemblage A, both assemblages commonly found in humans. Subsequent screening at the gdh and β-giardin loci resulted in amplification of only one of the 35 18S rRNA positive samples at the β-giardin locus. Sequencing at the β-giardin locus assigned the assemblage B 18S rRNA confirmed isolate to assemblage AI. The geographic distribution of sea lion populations sampled in relation to human settlements indicated that Giardia presence in sea lions was highest in populations less than 25 km from humans. Cryptosporidium was not detected by PCR screening in either wild colonies or captive sea lion populations. These data suggest that the presence of G. duodenalis in the endangered Australian sea lion is likely the result of dispersal from human sources. Multilocus molecular analyses are essential for the determination of G. duodenalis assemblages and subsequent inferences on transmission routes to endangered marine mammal populations. PMID:25426423

Giardia duodenalis and Cryptosporidium occurrence in Australian sea lions (Neophoca cinerea) exposed to varied levels of human interaction.

PubMed

Delport, Tiffany C; Asher, Amy J; Beaumont, Linda J; Webster, Koa N; Harcourt, Robert G; Power, Michelle L

2014-12-01

Giardia and Cryptosporidium are amongst the most common protozoan parasites identified as causing enteric disease in pinnipeds. A number of Giardia assemblages and Cryptosporidium species and genotypes are common in humans and terrestrial mammals and have also been identified in marine mammals. To investigate the occurrence of these parasites in an endangered marine mammal, the Australian sea lion (Neophoca cinerea), genomic DNA was extracted from faecal samples collected from wild populations (n = 271) in Southern and Western Australia and three Australian captive populations (n = 19). These were screened using PCR targeting the 18S rRNA of Giardia and Cryptosporidium. Giardia duodenalis was detected in 28 wild sea lions and in seven captive individuals. Successful sequencing of the 18S rRNA gene assigned 27 Giardia isolates to assemblage B and one to assemblage A, both assemblages commonly found in humans. Subsequent screening at the gdh and β-giardin loci resulted in amplification of only one of the 35 18S rRNA positive samples at the β-giardin locus. Sequencing at the β-giardin locus assigned the assemblage B 18S rRNA confirmed isolate to assemblage AI. The geographic distribution of sea lion populations sampled in relation to human settlements indicated that Giardia presence in sea lions was highest in populations less than 25 km from humans. Cryptosporidium was not detected by PCR screening in either wild colonies or captive sea lion populations. These data suggest that the presence of G. duodenalis in the endangered Australian sea lion is likely the result of dispersal from human sources. Multilocus molecular analyses are essential for the determination of G. duodenalis assemblages and subsequent inferences on transmission routes to endangered marine mammal populations.

Multilocus genotyping of Giardia duodenalis and Enterocytozoon bieneusi in dairy and native beef (Qinchuan) calves in Shaanxi province, northwestern China.

PubMed

Wang, X T; Wang, R J; Ren, G J; Yu, Z Q; Zhang, L X; Zhang, S Y; Lu, H; Peng, X Q; Zhao, G H

2016-03-01

Giardia duodenalis and Enterocytozoon bieneusi are two common protozoa that parasitize the intestinal epithelium of animals and humans. Calves have been identified as important reservoirs of these two pathogens, but limited data is available for these two pathogens in calves in China. In the present study, the prevalence and assemblages/genotypes of both parasites in calves of dairy and native beef (Qinchuan) cattle in Shaanxi province, northwestern China, were analyzed using multilocus genotyping (MLST). Of 371 fecal samples collected from calves (including 198 dairy calves and 173 Qinchuan calves), the respective overall prevalence of G. duodenalis and E. bieneusi was 18.87 (70 of 371) and 19.68 % (73 of 371). Both the zoonotic G. duodenalis assemblage A and animal adapted assemblage E were found in dairy and Qinchuan calves. Seventeen, eight, five, and two G. duodenalis subtypes were detected at the triose phosphate isomerase (tpi), β-giardin (bg), glutamate dehydrogenase (gdh), and small subunit ribosomal RNA (SSU-rRNA) loci, with five and two novel subtypes detected at the tpi and bg loci, forming 25 multiple genotypes (MLGs) (15 and 11 in dairy and Qinchuan calves, respectively). Of 73 samples that were positive for E. bieneusi at the ribosomal RNA internal transcribed spacer (ITS) locus, five ITS genotypes were found, including three known zoonotic genotypes (I, J, CHN1) and two novel genotypes (CSX1 and CSX2). MLST analysis of three microsatellite loci (MS1, MS3, MS7) and one minisatellite locus (MS4) detected six, two, two, and two genotypes at the MS1, MS3, MS4, and MS7 loci, respectively, forming ten MLGs (seven and four in dairy and Qinchuan calves, respectively). These results indicate complex population structures of G. duodenalis and E. bieneusi in calves in Shaanxi province and the zoonotic potential of these two pathogens in calves in this province.

Quality assessment of DNA derived from up to 30 years old formalin fixed paraffin embedded (FFPE) tissue for PCR-based methylation analysis using SMART-MSP and MS-HRM.

PubMed

Kristensen, Lasse S; Wojdacz, Tomasz K; Thestrup, Britta B; Wiuf, Carsten; Hager, Henrik; Hansen, Lise Lotte

2009-12-21

The High Resolution Melting (HRM) technology has recently been introduced as a rapid and robust analysis tool for the detection of DNA methylation. The methylation status of multiple tumor suppressor genes may serve as biomarkers for early cancer diagnostics, for prediction of prognosis and for prediction of response to treatment. Therefore, it is important that methodologies for detection of DNA methylation continue to evolve. Sensitive Melting Analysis after Real Time - Methylation Specific PCR (SMART-MSP) and Methylation Sensitive - High Resolution Melting (MS-HRM) are two methods for single locus DNA methylation detection based on HRM. Here, we have assessed the quality of DNA extracted from up to 30 years old Formalin Fixed Paraffin Embedded (FFPE) tissue for DNA methylation analysis using SMART-MSP and MS-HRM. The quality assessment was performed on DNA extracted from 54 Non-Small Cell Lung Cancer (NSCLC) samples derived from FFPE tissue, collected over 30 years and grouped into five years intervals. For each sample, the methylation levels of the CDKN2A (p16) and RARB promoters were estimated using SMART-MSP and MS-HRM assays designed to assess the methylation status of the same CpG positions. This allowed for a direct comparison of the methylation levels estimated by the two methods for each sample. CDKN2A promoter methylation levels were successfully determined by SMART-MSP and MS-HRM in all 54 samples. Identical methylation estimates were obtained by the two methods in 46 of the samples. The methylation levels of the RARB promoter were successfully determined by SMART-MSP in all samples. When using MS-HRM to assess RARB methylation five samples failed to amplify and 15 samples showed a melting profile characteristic for heterogeneous methylation. Twenty-seven of the remaining 34 samples, for which the methylation level could be estimated, gave the same result as observed when using SMART-MSP. MS-HRM and SMART-MSP can be successfully used for single locus methylation studies using DNA derived from up to 30 years old FFPE tissue. Furthermore, it can be expected that MS-HRM and SMART-MSP will provide similar methylation estimates when assays are designed to analyze the same CpG positions.

Distributed and Relative Nature of Professional Expertise

ERIC Educational Resources Information Center

Pillay, Hitendra; McCrindle, Andrea R.

2005-01-01

This exploratory study investigates the distributed nature and complexity of professional expertise by examining the patterns of cognitive processes in novices and experts who are using ultrasound technology to make diagnoses. The study aims to identify and provide an explanation for such patterns in light of the recent debate on the locus of…

Physical Localization of a Locus from Agropyron cristatum Conferring Resistance to Stripe Rust in Common Wheat

PubMed Central

Song, Liqiang; Han, Haiming; Zhou, Shenghui; Zhang, Jinpeng; Yang, Xinming; Li, Xiuquan; Liu, Weihua; Li, Lihui

2017-01-01

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat (Triticum aestivum L.) worldwide. Agropyron cristatum (L.) Gaertn. (2n = 28, PPPP), one of the wild relatives of wheat, exhibits resistance to stripe rust. In this study, wheat-A. cristatum 6P disomic addition line 4844-12 also exhibited resistance to stripe rust. To identify the stripe rust resistance locus from A. cristatum 6P, ten translocation lines, five deletion lines and the BC2F2 and BC3F2 populations of two wheat-A. cristatum 6P whole-arm translocation lines were tested with a mixture of two races of Pst in two sites during 2015–2016 and 2016–2017, being genotyped with genomic in situ hybridization (GISH) and molecular markers. The result indicated that the locus conferring stripe rust resistance was located on the terminal 20% of 6P short arm’s length. Twenty-nine 6P-specific sequence-tagged-site (STS) markers mapped on the resistance locus have been acquired, which will be helpful for the fine mapping of the stripe rust resistance locus. The stripe rust-resistant translocation lines were found to carry some favorable agronomic traits, which could facilitate their use in wheat improvement. Collectively, the stripe rust resistance locus from A. cristatum 6P could be a novel resistance source and the screened stripe rust-resistant materials will be valuable for wheat disease breeding. PMID:29137188

Physical Localization of a Locus from Agropyron cristatum Conferring Resistance to Stripe Rust in Common Wheat.

PubMed

Zhang, Zhi; Song, Liqiang; Han, Haiming; Zhou, Shenghui; Zhang, Jinpeng; Yang, Xinming; Li, Xiuquan; Liu, Weihua; Li, Lihui

2017-11-13

Stripe rust, caused by Puccinia striiformis f. sp. tritici ( Pst ), is one of the most destructive diseases of wheat ( Triticum aestivum L.) worldwide. Agropyron cristatum (L.) Gaertn. (2 n = 28, PPPP), one of the wild relatives of wheat, exhibits resistance to stripe rust. In this study, wheat- A . cristatum 6P disomic addition line 4844-12 also exhibited resistance to stripe rust. To identify the stripe rust resistance locus from A . cristatum 6P, ten translocation lines, five deletion lines and the BC₂F₂ and BC₃F₂ populations of two wheat- A . cristatum 6P whole-arm translocation lines were tested with a mixture of two races of Pst in two sites during 2015-2016 and 2016-2017, being genotyped with genomic in situ hybridization (GISH) and molecular markers. The result indicated that the locus conferring stripe rust resistance was located on the terminal 20% of 6P short arm's length. Twenty-nine 6P-specific sequence-tagged-site (STS) markers mapped on the resistance locus have been acquired, which will be helpful for the fine mapping of the stripe rust resistance locus. The stripe rust-resistant translocation lines were found to carry some favorable agronomic traits, which could facilitate their use in wheat improvement. Collectively, the stripe rust resistance locus from A . cristatum 6P could be a novel resistance source and the screened stripe rust-resistant materials will be valuable for wheat disease breeding.

Isolation, characterization, and cross-species amplification of polymorphic microsatellite markers for Pilosocereus machrisii (Cactaceae).

PubMed

Perez, Manolo F; Téo, Mariana F; Zappi, Daniela C; Taylor, Nigel P; Moraes, Evandro M

2011-08-01

Microsatellite primers were developed in Pilosocereus machrisii, a columnar cactus with a patchy distribution in eastern tropical South America, to assess its genetic diversity and population structure. Eleven microsatellite markers were developed, of which one was monomorphic among 51 individuals from two populations. The number of alleles per polymorphic locus ranged from two to eight, and the total number of alleles was 57. From the 11 isolated loci, nine were successfully amplified in the other four Pilosocereus species. The results showed that these markers will be useful for studies of genetic diversity, patterns of gene flow, and population genetic structure in P. machrisii, as well as across other congeneric species.

Comparison of STR profiling from low template DNA extracts with and without the consensus profiling method

PubMed Central

2012-01-01

Background The consensus profiling method was introduced to overcome the exaggerated stochastic effects associated with low copy number DNA typing. However, little empirical evidence has been provided which shows that a consensus profile, derived from dividing a sample into separate aliquots and including only alleles seen at least twice, gives the most informative profile, compared to a profile obtained by amplifying the entire low template DNA extract in one reaction. Therefore, this study aimed to investigate the quality of consensus profiles compared to profiles obtained using the whole low template extract for amplification. Methods A total of 100 pg and 25 pg DNA samples were amplified with the PowerPlex® ESI 16 Kits using 30 or 34 PCR cycles. A total of 100 pg and 25 pg DNA samples were then divided into three aliquots for a 34-cycle PCR and a consensus profile derived that included alleles that appeared in at least two of the replicates. Profiles from the non-split samples were compared to the consensus profiles focusing on peak heights, allele drop out, locus drop out and allele drop in. Results Performing DNA profiling on non-split extracts produced profiles with a higher percentage of correct loci compared to the consensus profiling technique. Consensus profiling did eliminate any spurious alleles from the final profile. However, there was a notable increase in allele and locus drop out when a LTDNA sample was divided prior to amplification. Conclusions The loss of information that occurs when a sample is split for amplification indicates that consensus profiling may not be producing the most informative DNA profile for samples where the template amount is limited. PMID:22748106

Contribution of GLC3A locus to Primary Congenital Glaucoma in Pakistani population

PubMed Central

Bashir, Rasheeda; Sanai, Mahrukh; Azeem, Adnan; Altaf, Imran; Saleem, Faiza; Naz, Sadaf

2014-01-01

Objectives: To check the contribution of GLC3A locus to primary congenital glaucoma in the Pakistani population. Methods: We enrolled twenty-nine sporadic cases and three families with multiple individuals affected with recessive primary congenital glaucoma in the year 2013. It was a genetic linkage study accomplished jointly in Department of Biotechnology of Lahore College for Women University and School of Biological Sciences, University of the Punjab, Lahore. Samples from all affected individuals were checked for homozygosity for alleles of microsatellite markers spanning CYP1B1 at GLC3A locus. Genotyping was performed with fluorescently labeled primers by capillary electrophoresis. For familial cases, linkage was evaluated by checking the co-segregation of the phenotype with the genotypes. Two-point LOD score was calculated for each microsatellite marker with MLINK. Results: Our study revealed that GLCA3 may contribute to glaucoma in 17% of the sporadic cases and patients in 2 of the 3 families. Conclusions: This data suggests that the GLC3A may make an important contribution to autosomal recessive primary congenital glaucoma in the Pakistani population. Genotyping and Sequencing of more families will be helpful to identify the common mutations in CYP1B1 in future. PMID:25674135

[Analysis of allele dropout at TH01 locus in paternity testing].

PubMed

Lai, Li; Shen, Xiao-li; Xue, Shi-jie; Hu, Jie

2013-10-01

To analyze allele dropout at TH01 locus in paternity testing in order to determine the accurate genotype. To use a two STR loci genotyping system to verify an abnormal genotype for the TH01 locus with PCR using specific primers, cloning and DNA sequencing. A rare allele at TH01 locus named 5.2, which was undetectable with PowerPlex 21 system, was detected with an Identifiler system. Genetic variations may result in rare alleles and loci loss. To avoid misjudgment, laboratories should have a variety of methods for detecting loci loss.

Note on guilt appeals in advertising: covariate effects of self-esteem and locus of control.

PubMed

Pinto, M B; Worobetz, N D

1992-02-01

A 1991 study by Pinto and Priest demonstrated the effectiveness of advertisements employing moderate levels of guilt in inducing guilt responses in subjects. Because individuals' responses to guilt are often influenced by their specific personality characteristics, researchers have pointed to the potential moderating effects of individual difference variables such as level of self-esteem and locus of control on individuals' susceptibility to guilt appeals. A study was conducted to evaluate the possibility that self-esteem and locus of control can act as covariates across three treatment levels of guilt advertising. From a sample of 57 working mothers, advertisements stimulating medium and high levels of guilt elicited significantly greater feelings of guilt in subjects than the control advertisement stimulating low guilt. However, the relationship between susceptibility to guilt appeals and self-esteem and locus of control was not observed to covary.

A support vector machine based test for incongruence between sets of trees in tree space

PubMed Central

2012-01-01

Background The increased use of multi-locus data sets for phylogenetic reconstruction has increased the need to determine whether a set of gene trees significantly deviate from the phylogenetic patterns of other genes. Such unusual gene trees may have been influenced by other evolutionary processes such as selection, gene duplication, or horizontal gene transfer. Results Motivated by this problem we propose a nonparametric goodness-of-fit test for two empirical distributions of gene trees, and we developed the software GeneOut to estimate a p-value for the test. Our approach maps trees into a multi-dimensional vector space and then applies support vector machines (SVMs) to measure the separation between two sets of pre-defined trees. We use a permutation test to assess the significance of the SVM separation. To demonstrate the performance of GeneOut, we applied it to the comparison of gene trees simulated within different species trees across a range of species tree depths. Applied directly to sets of simulated gene trees with large sample sizes, GeneOut was able to detect very small differences between two set of gene trees generated under different species trees. Our statistical test can also include tree reconstruction into its test framework through a variety of phylogenetic optimality criteria. When applied to DNA sequence data simulated from different sets of gene trees, results in the form of receiver operating characteristic (ROC) curves indicated that GeneOut performed well in the detection of differences between sets of trees with different distributions in a multi-dimensional space. Furthermore, it controlled false positive and false negative rates very well, indicating a high degree of accuracy. Conclusions The non-parametric nature of our statistical test provides fast and efficient analyses, and makes it an applicable test for any scenario where evolutionary or other factors can lead to trees with different multi-dimensional distributions. The software GeneOut is freely available under the GNU public license. PMID:22909268

Attitudes Toward Obese Persons and Weight Locus of Control in Chinese Nurses: A Cross-sectional Survey.

PubMed

Wang, Yan; Ding, Ye; Song, Daoping; Zhu, Daqiao; Wang, Jianrong

2016-01-01

Obese individuals frequently experience weight-related bias or discrimination-even in healthcare settings. Although obesity bias has been associated with several demographic factors, little is known about the association of weight locus of control with bias against overweight persons or about weight bias among Chinese health professionals. The aim of the study was to examine attitudes toward obese patients in a sample of Chinese registered nurses (RNs) and the relationship between weight bias and nurses' weight locus of control. RNs working in nine community health service centers across Shanghai, China, answered three self-report questionnaires: The Attitudes Toward Obese Persons Scale (ATOP), the External Weight Locus of Control Subscale (eWLOC) from the Dieting Belief Scale, and a sociodemographic profile. Hierarchical, stepwise, multiple regression was used to predict ATOP scores. From among 385 invited, a total of 297 RNs took part in the study (77.1% response rate). Participants scored an average of 71.04 on the ATOP, indicating slightly positive attitudes toward obese persons, and 30.08 on the eWLOC, indicating a belief in the uncontrollability of body weight. Using hierarchical, stepwise, multiple regression, two predictors of ATOP scores were statistically significant (eWLOC scores and status as a specialist rather than generalist nurse), but explained variance was low. Chinese RNs seemed to have relatively neutral or even slightly positive attitudes toward obese persons. Those nurses who believed that obesity was beyond the individual's control or worked in specialties were more likely to have positive attitudes toward obese people. Improved understanding of the comprehensive etiology of obesity is needed.

Identification of candidate regions for a novel Usher syndrome type II locus.

PubMed

Ben Rebeh, Imen; Benzina, Zeineb; Dhouib, Houria; Hadjamor, Imen; Amyere, Mustapha; Ayadi, Leila; Turki, Khalil; Hammami, Bouthaina; Kmiha, Noureddine; Kammoun, Hassen; Hakim, Bochra; Charfedine, Ilhem; Vikkula, Miikka; Ghorbel, Abdelmonem; Ayadi, Hammadi; Masmoudi, Saber

2008-09-19

Chronic diseases affecting the inner ear and the retina cause severe impairments to our communication systems. In more than half of the cases, Usher syndrome (USH) is the origin of these double defects. Patients with USH type II (USH2) have retinitis pigmentosa (RP) that develops during puberty, moderate to severe hearing impairment with downsloping pure-tone audiogram, and normal vestibular function. Four loci and three genes are known for USH2. In this study, we proposed to localize the gene responsible for USH2 in a consanguineous family of Tunisian origin. Affected members underwent detailed ocular and audiologic characterization. One Tunisian family with USH2 and 45 healthy controls unrelated to the family were recruited. Two affected and six unaffected family members attended our study. DNA samples of eight family members were genotyped with polymorphic markers. Two-point and multipoint LOD scores were calculated using Genehunter software v2.1. Sequencing was used to investigate candidate genes. Haplotype analysis showed no significant linkage to any known USH gene or locus. A genome-wide screen, using microsatellite markers, was performed, allowing the identification of three homozygous regions in chromosomes 2, 4, and 15. We further confirmed and refined these three regions using microsatellite and single-nucleotide polymorphisms. With recessive mode of inheritance, the highest multipoint LOD score of 1.765 was identified for the candidate regions on chromosomes 4 and 15. The chromosome 15 locus is large (55 Mb), underscoring the limited number of meioses in the consanguineous pedigree. Moreover, the linked, homozygous chromosome 15q alleles, unlike those of the chromosome 2 and 4 loci, are infrequent in the local population. Thus, the data strongly suggest that the novel locus for USH2 is likely to reside on 15q. Our data provide a basis for the localization and the identification of a novel gene implicated in USH2, most likely localized on 15q.

Two dominant loci determine resistance to Phomopsis cane lesions in F1 families of hybrid grapevines.

PubMed

Barba, Paola; Lillis, Jacquelyn; Luce, R Stephen; Travadon, Renaud; Osier, Michael; Baumgartner, Kendra; Wilcox, Wayne F; Reisch, Bruce I; Cadle-Davidson, Lance

2018-05-01

Rapid characterization of novel NB-LRR-associated resistance to Phomopsis cane spot on grapevine using high-throughput sampling and low-coverage sequencing for genotyping, locus mapping and transcriptome analysis provides insights into genetic resistance to a hemibiotrophic fungus. Phomopsis cane and leaf spot, caused by the hemibiotrophic fungus Diaporthe ampelina (syn = Phomopsis viticola), reduces the productivity in grapevines. Host resistance was studied on three F 1 families derived from crosses involving resistant genotypes 'Horizon', Illinois 547-1, Vitis cinerea B9 and V. vinifera 'Chardonnay'. All families had progeny with extremely susceptible phenotypes, developing lesions on both dormant canes and maturing fruit clusters. Segregation of symptoms was observed under natural levels of inoculum in the field, while phenotypes on green shoots were confirmed under controlled inoculations in greenhouse. High-density genetic maps were used to localize novel qualitative resistance loci named Rda1 and Rda2 from V. cinerea B9 and 'Horizon', respectively. Co-linearity between reference genetic and physical maps allowed localization of Rda2 locus between 1.5 and 2.4 Mbp on chromosome 7, and Rda1 locus between 19.3 and 19.6 Mbp of chromosome 15, which spans a cluster of five NB-LRR genes. Further dissection of this locus was obtained by QTL mapping of gene expression values 14 h after inoculation across a subset of the 'Chardonnay' × V. cinerea B9 progeny. This provided evidence for the association between transcript levels of two of these NB-LRR genes with Rda1, with increased NB-LRR expression among susceptible progeny. In resistant parent V. cinerea B9, inoculation with D. ampelina was characterized by up-regulation of SA-associated genes and down-regulation of ethylene pathways, suggesting an R-gene-mediated response. With dominant effects associated with disease-free berries and minimal symptoms on canes, Rda1 and Rda2 are promising loci for grapevine genetic improvement.

Evidence for balancing selection at the DAB locus in the axolotl, Ambystoma mexicanum.

PubMed

Richman, A D; Herrera, G; Reynoso, V H; Méndez, G; Zambrano, L

2007-12-01

The axolotl (Ambystoma mexicanum) has been characterized as immunodeficient, and the absence of major histocompatibility complex (MHC) class II polymorphism has been cited as a possible explanation. Here we present evidence for considerable allelic polymorphism at the MHC class II DAB locus for a sample of wild-caught axolotls. Evidence that these sequences are the product of balancing selection for disease resistance is discussed.

An Examination of the Influence of Self Efficacy, Locus of Control, and Perceptions of Parent Involvement on Academic Achievement of Urban High School Students

ERIC Educational Resources Information Center

Myree, Claudia

2011-01-01

Current research indicates that there is an on-going concern for the graduation rate of African American students in urban settings. This particular study sought to investigate the impact of students' self-efficacy, locus of control, and parental involvement on academic achievement via a targeted sample of urban African American high school…

Dogmatism, Locus of Control, Perceived Counselor Self-Efficacy, and the Theoretical Orientation of Students in a Master's Level Counseling Practicum

ERIC Educational Resources Information Center

Benesh, Andrew Christopher

2017-01-01

Purpose: The purpose of this study was to fill a gap in the literature by examining the relationship between dogmatism, locus of control, counselor self-efficacy, and counselor theoretical orientation in a sample of master's level practicum students. Method: A total of 45 master's practicum students completed a series of four instruments, the DOG…

Phylogeography of the sergeants Abudefduf sexfasciatus and A. vaigiensis reveals complex introgression patterns between two widespread and sympatric Indo-West Pacific reef fishes.

PubMed

Bertrand, Joris A M; Borsa, Philippe; Chen, Wei-Jen

2017-05-01

On evolutionary timescales, sea level oscillations lead to recurrent spatio-temporal variation in species distribution and population connectivity. In this situation, applying classical concepts of biogeography is challenging yet necessary to understand the mechanisms underlying biodiversity in highly diverse marine ecosystems such as coral reefs. We aimed at studying the outcomes of such complex biogeographic dynamics on reproductive isolation by sampling populations across a wide spatial range of a species-rich fish genus: the sergeants (Pomacentridae: Abudefduf). We generated a mutlilocus data set that included ten morpho-species from 32 Indo-West Pacific localities. We observed a pattern of mito-nuclear discordance in two common and widely distributed species: Abudefduf sexfasciatus and Abudefduf vaigiensis. The results showed three regional sublineages (Indian Ocean, Coral Triangle region, western Pacific) in A. sexfasciatus (0.6-1.5% divergence at cytb). The other species, A. vaigiensis, is polyphyletic and consists of three distinct genetic lineages (A, B and C) (9% divergence at cytb) whose geographic ranges overlap. Although A. vaigiensis A and A. sexfasciatus were found to be distinct based on nuclear information, A. vaigiensis A was found to be nested within A. sexfasciatus in the mitochondrial gene tree. A. sexfasciatus from the Coral Triangle region and A. vaigiensis A were not differentiated from each other at the mitochondrial locus. We then used coalescent-based simulation to characterize a spatially widespread but weak gene flow between the two species. We showed that these fishes are good candidates to investigate the evolutionary complexity of the discrepancies between phenotypic and genetic similarity in closely related species. © 2017 John Wiley & Sons Ltd.

Cloud computing for detecting high-order genome-wide epistatic interaction via dynamic clustering.

PubMed

Guo, Xuan; Meng, Yu; Yu, Ning; Pan, Yi

2014-04-10

Taking the advantage of high-throughput single nucleotide polymorphism (SNP) genotyping technology, large genome-wide association studies (GWASs) have been considered to hold promise for unravelling complex relationships between genotype and phenotype. At present, traditional single-locus-based methods are insufficient to detect interactions consisting of multiple-locus, which are broadly existing in complex traits. In addition, statistic tests for high order epistatic interactions with more than 2 SNPs propose computational and analytical challenges because the computation increases exponentially as the cardinality of SNPs combinations gets larger. In this paper, we provide a simple, fast and powerful method using dynamic clustering and cloud computing to detect genome-wide multi-locus epistatic interactions. We have constructed systematic experiments to compare powers performance against some recently proposed algorithms, including TEAM, SNPRuler, EDCF and BOOST. Furthermore, we have applied our method on two real GWAS datasets, Age-related macular degeneration (AMD) and Rheumatoid arthritis (RA) datasets, where we find some novel potential disease-related genetic factors which are not shown up in detections of 2-loci epistatic interactions. Experimental results on simulated data demonstrate that our method is more powerful than some recently proposed methods on both two- and three-locus disease models. Our method has discovered many novel high-order associations that are significantly enriched in cases from two real GWAS datasets. Moreover, the running time of the cloud implementation for our method on AMD dataset and RA dataset are roughly 2 hours and 50 hours on a cluster with forty small virtual machines for detecting two-locus interactions, respectively. Therefore, we believe that our method is suitable and effective for the full-scale analysis of multiple-locus epistatic interactions in GWAS.

Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system

PubMed Central

Hanson, Sara J.; Byrne, Kevin P.; Wolfe, Kenneth H.

2014-01-01

Saccharomyces cerevisiae has a complex system for switching the mating type of haploid cells, requiring the genome to have three mating-type (MAT)–like loci and a mechanism for silencing two of them. How this system originated is unknown, because the three-locus system is present throughout the family Saccharomycetaceae, whereas species in the sister Candida clade have only one locus and do not switch. Here we show that yeasts in a third clade, the methylotrophs, have a simpler two-locus switching system based on reversible inversion of a section of chromosome with MATa genes at one end and MATalpha genes at the other end. In Hansenula polymorpha the 19-kb invertible region lies beside a centromere so that, depending on the orientation, either MATa or MATalpha is silenced by centromeric chromatin. In Pichia pastoris, the orientation of a 138-kb invertible region puts either MATa or MATalpha beside a telomere and represses transcription of MATa2 or MATalpha2. Both species are homothallic, and inversion of their MAT regions can be induced by crossing two strains of the same mating type. The three-locus system of S. cerevisiae, which uses a nonconservative mechanism to replace DNA at MAT, likely evolved from a conservative two-locus system that swapped genes between expression and nonexpression sites by inversion. The increasing complexity of the switching apparatus, with three loci, donor bias, and cell lineage tracking, can be explained by continuous selection to increase sporulation ability in young colonies. Our results provide an evolutionary context for the diversity of switching and silencing mechanisms. PMID:25349420

Cloud computing for detecting high-order genome-wide epistatic interaction via dynamic clustering

PubMed Central

2014-01-01

Backgroud Taking the advan tage of high-throughput single nucleotide polymorphism (SNP) genotyping technology, large genome-wide association studies (GWASs) have been considered to hold promise for unravelling complex relationships between genotype and phenotype. At present, traditional single-locus-based methods are insufficient to detect interactions consisting of multiple-locus, which are broadly existing in complex traits. In addition, statistic tests for high order epistatic interactions with more than 2 SNPs propose computational and analytical challenges because the computation increases exponentially as the cardinality of SNPs combinations gets larger. Results In this paper, we provide a simple, fast and powerful method using dynamic clustering and cloud computing to detect genome-wide multi-locus epistatic interactions. We have constructed systematic experiments to compare powers performance against some recently proposed algorithms, including TEAM, SNPRuler, EDCF and BOOST. Furthermore, we have applied our method on two real GWAS datasets, Age-related macular degeneration (AMD) and Rheumatoid arthritis (RA) datasets, where we find some novel potential disease-related genetic factors which are not shown up in detections of 2-loci epistatic interactions. Conclusions Experimental results on simulated data demonstrate that our method is more powerful than some recently proposed methods on both two- and three-locus disease models. Our method has discovered many novel high-order associations that are significantly enriched in cases from two real GWAS datasets. Moreover, the running time of the cloud implementation for our method on AMD dataset and RA dataset are roughly 2 hours and 50 hours on a cluster with forty small virtual machines for detecting two-locus interactions, respectively. Therefore, we believe that our method is suitable and effective for the full-scale analysis of multiple-locus epistatic interactions in GWAS. PMID:24717145

Effect of individualized goal-setting on college biology students' locus of control

NASA Astrophysics Data System (ADS)

Schafer, John E.

This study investigated the effect of Individualized Goal-Setting A-T, relative to Classic A-T, on a student's locus of control (generalized and academic). This study also examined the effect of pretesting, relative to no pretesting, on a student's locus of control. Sixty students in an introductory, Audio-Tutorial, college zoology course were randomly assigned to treatment and control groups. Control groups (Classic A-T) completed the course in the usual manner. Treatment groups (IGS A-T) completed the course in the usual manner with one exception. That is, they used a different format for Optional Minicourse mastery. This new format released greater control to students over means as well as ends of minicourse mastery. Data were collected through use of the Solomon Four-Group design, with two levels of treatment (Classic A-T, IGS A-T) and two levels of pretesting (pretest, no pretest). Instruments included the Rotter I-E and Schafer Academic I-E Locus of Control Scales. Posttest scores were analyzed by a 2 × 2 multivariate analysis of variance (MANOVA).The following conclusions were made (p < 0.10).1IGS A-T, relative to Classic A-T, has no significant effect on a student's locus of control.2Pretesting, relative to no pretesting, has no significant effect on posttest locus of control.

NIST mixed stain study 3: signal intensity balance in commercial short tandem repeat multiplexes.

PubMed

Duewer, David L; Kline, Margaret C; Redman, Janette W; Butler, John M

2004-12-01

Short-tandem repeat (STR) allelic intensities were collected from more than 60 forensic laboratories for a suite of seven samples as part of the National Institute of Standards and Technology-coordinated 2001 Mixed Stain Study 3 (MSS3). These interlaboratory challenge data illuminate the relative importance of intrinsic and user-determined factors affecting the locus-to-locus balance of signal intensities for currently used STR multiplexes. To varying degrees, seven of the eight commercially produced multiplexes used by MSS3 participants displayed very similar patterns of intensity differences among the different loci probed by the multiplexes for all samples, in the hands of multiple analysts, with a variety of supplies and instruments. These systematic differences reflect intrinsic properties of the individual multiplexes, not user-controllable measurement practices. To the extent that quality systems specify minimum and maximum absolute intensities for data acceptability and data interpretation schema require among-locus balance, these intrinsic intensity differences may decrease the utility of multiplex results and surely increase the cost of analysis.

The powdery mildew resistance gene REN1 co-segregates with an NBS-LRR gene cluster in two Central Asian grapevines

PubMed Central

2009-01-01

Background Grape powdery mildew is caused by the North American native pathogen Erysiphe necator. Eurasian Vitis vinifera varieties were all believed to be susceptible. REN1 is the first resistance gene naturally found in cultivated plants of Vitis vinifera. Results REN1 is present in 'Kishmish vatkana' and 'Dzhandzhal kara', two grapevines documented in Central Asia since the 1920's. These cultivars have a second-degree relationship (half sibs, grandparent-grandchild, or avuncular), and share by descent the chromosome on which the resistance allele REN1 is located. The REN1 interval was restricted to 1.4 cM using 38 SSR markers distributed across the locus and the segregation of the resistance phenotype in two progenies of collectively 461 offspring, derived from either resistant parent. The boundary markers delimit a 1.4-Mbp sequence in the PN40024 reference genome, which contains 27 genes with known functions, 2 full-length coiled-coil NBS-LRR genes, and 9 NBS-LRR pseudogenes. In the REN1 locus of PN40024, NBS genes have proliferated through a mixture of segmental duplications, tandem gene duplications, and intragenic recombination between paralogues, indicating that the REN1 locus has been inherently prone to producing genetic variation. Three SSR markers co-segregate with REN1, the outer ones confining the 908-kb array of NBS-LRR genes. Kinship and clustering analyses based on genetic distances with susceptible cultivars representative of Central Asian Vitis vinifera indicated that 'Kishmish vatkana' and 'Dzhandzhal kara' fit well into local germplasm. 'Kishmish vatkana' also has a parent-offspring relationship with the seedless table grape 'Sultanina'. In addition, the distant genetic relatedness to rootstocks, some of which are derived from North American species resistant to powdery mildew and have been used worldwide to guard against phylloxera since the late 1800's, argues against REN1 being infused into Vitis vinifera from a recent interspecific hybridisation. Conclusion The REN1 gene resides in an NBS-LRR gene cluster tightly delimited by two flanking SSR markers, which can assist in the selection of this DNA block in breeding between Vitis vinifera cultivars. The REN1 locus has multiple layers of structural complexity compared with its two closely related paralogous NBS clusters, which are located some 5 Mbp upstream and 4 Mbp downstream of the REN1 interval on the same chromosome. PMID:20042081

HLA-DRB1 alleles in four Amerindian populations from Argentina and Paraguay

PubMed Central

2009-01-01

The major histocompatibility complex (MHC) is one of the biological systems of major polymorphisms. The study of HLA class II variability has allowed the identification of several alleles that are characteristic to Amerindian populations, and it is an excellent tool to define the relations and biological affinities among them. In this work, we analyzed the allelic distribution of the HLA-DRB1 class II locus in four Amerindian populations: Mapuche (n = 34) and Tehuelche (n = 23) from the Patagonian region of Argentina, and Wichi SV (n = 24) and Lengua (n = 17) from the Argentinean and Paraguayan Chaco regions, respectively. In all of these groups, relatively high frequencies of Amerindian HLA-DRB1 alleles were observed (DRB1*0403, DRB1*0407, DRB1*0411, DRB1*0417, DRB1*0802, DRB1*0901, DRB1*1402, DRB1*1406 and DRB1*1602). However, we also detected the presence of non-Amerindian variants in Mapuche (35%) and Tehuelche (22%). We compared our data with those obtained in six indigenous groups of the Argentinean Chaco region and in a sample from Buenos Aires City. The genetic distance dendrogram showed a clear-cut division between the Patagonian and Chaco populations, which formed two different clusters. In spite of their linguistic differences, it can be inferred that the biological affinities observed are in concordance with the geographic distributions and interethnic relations established among the groups studied. PMID:21637670

Isolation of Bdellovibrio sp. from soil samples in Mexico and their potential applications in control of pathogens.

PubMed

Oyedara, Omotayo Opemipo; De Luna-Santillana, Erick de Jesus; Olguin-Rodriguez, Omar; Guo, Xianwu; Mendoza-Villa, Marco Antonio; Menchaca-Arredondo, Jorge Luis; Elufisan, Temidayo Oluyomi; Garza-Hernandez, Javier Alfonso; Garcia Leon, Israel; Rodriguez-Perez, Mario Alberto

2016-12-01

In this study, two strains of Bdellovibrio were isolated from soil samples using the culture-dependent technique and two members of the family Enterobacteriaceae (Klebsiella sp. and Salmonella sp.) as prey. The Bdellovibrio strains were bacteriolytic, plaque-forming, and highly motile gram-negative bacteria. We identified and confirmed the Bdellovibrio strains using microscopy, PCR amplification, and sequencing of the 16S rRNA gene. They were observed to be different strains based on hit locus and prey range analyses. Here, the first report on Bdellovibrio strains isolated from soil in Mexico corroborates earlier report indicating that populations of Bdellovibrio found in soil are heterogeneous thereby the need to identify the various strains. © 2016 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

The genetic structure of the A mating-type locus of Lentinula edodes.

PubMed

Au, Chun Hang; Wong, Man Chun; Bao, Dapeng; Zhang, Meiyan; Song, Chunyan; Song, Wenhua; Law, Patrick Tik Wan; Kües, Ursula; Kwan, Hoi Shan

2014-02-10

The Shiitake mushroom, Lentinula edodes (Berk.) Pegler is a tetrapolar basidiomycete with two unlinked mating-type loci, commonly called the A and B loci. Identifying the mating-types in shiitake is important for enhancing the breeding and cultivation of this economically-important edible mushroom. Here, we identified the A mating-type locus from the first draft genome sequence of L. edodes and characterized multiple alleles from different monokaryotic strains. Two intron-length polymorphism markers were developed to facilitate rapid molecular determination of A mating-type. L. edodes sequences were compared with those of known tetrapolar and bipolar basidiomycete species. The A mating-type genes are conserved at the homeodomain region across the order Agaricales. However, we observed unique genomic organization of the locus in L. edodes which exhibits atypical gene order and multiple repetitive elements around its A locus. To our knowledge, this is the first known exception among Homobasidiomycetes, in which the mitochondrial intermediate peptidase (mip) gene is not closely linked to A locus. Copyright © 2013 Elsevier B.V. All rights reserved.

Biallelic Germline Transcription at the κ Immunoglobulin Locus

PubMed Central

Singh, Nandita; Bergman, Yehudit; Cedar, Howard; Chess, Andrew

2003-01-01

Rearrangement of antigen receptor genes generates a vast array of antigen receptors on lymphocytes. The establishment of allelic exclusion in immunoglobulin genes requires differential treatment of the two sequence identical alleles. In the case of the κ immunoglobulin locus, changes in chromatin structure, methylation, and replication timing of the two alleles are all potentially involved in regulating rearrangement. Additionally, germline transcription of the κ locus which precedes rearrangement has been proposed to reflect an opening of the chromatin structure rendering it available for rearrangement. As the initial restriction of rearrangement to one allele is critical to the establishment of allelic exclusion, a key question is whether or not germline transcription at the κ locus is monoallelic or biallelic. We have used a sensitive reverse transcription-polymerase chain reaction (RT-PCR) assay and an RNA–fluorescence in situ hybridization (FISH) to show that germline transcription of the κ locus is biallelic in wild-type immature B cells and in recombination activating gene (RAG)−/−, μ+ B cells. Therefore, germline transcription is unlikely to dictate which allele will be rearranged first and rather reflects a general opening on both alleles that must be accompanied by a mechanism allowing one of the two alleles to be rearranged first. PMID:12629064

Distinct self-interaction domains promote Multi Sex Combs accumulation in and formation of the Drosophila histone locus body.

PubMed

Terzo, Esteban A; Lyons, Shawn M; Poulton, John S; Temple, Brenda R S; Marzluff, William F; Duronio, Robert J

2015-04-15

Nuclear bodies (NBs) are structures that concentrate proteins, RNAs, and ribonucleoproteins that perform functions essential to gene expression. How NBs assemble is not well understood. We studied the Drosophila histone locus body (HLB), a NB that concentrates factors required for histone mRNA biosynthesis at the replication-dependent histone gene locus. We coupled biochemical analysis with confocal imaging of both fixed and live tissues to demonstrate that the Drosophila Multi Sex Combs (Mxc) protein contains multiple domains necessary for HLB assembly. An important feature of this assembly process is the self-interaction of Mxc via two conserved N-terminal domains: a LisH domain and a novel self-interaction facilitator (SIF) domain immediately downstream of the LisH domain. Molecular modeling suggests that the LisH and SIF domains directly interact, and mutation of either the LisH or the SIF domain severely impairs Mxc function in vivo, resulting in reduced histone mRNA accumulation. A region of Mxc between amino acids 721 and 1481 is also necessary for HLB assembly independent of the LisH and SIF domains. Finally, the C-terminal 195 amino acids of Mxc are required for recruiting FLASH, an essential histone mRNA-processing factor, to the HLB. We conclude that multiple domains of the Mxc protein promote HLB assembly in order to concentrate factors required for histone mRNA biosynthesis. © 2015 Terzo et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Evidence for bivariate linkage of obesity and HDL-C levels in the Framingham Heart Study.

PubMed

Arya, Rector; Lehman, Donna; Hunt, Kelly J; Schneider, Jennifer; Almasy, Laura; Blangero, John; Stern, Michael P; Duggirala, Ravindranath

2003-12-31

Epidemiological studies have indicated that obesity and low high-density lipoprotein (HDL) levels are strong cardiovascular risk factors, and that these traits are inversely correlated. Despite the belief that these traits are correlated in part due to pleiotropy, knowledge on specific genes commonly affecting obesity and dyslipidemia is very limited. To address this issue, we first conducted univariate multipoint linkage analysis for body mass index (BMI) and HDL-C to identify loci influencing variation in these phenotypes using Framingham Heart Study data relating to 1702 subjects distributed across 330 pedigrees. Subsequently, we performed bivariate multipoint linkage analysis to detect common loci influencing covariation between these two traits. We scanned the genome and identified a major locus near marker D6S1009 influencing variation in BMI (LOD = 3.9) using the program SOLAR. We also identified a major locus for HDL-C near marker D2S1334 on chromosome 2 (LOD = 3.5) and another region near marker D6S1009 on chromosome 6 with suggestive evidence for linkage (LOD = 2.7). Since these two phenotypes have been independently mapped to the same region on chromosome 6q, we used the bivariate multipoint linkage approach using SOLAR. The bivariate linkage analysis of BMI and HDL-C implicated the genetic region near marker D6S1009 as harboring a major gene commonly influencing these phenotypes (bivariate LOD = 6.2; LODeq = 5.5) and appears to improve power to map the correlated traits to a region, precisely. We found substantial evidence for a quantitative trait locus with pleiotropic effects, which appears to influence both BMI and HDL-C phenotypes in the Framingham data.

Use of Whole-Genome Phylogeny and Comparisons for Development of a Multiplex PCR Assay To Identify Sequence Type 36 Vibrio parahaemolyticus.

PubMed

Whistler, Cheryl A; Hall, Jeffrey A; Xu, Feng; Ilyas, Saba; Siwakoti, Puskar; Cooper, Vaughn S; Jones, Stephen H

2015-06-01

Vibrio parahaemolyticus sequence type 36 (ST36) strains that are native to the Pacific Ocean have recently caused multistate outbreaks of gastroenteritis linked to shellfish harvested from the Atlantic Ocean. Whole-genome comparisons of 295 genomes of V. parahaemolyticus, including several traced to northeastern U.S. sources, were used to identify diagnostic loci, one putatively encoding an endonuclease (prp), and two others potentially conferring O-antigenic properties (cps and flp). The combination of all three loci was present in only one clade of closely related strains of ST36, ST59, and one additional unknown sequence type. However, each locus was also identified outside this clade, with prp and flp occurring in only two nonclade isolates and cps in four. Based on the distribution of these loci in sequenced genomes, prp identified clade strains with >99% accuracy, but the addition of one more locus increased accuracy to 100%. Oligonucleotide primers targeting prp and cps were combined in a multiplex PCR method that defines species using the tlh locus and determines the presence of both the tdh and trh hemolysin-encoding genes, which are also present in ST36. Application of the method in vitro to a collection of 94 clinical isolates collected over a 4-year period in three northeastern U.S. states and 87 environmental isolates revealed that the prp and cps amplicons were detected only in clinical isolates identified as belonging to the ST36 clade and in no environmental isolates from the region. The assay should improve detection and surveillance, thereby reducing infections. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Two different secondary metabolism gene clusters occupied the same ancestral locus in fungal dermatophytes of the arthrodermataceae.

PubMed

Zhang, Han; Rokas, Antonis; Slot, Jason C

2012-01-01

Dermatophyte fungi of the family Arthrodermataceae (Eurotiomycetes) colonize keratinized tissue, such as skin, frequently causing superficial mycoses in humans and other mammals, reptiles, and birds. Competition with native microflora likely underlies the propensity of these dermatophytes to produce a diversity of antibiotics and compounds for scavenging iron, which is extremely scarce, as well as the presence of an unusually large number of putative secondary metabolism gene clusters, most of which contain non-ribosomal peptide synthetases (NRPS), in their genomes. To better understand the historical origins and diversification of NRPS-containing gene clusters we examined the evolution of a variable locus (VL) that exists in one of three alternative conformations among the genomes of seven dermatophyte species. The first conformation of the VL (termed VLA) contains only 539 base pairs of sequence and lacks protein-coding genes, whereas the other two conformations (termed VLB and VLC) span 36 Kb and 27 Kb and contain 12 and 10 genes, respectively. Interestingly, both VLB and VLC appear to contain distinct secondary metabolism gene clusters; VLB contains a NRPS gene as well as four porphyrin metabolism genes never found to be physically linked in the genomes of 128 other fungal species, whereas VLC also contains a NRPS gene as well as several others typically found associated with secondary metabolism gene clusters. Phylogenetic evidence suggests that the VL locus was present in the ancestor of all seven species achieving its present distribution through subsequent differential losses or retentions of specific conformations. We propose that the existence of variable loci, similar to the one we studied, in fungal genomes could potentially explain the dramatic differences in secondary metabolic diversity between closely related species of filamentous fungi, and contribute to host adaptation and the generation of metabolic diversity.

Comparing health locus of control in patients with Spasmodic Dysphonia, Functional Dysphonia and Nonlaryngeal Dystonia.

PubMed

Haselden, Karen; Powell, Theresa; Drinnan, Mike; Carding, Paul

2009-11-01

Locus of Control (LoC) refers to an individuals' perception of whether they are in control of life events. Health Locus of Control refers to whether someone feels they have influence over their health. Health Locus of Control has not been studied in any depth in voice-disordered patients. The objective of this study was to examine Health Locus of Control in three patient groups: (1) Spasmodic Dysphonia, (2) Functional Dysphonia and (3) a nondysphonic group with Nonlaryngeal Dystonia. LoC was measured and compared in a total of 57 patients using the Multidimensional Health Locus of Control Scales (diagnostic specific) Form C. Internal, Chance, and Powerful others LoC were measured and comparisons were made using one-way analysis of variance. Contrary to expectations Internal LoC was found to be significantly higher in the Functional Dysphonia group when compared to the other two groups. There was no significant difference between the groups in Chance or Powerful others LoC. The two organic groups, Spasmodic Dysphonia and Nonlaryngeal Dystonia, were more alike in Internal Health Locus of Control than the Functional Dysphonia group. The diagnostic nature of the groups was reflected in their LoC scores rather than their voice loss. These results contribute to the debate about the etiology of Spasmodic Dysphonia and will be of interest to those involved in the psychology of voice and those managing voice-disordered patients.

A Symmetric Two-Locus Fertility Model

PubMed Central

Feldman, Marcus W.; Liberman, Uri

1985-01-01

A model in which selection is mediated by differential fertilities among the genotypes at two diallelic loci is proposed. Fertility depends only on the number of heterozygous loci participating in the mating. Classes analogous to symmetric equilibria in symmetric viability models are determined explicitly and shown to exhibit stability behavior very different from the viability results. Linkage equilibrium is shown to occur in a relatively asymmetric fashion and to overlap in stability with linkage disequilibrium. In many cases single-locus or two-locus polymorphism is shown to be stable simultaneously with chromosome fixation even under very tight linkage. It is suggested that historical effects may be of great significance in the evolution of systems in which fertility is the primary agent of natural selection. PMID:3967817

The Star Formation Demographics of Galaxies in the Local Volume

NASA Astrophysics Data System (ADS)

Lee, Janice C.; Kennicutt, Robert C.; Funes, S. J., José G.; Sakai, Shoko; Akiyama, Sanae

2007-12-01

We examine the connections between the current global star formation activity, luminosity, dynamical mass, and morphology of galaxies in the Local Volume, using Hα data from the 11 Mpc Hα and Ultraviolet Galaxy Survey (11HUGS). Taking the equivalent width (EW) of the Hα emission line as a tracer of the specific star formation rate, we analyze the distribution of galaxies in the MB-EW and rotational velocity (Vmax)-EW planes. Star-forming galaxies show two characteristic transitions in these planes. A narrowing of the galaxy locus occurs at MB~-15 and Vmax~50 km s-1, where the scatter in the logarithmic EWs drops by a factor of 2 as the luminosities/masses increase, and galaxy morphologies shift from predominately irregular to late-type spiral. Another transition occurs at MB~-19 and Vmax~120 km s-1, above which the sequence turns off toward lower EWs and becomes mostly populated by intermediate- and early-type bulge-prominent spirals. Between these two transitions, the mean logarithmic EW appears to remain constant at 30 Å. We comment on how these features reflect established empirical relationships, and provide clues for identifying the large-scale physical processes that both drive and regulate star formation, with emphasis on the low-mass galaxies which dominate our approximately volume-limited sample.

Genome-wide association study of rice grain width variation.

PubMed

Zheng, Xiao-Ming; Gong, Tingting; Ou, Hong-Ling; Xue, Dayuan; Qiao, Weihua; Wang, Junrui; Liu, Sha; Yang, Qingwen; Olsen, Kenneth M

2018-04-01

Seed size is variable within many plant species, and understanding the underlying genetic factors can provide insights into mechanisms of local environmental adaptation. Here we make use of the abundant genomic and germplasm resources available for rice (Oryza sativa) to perform a large-scale genome-wide association study (GWAS) of grain width. Grain width varies widely within the crop and is also known to show climate-associated variation across populations of its wild progenitor. Using a filtered dataset of >1.9 million genome-wide SNPs in a sample of 570 cultivated and wild rice accessions, we performed GWAS with two complementary models, GLM and MLM. The models yielded 10 and 33 significant associations, respectively, and jointly yielded seven candidate locus regions, two of which have been previously identified. Analyses of nucleotide diversity and haplotype distributions at these loci revealed signatures of selection and patterns consistent with adaptive introgression of grain width alleles across rice variety groups. The results provide a 50% increase in the total number of rice grain width loci mapped to date and support a polygenic model whereby grain width is shaped by gene-by-environment interactions. These loci can potentially serve as candidates for studies of adaptive seed size variation in wild grass species.

Work stress and emotional exhaustion in nurses: the mediating role of internal locus of control.

PubMed

Partlak Günüşen, Neslihan; Ustün, Besti; Erdem, Sabri

2014-01-01

Burnout is a major problem for nursing. There is a strong relationship between work stress and emotional exhaustion. Although studies report a negative correlation between the internal locus of control and emotional exhaustion and work stress, the number of studies available on the subject is limited. This study intends to examine the extent to which the relationship between work stress and emotional exhaustion is mediated by nurses' internal locus of control. The study adopted a cross-sectional survey design. The data were analyzed using structural equation modeling techniques. The study sample consisted of 347 nurses who worked in a university hospital in Izmir, Turkey and who agreed to participate in the study. The Work-Related Strain Inventory was used to evaluate the nurses' work stress level, Maslach Burnout Inventory was used to evaluate their emotional exhaustion levels, and the Locus of Control Scale was used to evaluate the internal locus of control. The variables of the study were based on the Neuman Systems Model. Work stress was positively related to internal locus of control (β3 = .21, p < .001), which was, in turn, negatively associated with emotional exhaustion (β = -.03, p > 0.1). Internal locus of control was negatively related to emotional exhaustion (β = -.14, p < .001). Work stress is directly (β = .87, p < .001) and indirectly related to emotional exhaustion (mediated by internal locus of control β = .84, p < .001). Work stress is directly (β = .87, p < .001) and indirectly related to emotional exhaustion (mediated by internal locus of control, β = .84, p < .001). Although the relationship between emotional exhaustion and work stress was mediated, the impact of internal locus of control was limited. It is recommended that different variables be included in future studies so that they can mediate the relationship between work stress and emotional exhaustion.

Inferring mechanisms of copy number change from haplotype structures at the human DEFA1A3 locus.

PubMed

Black, Holly A; Khan, Fayeza F; Tyson, Jess; Al Armour, John

2014-07-21

The determination of structural haplotypes at copy number variable regions can indicate the mechanisms responsible for changes in copy number, as well as explain the relationship between gene copy number and expression. However, obtaining spatial information at regions displaying extensive copy number variation, such as the DEFA1A3 locus, is complex, because of the difficulty in the phasing and assembly of these regions. The DEFA1A3 locus is intriguing in that it falls within a region of high linkage disequilibrium, despite its high variability in copy number (n = 3-16); hence, the mechanisms responsible for changes in copy number at this locus are unclear. In this study, a region flanking the DEFA1A3 locus was sequenced across 120 independent haplotypes with European ancestry, identifying five common classes of DEFA1A3 haplotype. Assigning DEFA1A3 class to haplotypes within the 1000 Genomes project highlights a significant difference in DEFA1A3 class frequencies between populations with different ancestry. The features of each DEFA1A3 class, for example, the associated DEFA1A3 copy numbers, were initially assessed in a European cohort (n = 599) and replicated in the 1000 Genomes samples, showing within-class similarity, but between-class and between-population differences in the features of the DEFA1A3 locus. Emulsion haplotype fusion-PCR was used to generate 61 structural haplotypes at the DEFA1A3 locus, showing a high within-class similarity in structure. Structural haplotypes across the DEFA1A3 locus indicate that intra-allelic rearrangement is the predominant mechanism responsible for changes in DEFA1A3 copy number, explaining the conservation of linkage disequilibrium across the locus. The identification of common structural haplotypes at the DEFA1A3 locus could aid studies into how DEFA1A3 copy number influences expression, which is currently unclear.

The allele-frequency spectrum in a decoupled Moran model with mutation, drift, and directional selection, assuming small mutation rates.

PubMed

Vogl, Claus; Clemente, Florian

2012-05-01

We analyze a decoupled Moran model with haploid population size N, a biallelic locus under mutation and drift with scaled forward and backward mutation rates θ(1)=μ(1)N and θ(0)=μ(0)N, and directional selection with scaled strength γ=sN. With small scaled mutation rates θ(0) and θ(1), which is appropriate for single nucleotide polymorphism data in highly recombining regions, we derive a simple approximate equilibrium distribution for polymorphic alleles with a constant of proportionality. We also put forth an even simpler model, where all mutations originate from monomorphic states. Using this model we derive the sojourn times, conditional on the ancestral and fixed allele, and under equilibrium the distributions of fixed and polymorphic alleles and fixation rates. Furthermore, we also derive the distribution of small samples in the diffusion limit and provide convenient recurrence relations for calculating this distribution. This enables us to give formulas analogous to the Ewens-Watterson estimator of θ for biased mutation rates and selection. We apply this theory to a polymorphism dataset of fourfold degenerate sites in Drosophila melanogaster. Copyright © 2012 Elsevier Inc. All rights reserved.

Effects of the Ordering of Natural Selection and Population Regulation Mechanisms on Wright-Fisher Models

PubMed Central

He, Zhangyi; Beaumont, Mark; Yu, Feng

2017-01-01

We explore the effect of different mechanisms of natural selection on the evolution of populations for one- and two-locus systems. We compare the effect of viability and fecundity selection in the context of the Wright-Fisher model with selection under the assumption of multiplicative fitness. We show that these two modes of natural selection correspond to different orderings of the processes of population regulation and natural selection in the Wright-Fisher model. We find that under the Wright-Fisher model these two different orderings can affect the distribution of trajectories of haplotype frequencies evolving with genetic recombination. However, the difference in the distribution of trajectories is only appreciable when the population is in significant linkage disequilibrium. We find that as linkage disequilibrium decays the trajectories for the two different models rapidly become indistinguishable. We discuss the significance of these findings in terms of biological examples of viability and fecundity selection, and speculate that the effect may be significant when factors such as gene migration maintain a degree of linkage disequilibrium. PMID:28500051

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 imputed under our model can be investigated in additional subsequent analyses, our method will be useful for preparing data for applications in diverse contexts in population genetics and molecular ecology. PMID:22851645

Genetic mapping of the female mimic morph locus in the ruff

PubMed Central

2013-01-01

Background Ruffs (Aves: Philomachus pugnax) possess a genetic polymorphism for male mating behaviour resulting in three permanent alternative male reproductive morphs: (i) territorial ‘Independents’, (ii) non-territorial ‘Satellites’, and (iii) female-mimicking ‘Faeders’. Development into independent or satellite morphs has previously been shown to be due to a single-locus, two-allele autosomal Mendelian mode of inheritance at the Satellite locus. Here, we use linkage analysis to map the chromosomal location of the Faeder locus, which controls development into the Faeder morph, and draw further conclusions about candidate genes, assuming shared synteny with other birds. Results Segregation data on the Faeder locus were obtained from captive-bred pedigrees comprising 64 multi-generation families (N = 381). There was no evidence that the Faeder locus was linked to the Satellite locus, but it was linked with microsatellite marker Ppu020. Comparative mapping of ruff microsatellite markers against the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genomes places the Ppu020 and Faeder loci on a region of chromosome 11 that includes the Melanocortin-1 receptor (MC1R) gene, which regulates colour polymorphisms in numerous birds and other vertebrates. Melanin-based colouration varies with life-history strategies in ruffs and other species, thus the MC1R gene is a strong candidate to play a role in alternative male morph determination. Conclusion Two unlinked loci appear to control behavioural development in ruffs. The Faeder locus is linked to Ppu020, which, assuming synteny, is located on avian chromosome 11. MC1R is a candidate gene involved in alternative male morph determination in ruffs. PMID:24256185

Interrelationships of Heterozygosity, Growth Rate and Heterozygote Deficiencies in the Coot Clam, Mulinia Lateralis

PubMed Central

Gaffney, P. M.; Scott, T. M.; Koehn, R. K.; Diehl, W. J.

1990-01-01

Allozyme surveys of marine invertebrates commonly report heterozygote deficiencies, a correlation between multiple locus heterozygosity and size, or both. Hypotheses advanced to account for these phenomena include inbreeding, null alleles, selection, spatial or temporal Wahlund effects, aneuploidy and molecular imprinting. Previous studies have been unable to clearly distinguish among these alternative hypotheses. This report analyzes a large data set (1906 individuals, 15 allozyme loci) from a single field collection of the coot clam Mulinia lateralis and demonstrates (1) significant heterozygote deficiencies at 13 of 15 loci, (2) a correlation between the magnitude of heterozygote deficiency at a locus and the effect of heterozygosity at that locus on shell length, and (3) a distribution of multilocus heterozygosity which deviates from that predicted by observed single-locus heterozygosities. A critical examination of the abovementioned hypotheses as sources of these findings rules out inbreeding, null alleles, aneuploidy, population mixing and imprinting as sole causes. The pooling of larval subpopulations subjected to varying degrees of selection, aneuploidy or imprinting could account for the patterns observed in this study. PMID:2311919

USH1H, a novel locus for type I Usher syndrome, maps to chromosome 15q22-23.

PubMed

Ahmed, Z M; Riazuddin, S; Khan, S N; Friedman, P L; Riazuddin, S; Friedman, T B

2009-01-01

Usher syndrome (USH) is a hereditary disorder associated with sensorineural hearing impairment, progressive loss of vision attributable to retinitis pigmentosa (RP) and variable vestibular function. Three clinical types have been described with type I (USH1) being the most severe. To date, six USH1 loci have been reported. We ascertained two large Pakistani consanguineous families segregating profound hearing loss, vestibular dysfunction, and RP, the defining features of USH1. In these families, we excluded linkage of USH to the 11 known USH loci and subsequently performed a genome-wide linkage screen. We found a novel USH1 locus designated USH1H that mapped to chromosome 15q22-23 in a 4.92-cM interval. This locus overlaps the non-syndromic deafness locus DFNB48 raising the possibility that the two disorders may be caused by allelic mutations.

Distribution of the messenger RNA for the small conductance calcium-activated potassium channel SK3 in the adult rat brain and correlation with immunoreactivity.

PubMed

Tacconi, S; Carletti, R; Bunnemann, B; Plumpton, C; Merlo Pich, E; Terstappen, G C

2001-01-01

Small conductance calcium-activated potassium channels are voltage independent potassium channels which modulate the firing patterns of neurons by activating the slow component of the afterhyperpolarization. The genes encoding a family of small conductance calcium-activated potassium channels have been cloned and up to now three known members have been described and named small conductance calcium-activated potassium channel type 1, small conductance calcium-activated potassium channel type 2 and small conductance calcium-activated potassium channel type 3; the distribution of their messenger RNA in the rat CNS has already been performed but only in a limited detail. The present study represents the first detailed analysis of small conductance calcium-activated potassium channel type 3 mRNA distribution in the adult rat brain and resulted in a strong to moderate expression of signal in medial habenular nucleus, substantia nigra compact part, suprachiasmatic nucleus, ventral tegmental area, lateral septum, dorsal raphe and locus coeruleus. Immunohistological experiments were also performed and confirmed the presence of small conductance calcium-activated potassium channel type 3 protein in medial habenular nucleus, locus coeruleus and dorsal raphe. Given the importance of dorsal raphe, locus coeruleus and substantia nigra/ventral tegmental area for serotonergic, noradrenergic and dopaminergic transmission respectively, our results pose the morphological basis for further studies on the action of small conductance calcium-activated potassium channel type 3 in serotonergic, noradrenergic and dopaminergic transmission.

Predictors of seasonal influenza vaccination behaviour among nurses and implications for interventions to increase vaccination uptake: A cross-sectional survey.

PubMed

Kan, Ting; Ai, Jiaqi; Zhang, Jing; Liu, Xiaohong

2018-03-01

Vaccination has been proven the most effective method to prevent seasonal influenza. Nurses' vaccination can provide protection against influenza not only for themselves but also for patients they take care of. However, vaccination coverage of nurses is suboptimal worldwide, especially in China. The influencing factors need to be explored so as to develop specific, workable strategies to improve nurses' vaccination behaviour. To explore predictors of their vaccination behaviour, identify the motivators and barriers of vaccination, and provide implications for future interventions. A cross-sectional convenience sampling questionnaire survey. Nine hospitals including five tertiary hospitals, two secondary hospitals, and two primary hospitals in Shanghai, China. A total of 1000 nurses from the nine hospitals were invited to participate in this survey. Among them, 921 nurses responded and 895 returned valid questionnaires that were used in data analysis. The Chinese version of the King's Nurses' Influenza Vaccination Questionnaire was used as the survey instrument and distributed to the participants during February-November 2012. Descriptive statistics, univariate analyses, and multivariate analyses were conducted to explore the predictors of nurses' vaccination behaviour. Overall, 8.8% of the respondents received seasonal influenza vaccination in the past influenza season (2011/2012 season). Nurses had averagely received 0.38 ± 0.71 influenza vaccines during the past five influenza seasons (2007/2008 to 2011/2012 season). Predictors of nurses' vaccination status were clinical specialty, knowledge about influenza vaccination [1.331 (1.102, 1.608), p = 0.003], internal health locus of control [0.910 (0.845, 0.980), p = 0.013], chance health locus of control [1.075 (1.023, 1.130), p = 0.004]and powerful others health of locus control [1.166 (1.083, 1.255), p < 0.001]. Predictors of their vaccination times were hospital level, clinical specialty, and knowledge about influenza vaccination [1.458 (1.242, 1.711), p < 0.001]. Self-protection was the most common cited reason for getting vaccinated, and "no need" was cited as the most common refusal reason. This is the first well-designed study conducted in mainland China to explore nurses' vaccination behaviour against seasonal influenza. Vaccination coverage in this population was suboptimal. Mandatory vaccination policy should be implemented and attempts of multi-faceted interventions including specific education might also be needed. Copyright © 2017 Elsevier Ltd. All rights reserved.

The influence of locus number and information content on species delimitation: an empirical test case in an endangered Mexican salamander.

PubMed

Hime, Paul M; Hotaling, Scott; Grewelle, Richard E; O'Neill, Eric M; Voss, S Randal; Shaffer, H Bradley; Weisrock, David W

2016-12-01

Perhaps the most important recent advance in species delimitation has been the development of model-based approaches to objectively diagnose species diversity from genetic data. Additionally, the growing accessibility of next-generation sequence data sets provides powerful insights into genome-wide patterns of divergence during speciation. However, applying complex models to large data sets is time-consuming and computationally costly, requiring careful consideration of the influence of both individual and population sampling, as well as the number and informativeness of loci on species delimitation conclusions. Here, we investigated how locus number and information content affect species delimitation results for an endangered Mexican salamander species, Ambystoma ordinarium. We compared results for an eight-locus, 137-individual data set and an 89-locus, seven-individual data set. For both data sets, we used species discovery methods to define delimitation models and species validation methods to rigorously test these hypotheses. We also used integrated demographic model selection tools to choose among delimitation models, while accounting for gene flow. Our results indicate that while cryptic lineages may be delimited with relatively few loci, sampling larger numbers of loci may be required to ensure that enough informative loci are available to accurately identify and validate shallow-scale divergences. These analyses highlight the importance of striking a balance between dense sampling of loci and individuals, particularly in shallowly diverged lineages. They also suggest the presence of a currently unrecognized, endangered species in the western part of A. ordinarium's range. © 2016 John Wiley & Sons Ltd.

Genome-Wide Association Analysis of Young-Onset Stroke Identifies a Locus on Chromosome 10q25 Near HABP2.

PubMed

Cheng, Yu-Ching; Stanne, Tara M; Giese, Anne-Katrin; Ho, Weang Kee; Traylor, Matthew; Amouyel, Philippe; Holliday, Elizabeth G; Malik, Rainer; Xu, Huichun; Kittner, Steven J; Cole, John W; O'Connell, Jeffrey R; Danesh, John; Rasheed, Asif; Zhao, Wei; Engelter, Stefan; Grond-Ginsbach, Caspar; Kamatani, Yoichiro; Lathrop, Mark; Leys, Didier; Thijs, Vincent; Metso, Tiina M; Tatlisumak, Turgut; Pezzini, Alessandro; Parati, Eugenio A; Norrving, Bo; Bevan, Steve; Rothwell, Peter M; Sudlow, Cathie; Slowik, Agnieszka; Lindgren, Arne; Walters, Matthew R; Jannes, Jim; Shen, Jess; Crosslin, David; Doheny, Kimberly; Laurie, Cathy C; Kanse, Sandip M; Bis, Joshua C; Fornage, Myriam; Mosley, Thomas H; Hopewell, Jemma C; Strauch, Konstantin; Müller-Nurasyid, Martina; Gieger, Christian; Waldenberger, Melanie; Peters, Annette; Meisinger, Christine; Ikram, M Arfan; Longstreth, W T; Meschia, James F; Seshadri, Sudha; Sharma, Pankaj; Worrall, Bradford; Jern, Christina; Levi, Christopher; Dichgans, Martin; Boncoraglio, Giorgio B; Markus, Hugh S; Debette, Stephanie; Rolfs, Arndt; Saleheen, Danish; Mitchell, Braxton D

2016-02-01

Although a genetic contribution to ischemic stroke is well recognized, only a handful of stroke loci have been identified by large-scale genetic association studies to date. Hypothesizing that genetic effects might be stronger for early- versus late-onset stroke, we conducted a 2-stage meta-analysis of genome-wide association studies, focusing on stroke cases with an age of onset <60 years. The discovery stage of our genome-wide association studies included 4505 cases and 21 968 controls of European, South-Asian, and African ancestry, drawn from 6 studies. In Stage 2, we selected the lead genetic variants at loci with association P<5×10(-6) and performed in silico association analyses in an independent sample of ≤1003 cases and 7745 controls. One stroke susceptibility locus at 10q25 reached genome-wide significance in the combined analysis of all samples from the discovery and follow-up stages (rs11196288; odds ratio =1.41; P=9.5×10(-9)). The associated locus is in an intergenic region between TCF7L2 and HABP2. In a further analysis in an independent sample, we found that 2 single nucleotide polymorphisms in high linkage disequilibrium with rs11196288 were significantly associated with total plasma factor VII-activating protease levels, a product of HABP2. HABP2, which encodes an extracellular serine protease involved in coagulation, fibrinolysis, and inflammatory pathways, may be a genetic susceptibility locus for early-onset stroke. © 2016 American Heart Association, Inc.

Persistence of the same genetic type of Mycoplasma hyopneumoniae in a closed herd for at least two years.

PubMed

Rebaque, Florencia; Camacho, Pablo; Parada, Julián; Lucchesi, Paula; Ambrogi, Arnaldo; Tamiozzo, Pablo

2017-10-20

Two cross-sectional studies were carried out in 2013 and 2015 monitoring for Mycoplasma hyopneumoniae presence in a swine farm. In these studies, the genetic diversity of M. hyopneumoniae was assessed in clinical specimens using a Multiple Locus Variable-number tandem repeat Analysis (MLVA) targeting P97 R1, P146 R3 and H4 loci. The samples from August 2015 showed the MLVA profile prevalent in June 2013, therefore it can be concluded that a same genetic type of M. hyopneumoniae can persist for at least two years in a closed herd. In addition, the nested PCR reactions implemented in this study showed to be useful for MLVA typing in non-invasive clinical samples. Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

FHSA-SED: Two-Locus Model Detection for Genome-Wide Association Study with Harmony Search Algorithm.

PubMed

Tuo, Shouheng; Zhang, Junying; Yuan, Xiguo; Zhang, Yuanyuan; Liu, Zhaowen

2016-01-01

Two-locus model is a typical significant disease model to be identified in genome-wide association study (GWAS). Due to intensive computational burden and diversity of disease models, existing methods have drawbacks on low detection power, high computation cost, and preference for some types of disease models. In this study, two scoring functions (Bayesian network based K2-score and Gini-score) are used for characterizing two SNP locus as a candidate model, the two criteria are adopted simultaneously for improving identification power and tackling the preference problem to disease models. Harmony search algorithm (HSA) is improved for quickly finding the most likely candidate models among all two-locus models, in which a local search algorithm with two-dimensional tabu table is presented to avoid repeatedly evaluating some disease models that have strong marginal effect. Finally G-test statistic is used to further test the candidate models. We investigate our method named FHSA-SED on 82 simulated datasets and a real AMD dataset, and compare it with two typical methods (MACOED and CSE) which have been developed recently based on swarm intelligent search algorithm. The results of simulation experiments indicate that our method outperforms the two compared algorithms in terms of detection power, computation time, evaluation times, sensitivity (TPR), specificity (SPC), positive predictive value (PPV) and accuracy (ACC). Our method has identified two SNPs (rs3775652 and rs10511467) that may be also associated with disease in AMD dataset.

FHSA-SED: Two-Locus Model Detection for Genome-Wide Association Study with Harmony Search Algorithm

PubMed Central

Tuo, Shouheng; Zhang, Junying; Yuan, Xiguo; Zhang, Yuanyuan; Liu, Zhaowen

2016-01-01

Motivation Two-locus model is a typical significant disease model to be identified in genome-wide association study (GWAS). Due to intensive computational burden and diversity of disease models, existing methods have drawbacks on low detection power, high computation cost, and preference for some types of disease models. Method In this study, two scoring functions (Bayesian network based K2-score and Gini-score) are used for characterizing two SNP locus as a candidate model, the two criteria are adopted simultaneously for improving identification power and tackling the preference problem to disease models. Harmony search algorithm (HSA) is improved for quickly finding the most likely candidate models among all two-locus models, in which a local search algorithm with two-dimensional tabu table is presented to avoid repeatedly evaluating some disease models that have strong marginal effect. Finally G-test statistic is used to further test the candidate models. Results We investigate our method named FHSA-SED on 82 simulated datasets and a real AMD dataset, and compare it with two typical methods (MACOED and CSE) which have been developed recently based on swarm intelligent search algorithm. The results of simulation experiments indicate that our method outperforms the two compared algorithms in terms of detection power, computation time, evaluation times, sensitivity (TPR), specificity (SPC), positive predictive value (PPV) and accuracy (ACC). Our method has identified two SNPs (rs3775652 and rs10511467) that may be also associated with disease in AMD dataset. PMID:27014873

STBase: one million species trees for comparative biology.

PubMed

McMahon, Michelle M; Deepak, Akshay; Fernández-Baca, David; Boss, Darren; Sanderson, Michael J

2015-01-01

Comprehensively sampled phylogenetic trees provide the most compelling foundations for strong inferences in comparative evolutionary biology. Mismatches are common, however, between the taxa for which comparative data are available and the taxa sampled by published phylogenetic analyses. Moreover, many published phylogenies are gene trees, which cannot always be adapted immediately for species level comparisons because of discordance, gene duplication, and other confounding biological processes. A new database, STBase, lets comparative biologists quickly retrieve species level phylogenetic hypotheses in response to a query list of species names. The database consists of 1 million single- and multi-locus data sets, each with a confidence set of 1000 putative species trees, computed from GenBank sequence data for 413,000 eukaryotic taxa. Two bodies of theoretical work are leveraged to aid in the assembly of multi-locus concatenated data sets for species tree construction. First, multiply labeled gene trees are pruned to conflict-free singly-labeled species-level trees that can be combined between loci. Second, impacts of missing data in multi-locus data sets are ameliorated by assembling only decisive data sets. Data sets overlapping with the user's query are ranked using a scheme that depends on user-provided weights for tree quality and for taxonomic overlap of the tree with the query. Retrieval times are independent of the size of the database, typically a few seconds. Tree quality is assessed by a real-time evaluation of bootstrap support on just the overlapping subtree. Associated sequence alignments, tree files and metadata can be downloaded for subsequent analysis. STBase provides a tool for comparative biologists interested in exploiting the most relevant sequence data available for the taxa of interest. It may also serve as a prototype for future species tree oriented databases and as a resource for assembly of larger species phylogenies from precomputed trees.

Subspecific affinities and conservation genetics of western big-eared bats (Corynorhinus townsendii pallescens) at the edge of their distributional range

USGS Publications Warehouse

Smith, S.J.; Leslie, David M.; Hamilton, M.J.; Lack, Justin B.; Van Den Bussche, Ronald A.

2008-01-01

Subspecific affinities, determination of population boundaries, and levels of population connectedness are of critical importance for the development of management and conservation planning. We used variation at a mitochondrial locus and 5 biparentally inherited nuclear loci to determine partitioning of genetic variation of western big-eared bats (Corynorhinus townsendii) within and among caves occurring in a fragmented landscape of gypsum deposits in western Oklahoma. To accomplish this objective, we first performed a phylogenetic analysis based on the mitochondrial locus of western big-eared bats from a large portion of their range. This analysis indicated that western big-eared bats at the periphery of the distribution in western Oklahoma share phylogenetic affinities with the most geographically restricted subspecies, C. t. pallescens. Because C. townsendii is rare in Oklahoma and is listed as a species of special concern, this finding provides additional support for the continued protection of this species in Oklahoma. Within western Oklahoma, we failed to detect significant differentiation among any caves for the biparentally inherited microsatellite data. However, the mitochondrial locus exhibited significant levels of genetic differentiation among caves, with the highest level of differentiation occurring between caves within the disjunct distributions of gypsum (??ST = 38.76%). Although a significant amount of genetic differentiation was detected between populations on the 2 disjunct distributions of gypsum deposits, Analysis with the program Migrate suggested high levels of asymmetric gene flow among some populations. Our results provide a greater understanding of the population dynamics of western big-eared bats on the periphery of their range and highlight the importance of continued monitoring and study of this taxon. ?? 2008 American Society of Mammalogists.

Mapping genes underlying ethnic differences in disease risk by linkage disequilibrium in recently admixed populations.

PubMed Central

McKeigue, P M

1997-01-01

Where recent admixture has occurred between two populations that have different disease rates for genetic reasons, family-based association studies can be used to map the genes underlying these differences, if the ancestry of the alleles at each locus examined can be assigned to one of the two founding populations. This article explores the statistical power and design requirements of this approach. Markers suitable for assigning the ancestry of genomic regions could be defined by grouping alleles at closely spaced microsatellite loci into haplotypes, or generated by representational difference analysis. For a given relative risk between populations, the sample size required to detect a disease locus that accounts for this relative risk by linkage-disequilibrium mapping in an admixed population is not critically dependent on assumptions about genotype penetrances or allele frequencies. Using the transmission-disequilibrium test to search the genome for a locus that accounts for a relative risk of between 2 and 3 in a high-risk population, compared with a low-risk population, generally requires between 150 and 800 case-parent pairs of mixed descent. The optimal strategy is to conduct an initial study using markers spaced at < or = 10 cM with cases from the second and third generations of mixed descent, and then to map the disease loci more accurately in a subsequent study of a population with a longer history of admixture. This approach has greater statistical power than allele-sharing designs and has obvious applications to the genetics of hypertension, non-insulin-dependent diabetes, and obesity. PMID:8981962

Delimiting Species-Poor Data Sets using Single Molecular Markers: A Study of Barcode Gaps, Haplowebs and GMYC.

PubMed

Dellicour, Simon; Flot, Jean-François

2015-11-01

Most single-locus molecular approaches to species delimitation available to date have been designed and tested on data sets comprising at least tens of species, whereas the opposite case (species-poor data sets for which the hypothesis that all individuals are conspecific cannot by rejected beforehand) has rarely been the focus of such attempts. Here we compare the performance of barcode gap detection, haplowebs and generalized mixed Yule-coalescent (GMYC) models to delineate chimpanzees and bonobos using nuclear sequence markers, then apply these single-locus species delimitation methods to data sets of one, three, or six species simulated under a wide range of population sizes, speciation rates, mutation rates and sampling efforts. Our results show that barcode gap detection and GMYC models are unable to delineate species properly in data sets composed of one or two species, two situations in which haplowebs outperform them. For data sets composed of three or six species, bGMYC and haplowebs outperform the single-threshold and multiple-threshold versions of GMYC, whereas a clear barcode gap is only observed when population sizes and speciation rates are both small. The latter conditions represent a "sweet spot" for molecular taxonomy where all the single-locus approaches tested work well; however, the performance of these methods decreases strongly when population sizes and speciation rates are high, suggesting that multilocus approaches may be necessary to tackle such cases. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Genetic characterization of the partial mitochondrial cytochrome oxidase c subunit I (cox 1) gene of the zoonotic parasitic nematode, Ancylostoma ceylanicum from humans, dogs and cats.

PubMed

Ngui, Romano; Mahdy, Mohammed A K; Chua, Kek Heng; Traub, Rebecca; Lim, Yvonne A L

2013-10-01

Ancylostoma ceylanicum is the only zoonotic hookworm species that is able to produce patent infections in humans with the majority of cases reported in South East Asia. Over the past few years, there have been an increasing number of studies investigating the prevalence of this parasitic zoonosis using molecular diagnostic tools and a single genetic locus as marker for species identification. As there can be limitations in using a single genetic locus for epidemiological studies and genetic discrimination, the complementary use of a more variable locus will provide additional evidence to support the zoonotic exchange of hookworm species between humans and animals. In the present study, the cytochrome c oxidase subunit 1 (cox 1) sequence of A. ceylanicum from positive human and animal fecal samples were determined and compared with published reference sequences. Phylogenetic analysis demonstrated that isolates of A. ceylanicum were divided into two clusters, one consisting 3 human isolates and the other comprising 19 isolates of human and animal origin from different geographical locations within Malaysia. The two groups of A. ceylanicum could be distinguished from one another through five fixed nucleotide differences at locations 891, 966, 1008, 1077 and 1083. The detection of genetically distinct groups and considerable level of genetic variation within the cox 1 sequence of A. ceylanicum might suggest potential haplotype-linked differences in zoonotic, epidemiological and pathobiological characteristics, a hypothesis that still needs further investigation. Copyright © 2013 Elsevier B.V. All rights reserved.

Genotypic Diversity of Mycobacterium tuberculosis Clinical Isolates in the Multiethnic Area of the Xinjiang Uygur Autonomous Region in China.

PubMed

Liu, Jie; Li, Junlian; Liu, Jiao; Zhao, Xiuqin; Lian, Lulu; Liu, Haican; Lu, Bing; Yu, Qin; Zhang, Jingrui; Qi, Yingcheng; Wan, Kanglin

2017-01-01

Objectives. We studied the genetic diversity of clinical isolates from patients with tuberculosis in the multiethnic area of Xinjiang autonomous region in China. A total of 311 clinical M. tuberculosis isolates were collected in 2006 and 2011 and genotyped by two genotyping methods. All isolates were grouped into 68 distinct spoligotypes using the spoligotyping method. The Beijing family was dominant, followed by T1 and CAS. MIRU-VNTR results showed that a total of 195 different VNTR types were identified. Ten of the 15 loci were highly or moderately discriminant according to their HGDI scores, and 13 loci had good discriminatory power in non-Beijing family strains, whereas only two loci had good discriminatory power in Beijing family strains. Chi-square tests demonstrated that there were no correlations between four characteristics (sex, age, type of case, and treatment history) and the Beijing family. In summary, Beijing family strains were predominant in Xinjiang, and the VNTR-15 China locus-set was suitable for genotyping all Xinjiang strains, but not for the Beijing family strains. Thus, these data suggested that different genotype distributions may exist in different regions; MLVA locus-sets should be adjusted accordingly, with newly added loci to increase resolution if necessary.

Asymmetrical booster ascent guidance and control system design study. Volume 4: Sampled data stability analysis program (SADSAP) user's guide. [space shuttle development

NASA Technical Reports Server (NTRS)

Wilson, J. L.

1974-01-01

A users guide to the Sampled Data Stability Analysis Program (SADSAP) is provided. This program is a general purpose sampled data Stability Analysis Program capable of providing frequency response on root locus data.

Development of microsatellite markers to genetically differentiate populations of Octopus minor from Korea and China.

PubMed

Kang, Jung-Ha; Kim, Yi-Kyung; Park, Jung-Youn; An, Chel-Min; Jun, Je-Chun

2012-08-01

Of the more than 300 octopus species, Octopus minor is one of the most popular and economically important species in Eastern Asia, including Korea, along with O. vulgaris, O. ocellatus, and O. aegina. We developed 19 microsatellite markers from Octopus minor and eight polymorphic markers were developed to analyze the genetic diversity and relationships among four octopus populations from Korea and three from China. The number of alleles per locus varied from 10 to 49, and allelic richness per locus ranged from 2 to 16.4 across all populations. The average allele number among the populations was 11.1, with a minimum of 8.3 and a maximum of 13.6. The mean allelic richness was 8.7 in all populations. The Hardy-Weinberg equilibrium (HWE) test revealed significant deviation in 19 of the 56 single-locus sites, and null alleles were presumed in five of eight loci. The pairwise F ( ST ) values between populations from Korea and China differed significantly in all pairwise comparisons. The genetic distances between the China and Korea samples ranged from 0.161 to 0.454. The genetic distances among the populations from Korea ranged from 0.033 to 0.090, with an average of 0.062; those among populations from China ranged from 0.191 to 0.316, with an average of 0.254. The populations from Korea and China formed clearly separated into clusters via an unweighted pair group method with arithmetic mean dendrogram. Furthermore, a population from muddy flats on the western coast of the Korean Peninsula and one from a rocky area on Jeju Island formed clearly separated subclusters. An assignment test based on the allele distribution discriminated between the Korean and Chinese origins with 96.9 % accuracy.

[Monitoring microbiological safety of small systems of water distribution. Comparison of two sampling programs in a town in central Italy].

PubMed

Papini, Paolo; Faustini, Annunziata; Manganello, Rosa; Borzacchi, Giancarlo; Spera, Domenico; Perucci, Carlo A

2005-01-01

To determine the frequency of sampling in small water distribution systems (<5,000 inhabitants) and compare the results according to different hypotheses in bacteria distribution. We carried out two sampling programs to monitor the water distribution system in a town in Central Italy between July and September 1992; the Poisson distribution assumption implied 4 water samples, the assumption of negative binomial distribution implied 21 samples. Coliform organisms were used as indicators of water safety. The network consisted of two pipe rings and two wells fed by the same water source. The number of summer customers varied considerably from 3,000 to 20,000. The mean density was 2.33 coliforms/100 ml (sd= 5.29) for 21 samples and 3 coliforms/100 ml (sd= 6) for four samples. However the hypothesis of homogeneity was rejected (p-value <0.001) and the probability of II type error with the assumption of heterogeneity was higher with 4 samples (beta= 0.24) than with 21 (beta= 0.05). For this small network, determining the samples' size according to heterogeneity hypothesis strengthens the statement that water is drinkable compared with homogeneity assumption.

Locus coeruleus and dopaminergic consolidation of everyday memory.

PubMed

Takeuchi, Tomonori; Duszkiewicz, Adrian J; Sonneborn, Alex; Spooner, Patrick A; Yamasaki, Miwako; Watanabe, Masahiko; Smith, Caroline C; Fernández, Guillén; Deisseroth, Karl; Greene, Robert W; Morris, Richard G M

2016-09-15

The retention of episodic-like memory is enhanced, in humans and animals, when something novel happens shortly before or after encoding. Using an everyday memory task in mice, we sought the neurons mediating this dopamine-dependent novelty effect, previously thought to originate exclusively from the tyrosine-hydroxylase-expressing (TH + ) neurons in the ventral tegmental area. Here we report that neuronal firing in the locus coeruleus is especially sensitive to environmental novelty, locus coeruleus TH + neurons project more profusely than ventral tegmental area TH + neurons to the hippocampus, optogenetic activation of locus coeruleus TH + neurons mimics the novelty effect, and this novelty-associated memory enhancement is unaffected by ventral tegmental area inactivation. Surprisingly, two effects of locus coeruleus TH + photoactivation are sensitive to hippocampal D 1 /D 5 receptor blockade and resistant to adrenoceptor blockade: memory enhancement and long-lasting potentiation of synaptic transmission in CA1 ex vivo. Thus, locus coeruleus TH + neurons can mediate post-encoding memory enhancement in a manner consistent with possible co-release of dopamine in the hippocampus.

Length Variation of Cag/Caa Trinucleotide Repeats in Natural Populations of Drosophila Melanogaster and Its Relation to the Recombination Rate

PubMed Central

Michalakis, Y.; Veuille, M.

1996-01-01

Eleven genes distributed along the Drosophila melanogaster chromosome 2 and showing exonic tandem repeats of glutamine codons (CAG or CAA) were surveyed for length variation in a sample of four European and African populations. Only one gene was monomorphic. Eight genes were polymorphic in all populations, with a total number of alleles varying between five and 12 for 120 chromosomes. The average heterozygozity per locus and population was 0.41. Selective neutrality in length variation could not be rejected under the assumptions of the infinite allele model. Significant population subdivision was found though no geographical pattern emerged, all populations being equally different. Significant linkage disequilibrium was found in four out of seven cases where the genetic distance between loci was <1 cM and was negligible when the distance was larger. There is evidence that these associations were established after the populations separated. An unexpected result was that variation at each locus was independent of the coefficient of exchange, although the latter ranged from zero to the relatively high value of 6.7%. This would indicate that background selection and selective hitchhiking, which are thought to affect levels of nucleotide substitution polymorphism, have no effect on trinucleotide repeat variation. PMID:8844158

Batrachochytrium dendrobatidis Shows High Genetic Diversity and Ecological Niche Specificity among Haplotypes in the Maya Mountains of Belize

PubMed Central

Kaiser, Kristine; Pollinger, John

2012-01-01

The amphibian pathogen Batrachochytrium dendrobatidis (Bd) has been implicated in amphibian declines around the globe. Although it has been found in most countries in Central America, its presence has never been assessed in Belize. We set out to determine the range, prevalence, and diversity of Bd using quantitative PCR (qPCR) and sequencing of a portion of the 5.8 s and ITS1-2 regions. Swabs were collected from 524 amphibians of at least 26 species in the protected areas of the Maya Mountains of Belize. We sequenced a subset of 72 samples that had tested positive for Bd by qPCR at least once; 30 samples were verified as Bd. Eight unique Bd haplotypes were identified in the Maya Mountains, five of which were previously undescribed. We identified unique ecological niches for the two most broadly distributed haplotypes. Combined with data showing differing virulence shown in different strains in other studies, the 5.8 s - ITS1-2 region diversity found in this study suggests that there may be substantial differences among populations or haplotypes. Future work should focus on whether specific haplotypes for other genomic regions and possibly pathogenicity can be associated with haplotypes at this locus, as well as the integration of molecular tools with other ecological tools to elucidate the ecology and pathogenicity of Bd. PMID:22389681

A New Perspective on Polyploid Fragaria (Strawberry) Genome Composition Based on Large-Scale, Multi-Locus Phylogenetic Analysis

PubMed Central

Yang, Yilong

2017-01-01

Abstract The subgenomic compositions of the octoploid (2n = 8× = 56) strawberry (Fragaria) species, including the economically important cultivated species Fragaria x ananassa, have been a topic of long-standing interest. Phylogenomic approaches utilizing next-generation sequencing technologies offer a new window into species relationships and the subgenomic compositions of polyploids. We have conducted a large-scale phylogenetic analysis of Fragaria (strawberry) species using the Fluidigm Access Array system and 454 sequencing platform. About 24 single-copy or low-copy nuclear genes distributed across the genome were amplified and sequenced from 96 genomic DNA samples representing 16 Fragaria species from diploid (2×) to decaploid (10×), including the most extensive sampling of octoploid taxa yet reported. Individual gene trees were constructed by different tree-building methods. Mosaic genomic structures of diploid Fragaria species consisting of sequences at different phylogenetic positions were observed. Our findings support the presence in octoploid species of genetic signatures from at least five diploid ancestors (F. vesca, F. iinumae, F. bucharica, F. viridis, and at least one additional allele contributor of unknown identity), and questions the extent to which distinct subgenomes are preserved over evolutionary time in the allopolyploid Fragaria species. In addition, our data support divergence between the two wild octoploid species, F. virginiana and F. chiloensis. PMID:29045639

Identification of a novel polymorphism in X-linked sterol-4-alpha-carboxylate 3-dehydrogenase (Nsdhl) associated with reduced high-density lipoprotein cholesterol levels in I/LnJ mice.

PubMed

Bautz, David J; Broman, Karl W; Threadgill, David W

2013-10-03

Loci controlling plasma lipid concentrations were identified by performing a quantitative trait locus analysis on genotypes from 233 mice from a F2 cross between KK/HlJ and I/LnJ, two strains known to differ in their high-density lipoprotein (HDL) cholesterol levels. When fed a standard diet, HDL cholesterol concentration was affected by two significant loci, the Apoa2 locus on Chromosome (Chr) 1 and a novel locus on Chr X, along with one suggestive locus on Chr 6. Non-HDL concentration also was affected by loci on Chr 1 and X along with a suggestive locus on Chr 3. Additional loci that may be sex-specific were identified for HDL cholesterol on Chr 2, 3, and 4 and for non-HDL cholesterol on Chr 5, 7, and 14. Further investigation into the potential causative gene on Chr X for reduced HDL cholesterol levels revealed a novel, I/LnJ-specific nonsynonymous polymorphism in Nsdhl, which codes for sterol-4-alpha-carboxylate 3-dehydrogenase in the cholesterol synthesis pathway. Although many lipid quantitative trait locus have been reported previously, these data suggest there are additional genes left to be identified that control lipid levels and that can provide new pharmaceutical targets.

Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species

PubMed Central

Chen, Shilin; Yao, Hui; Han, Jianping; Liu, Chang; Song, Jingyuan; Shi, Linchun; Zhu, Yingjie; Ma, Xinye; Gao, Ting; Pang, Xiaohui; Luo, Kun; Li, Ying; Li, Xiwen; Jia, Xiaocheng; Lin, Yulin; Leon, Christine

2010-01-01

Background The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL + matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over. Methodology/Principal Findings Here, we compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species. Our ranking criteria included PCR amplification efficiency, differential intra- and inter-specific divergences, and the DNA barcoding gap. Our data suggest that the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications. Furthermore, we tested the discrimination ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the ITS2 was 92.7% at the species level. Conclusions The ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species. We also propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa. PMID:20062805

Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.).

PubMed Central

Garris, Amanda J; McCouch, Susan R; Kresovich, Stephen

2003-01-01

To assess the usefulness of linkage disequilibrium mapping in an autogamous, domesticated species, we have characterized linkage disequilibrium in the candidate region for xa5, a recessive gene conferring race-specific resistance to bacterial blight in rice. This trait and locus have good mapping information, a tractable phenotype, and available sequence data, but no cloned gene. We sampled 13 short segments from the 70-kb candidate region in 114 accessions of Oryza sativa. Five additional segments were sequenced from the adjacent 45-kb region in resistant accessions to estimate the distance at which linkage disequilibrium decays. The data show significant linkage disequilibrium between sites 100 kb apart. The presence of the xa5 resistant reaction in two ecotypes and in accessions with different haplotypes in the candidate region may indicate multiple origins or genetic heterogeneity for resistance. In addition, genetic differentiation between ecotypes emphasizes the need for controlling for population structure in the design of linkage disequilibrium studies in rice. PMID:14573486

Microsatellites identify depredated waterfowl remains from glaucous gull stomachs

USGS Publications Warehouse

Scribner, K.T.; Bowman, Timothy D.

1998-01-01

Prey remains can provide valuable sources of information regarding causes of predation and the species composition of a predator's diet. Unfortunately, the highly degraded state of many prey samples from gastrointestinal tracts often precludes unambiguous identification. We describe a procedure by which PCR amplification of taxonomically informative microsatellite loci were used to identify species of waterfowl predated by glaucous gulls (Larus hyperboreus). We found that one microsatellite locus unambiguously distinguished between species of the subfamily Anserinae (whistling ducks, geese and swans) and those of the subfamily Anatidae (all other ducks). An additional locus distinguished the remains of all geese and swan species known to nest on the Yukon-Kuskokwim delta in western Alaska. The study focused on two waterfowl species which have experienced precipitous declines in population numbers: emperor geese (Chen canagica) and spectacled eiders (Somateria fischeri). No evidence of predation on spectacled eiders was observed. Twenty-six percent of all glaucous gull stomachs examined contained the remains of juvenile emperor geese.

Lexical Access and Dual-Task Performance: Determining the Locus of the Bottleneck

NASA Technical Reports Server (NTRS)

Allen, Phil

2004-01-01

During the two years of funding for NASA Grant "NCC21325, Lexical access and dual-task performance: Determining the locus of the bottleneck," we completed three experiments involving the psychological refractory period (PRP) and word frequency.

Microstructure and tuber properties of potato varieties with different genetic profiles.

PubMed

Romano, Annalisa; Masi, Paolo; Aversano, Riccardo; Carucci, Francesca; Palomba, Sara; Carputo, Domenico

2018-01-15

The objectives of this research were to study tuber starch characteristics and chemical - thermal properties of 21 potato varieties, and to determine their genetic diversity through SSR markers. Starch granular size varied among samples, with a wide diameter distribution (5-85μm), while granule shapes were similar. Differential Scanning Calorimeter analysis showed that the transition temperatures (69°C-74°C) and enthalpies of gelatinization (0.9J/g-3.8J/g) of tubers were also variety dependent. SSR analysis allowed the detection of 157 alleles across all varieties, with an average value of 6.8 alleles per locus. Variety-specific alleles were also identified. SSR-based cluster analysis revealed that varieties with interesting quality attributes were distributed among all clusters and sub-clusters, suggesting that the genetic basis of traits analyzed may differ among our varieties. The information obtained in this study may be useful to identify and develop varieties with slowly digestible starch. Copyright © 2017 Elsevier Ltd. All rights reserved.

Directional genetic selection by pulp mill effluent on multiple natural populations of three-spined stickleback (Gasterosteus aculeatus).

PubMed

Lind, Emma E; Grahn, Mats

2011-05-01

Contamination can cause a rapid environmental change which may require populations to respond with evolutionary changes. To evaluate the effects of pulp mill effluents on population genetics, we sampled three-spined sticklebacks (Gasterosteus aculeatus) near four pulp mills and four adjacent reference sites and analyzed Amplified Fragment Length Polymorphism (AFLP) to compare genetic variability. A fine scale genetic structure was detected and samples from polluted sites separated from reference sites in multidimensional scaling plots (P<0.005, 1000 permutations) and locus-by-locus Analysis of Molecular Variance (AMOVA) further confirmed that habitats are significantly separated (F(ST)=0.021, P<0.01, 1023 permutations). The amount of genetic variation between populations did not differ between habitats, and populations from both habitats had similar levels of heterozygosity (polluted sites Nei's Hs=0.11, reference sites Nei's Hs=0.11). Still, pairwise F(ST): s between three, out of four, pairs of polluted-reference sites were significant. A F(ST)-outlier analysis showed that 21 (8.4%) loci were statistically different from a neutral distribution at the P<0.05 level and therefore indicated to be under divergent selection. When removing 13 F(ST)-outlier loci, significant at the P<0.01 level, differentiation between habitats disappeared in a multidimensional scaling plot. In conclusion, pulp mill effluence has acted as a selective agent on natural populations of G. aculeatus, causing a convergence in genotype composition change at multiple sites in an open environment. © The Author(s) 2011. This article is published with open access at Springerlink.com

A two-locus model of spatially varying stabilizing or directional selection on a quantitative trait

PubMed Central

Geroldinger, Ludwig; Bürger, Reinhard

2014-01-01

The consequences of spatially varying, stabilizing or directional selection on a quantitative trait in a subdivided population are studied. A deterministic two-locus two-deme model is employed to explore the effects of migration, the degree of divergent selection, and the genetic architecture, i.e., the recombination rate and ratio of locus effects, on the maintenance of genetic variation. The possible equilibrium configurations are determined as functions of the migration rate. They depend crucially on the strength of divergent selection and the genetic architecture. The maximum migration rates are investigated below which a stable fully polymorphic equilibrium or a stable single-locus polymorphism can exist. Under stabilizing selection, but with different optima in the demes, strong recombination may facilitate the maintenance of polymorphism. However usually, and in particular with directional selection in opposite direction, the critical migration rates are maximized by a concentrated genetic architecture, i.e., by a major locus and a tightly linked minor one. Thus, complementing previous work on the evolution of genetic architectures in subdivided populations subject to diversifying selection, it is shown that concentrated architectures may aid the maintenance of polymorphism. Conditions are obtained when this is the case. Finally, the dependence of the phenotypic variance, linkage disequilibrium, and various measures of local adaptation and differentiation on the parameters is elaborated. PMID:24726489

A two-locus model of spatially varying stabilizing or directional selection on a quantitative trait.

PubMed

Geroldinger, Ludwig; Bürger, Reinhard

2014-06-01

The consequences of spatially varying, stabilizing or directional selection on a quantitative trait in a subdivided population are studied. A deterministic two-locus two-deme model is employed to explore the effects of migration, the degree of divergent selection, and the genetic architecture, i.e., the recombination rate and ratio of locus effects, on the maintenance of genetic variation. The possible equilibrium configurations are determined as functions of the migration rate. They depend crucially on the strength of divergent selection and the genetic architecture. The maximum migration rates are investigated below which a stable fully polymorphic equilibrium or a stable single-locus polymorphism can exist. Under stabilizing selection, but with different optima in the demes, strong recombination may facilitate the maintenance of polymorphism. However usually, and in particular with directional selection in opposite direction, the critical migration rates are maximized by a concentrated genetic architecture, i.e., by a major locus and a tightly linked minor one. Thus, complementing previous work on the evolution of genetic architectures in subdivided populations subject to diversifying selection, it is shown that concentrated architectures may aid the maintenance of polymorphism. Conditions are obtained when this is the case. Finally, the dependence of the phenotypic variance, linkage disequilibrium, and various measures of local adaptation and differentiation on the parameters is elaborated. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate.

PubMed

Jasinska, Anna J; Zelaya, Ivette; Service, Susan K; Peterson, Christine B; Cantor, Rita M; Choi, Oi-Wa; DeYoung, Joseph; Eskin, Eleazar; Fairbanks, Lynn A; Fears, Scott; Furterer, Allison E; Huang, Yu S; Ramensky, Vasily; Schmitt, Christopher A; Svardal, Hannes; Jorgensen, Matthew J; Kaplan, Jay R; Villar, Diego; Aken, Bronwen L; Flicek, Paul; Nag, Rishi; Wong, Emily S; Blangero, John; Dyer, Thomas D; Bogomolov, Marina; Benjamini, Yoav; Weinstock, George M; Dewar, Ken; Sabatti, Chiara; Wilson, Richard K; Jentsch, J David; Warren, Wesley; Coppola, Giovanni; Woods, Roger P; Freimer, Nelson B

2017-12-01

By analyzing multitissue gene expression and genome-wide genetic variation data in samples from a vervet monkey pedigree, we generated a transcriptome resource and produced the first catalog of expression quantitative trait loci (eQTLs) in a nonhuman primate model. This catalog contains more genome-wide significant eQTLs per sample than comparable human resources and identifies sex- and age-related expression patterns. Findings include a master regulatory locus that likely has a role in immune function and a locus regulating hippocampal long noncoding RNAs (lncRNAs), whose expression correlates with hippocampal volume. This resource will facilitate genetic investigation of quantitative traits, including brain and behavioral phenotypes relevant to neuropsychiatric disorders.

Teacher psychological needs, locus of control and engagement.

PubMed

Betoret, Fernando Doménech

2013-01-01

This study examines the relationships among psychological needs, locus of control and engagement in a sample of 282 Spanish secondary school teachers. Nine teacher needs were identified based on the study of Bess (1977) and on the Self-Determination Theory (Deci & Ryan, 1985, 2000, 2002). Self-report questionnaires were used to measure the construct selected for this study and their interrelationships were examined by conducting hierarchical regression analyses. An analysis of teacher responses using hierarchical regression reveals that psychological needs have significant positive effects on the three engagement dimensions (vigor, dedication and absorption). Furthermore, the results show the moderator role played by locus of control in the relationship between teacher psychological needs and the so-called core of engagement (vigor and dedication). Finally, practical implications are discussed.

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.

Effective application of multiple locus variable number of tandem repeats analysis to tracing Staphylococcus aureus in food-processing environment.

PubMed

Rešková, Z; Koreňová, J; Kuchta, T

2014-04-01

A total of 256 isolates of Staphylococcus aureus were isolated from 98 samples (34 swabs and 64 food samples) obtained from small or medium meat- and cheese-processing plants in Slovakia. The strains were genotypically characterized by multiple locus variable number of tandem repeats analysis (MLVA), involving multiplex polymerase chain reaction (PCR) with subsequent separation of the amplified DNA fragments by an automated flow-through gel electrophoresis. With the panel of isolates, MLVA produced 31 profile types, which was a sufficient discrimination to facilitate the description of spatial and temporal aspects of contamination. Further data on MLVA discrimination were obtained by typing a subpanel of strains by multiple locus sequence typing (MLST). MLVA coupled to automated electrophoresis proved to be an effective, comparatively fast and inexpensive method for tracing S. aureus contamination of food-processing factories. Subspecies genotyping of microbial contaminants in food-processing factories may facilitate identification of spatial and temporal aspects of the contamination. This may help to properly manage the process hygiene. With S. aureus, multiple locus variable number of tandem repeats analysis (MLVA) proved to be an effective method for the purpose, being sufficiently discriminative, yet comparatively fast and inexpensive. The application of automated flow-through gel electrophoresis to separation of DNA fragments produced by multiplex PCR helped to improve the accuracy and speed of the method. © 2013 The Society for Applied Microbiology.

Habitat and Host Indicate Lineage Identity in Colletotrichum gloeosporioides s.l. from Wild and Agricultural Landscapes in North America

PubMed Central

Doyle, Vinson P.; Oudemans, Peter V.; Rehner, Stephen A.; Litt, Amy

2013-01-01

Understanding the factors that drive the evolution of pathogenic fungi is central to revealing the mechanisms of virulence and host preference, as well as developing effective disease control measures. Prerequisite to these pursuits is the accurate delimitation of species boundaries. Colletotrichum gloeosporioides s.l. is a species complex of plant pathogens and endophytic fungi for which reliable species recognition has only recently become possible through a multi-locus phylogenetic approach. By adopting an intensive regional sampling strategy encompassing multiple hosts within and beyond agricultural zones associated with cranberry (Vaccinium macrocarpon Aiton), we have integrated North America strains of Colletotrichum gloeosporioides s.l. from these habitats into a broader phylogenetic framework. We delimit species on the basis of genealogical concordance phylogenetic species recognition (GCPSR) and quantitatively assess the monophyly of delimited species at each of four nuclear loci and in the combined data set with the genealogical sorting index (gsi). Our analysis resolved two principal lineages within the species complex. Strains isolated from cranberry and sympatric host plants are distributed across both of these lineages and belong to seven distinct species or terminal clades. Strains isolated from V. macrocarpon in commercial cranberry beds belong to four species, three of which are described here as new. Another species, C. rhexiae Ellis & Everh., is epitypified. Intensive regional sampling has revealed a combination of factors, including the host species from which a strain has been isolated, the host organ of origin, and the habitat of the host species, as useful indicators of species identity in the sampled regions. We have identified three broadly distributed temperate species, C. fructivorum, C. rhexiae, and C. nupharicola, that could be useful for understanding the microevolutionary forces that may lead to species divergence in this important complex of endophytes and plant pathogens. PMID:23671594

Multi-locus variable-number tandem repeat analysis of Chinese Brucella strains isolated from 1953 to 2013.

PubMed

Tian, Guo-Zhong; Cui, Bu-Yun; Piao, Dong-Ri; Zhao, Hong-Yan; Li, Lan-Yu; Liu, Xi; Xiao, Pei; Zhao, Zhong-Zhi; Xu, Li-Qing; Jiang, Hai; Li, Zhen-Jun

2017-05-02

Brucellosis was a common human and livestock disease caused by Brucella strains, the category B priority pathogens by the US Center for Disease Control (CDC). Identified as a priority disease in human and livestock populations, the increasing incidence in recent years in China needs urgent control measures for this disease but the molecular background important for monitoring the epidemiology of Brucella strains at the national level is still lacking. A total of 600 Brucella isolates collected during 60 years (from 1953 to 2013) in China were genotyped by multiple locus variable-number tandem repeat analysis (MLVA) and the variation degree of MLVA11 loci was calculated by the Hunter Gaston Diversity Index (HGDI) values. The charts and map were processed by Excel 2013, and cluster analysis and epidemiological distribution was performed using BioNumerics (version 5.1). The 600 representative Brucella isolates fell into 104 genotypes with 58 singleton genotypes by the MLVA11 assay, including B. melitensis biovars 2 and 3 (five main genotypes), B. abortus biovars 1 and 3 (two main genotypes), B. suis biovars 1 and 3 (three main genotypes), and B. canis (two main genotypes) respectively. While most B. suis biovar 1 and biovar 3 were respectively found in northern provinces and southern provinces, B. melitensis and B. abortus strains were dominant in China. Canine Brucellosis was only found in animals without any human cases reported. Eight Brucellosis epidemic peaks emerged during the 60 years between 1953 and 2013: 1955 - 1959, 1962 - 1969, 1971 - 1975, 1977 - 1983, 1985 - 1989, 1992 - 1997, 2000 - 2008 and 2010 - 2013 in China. Brucellosis has its unique molecular epidemiological patterns with specific spatial and temporal distribution according to MLVA. IDOP-D-16-00101.

A robust and efficient statistical method for genetic association studies using case and control samples from multiple cohorts

PubMed Central

2013-01-01

Background The theoretical basis of genome-wide association studies (GWAS) is statistical inference of linkage disequilibrium (LD) between any polymorphic marker and a putative disease locus. Most methods widely implemented for such analyses are vulnerable to several key demographic factors and deliver a poor statistical power for detecting genuine associations and also a high false positive rate. Here, we present a likelihood-based statistical approach that accounts properly for non-random nature of case–control samples in regard of genotypic distribution at the loci in populations under study and confers flexibility to test for genetic association in presence of different confounding factors such as population structure, non-randomness of samples etc. Results We implemented this novel method together with several popular methods in the literature of GWAS, to re-analyze recently published Parkinson’s disease (PD) case–control samples. The real data analysis and computer simulation show that the new method confers not only significantly improved statistical power for detecting the associations but also robustness to the difficulties stemmed from non-randomly sampling and genetic structures when compared to its rivals. In particular, the new method detected 44 significant SNPs within 25 chromosomal regions of size < 1 Mb but only 6 SNPs in two of these regions were previously detected by the trend test based methods. It discovered two SNPs located 1.18 Mb and 0.18 Mb from the PD candidates, FGF20 and PARK8, without invoking false positive risk. Conclusions We developed a novel likelihood-based method which provides adequate estimation of LD and other population model parameters by using case and control samples, the ease in integration of these samples from multiple genetically divergent populations and thus confers statistically robust and powerful analyses of GWAS. On basis of simulation studies and analysis of real datasets, we demonstrated significant improvement of the new method over the non-parametric trend test, which is the most popularly implemented in the literature of GWAS. PMID:23394771

Parental interest in children's education, children's self-esteem and locus of control, and later educational attainment: twenty-six year follow-up of the 1970 British Birth Cohort.

PubMed

Flouri, Eirini

2006-03-01

Few studies have investigated if mother's interest and father's interest in child's education are linked to educational attainment via their impact on child's self-esteem and locus of control. (1) To investigate (after controlling for known confounding factors) the long-term effect of mother's and father's interest in child's education at age 10 and child's locus of control and self-esteem at age 10 in educational attainment at age 26; and (2) to explore if mother's interest and father's interest in child's education are linked to child's educational attainment via their effect in increasing child's self-esteem and internal locus of control. The study used longitudinal data from sweeps of the 1970 British Cohort Study (BCS70). The initial sample was those 1,737 men and 2,033 women with valid data on age 10 self-esteem, locus of control, father's interest, mother's interest, and age 26 educational attainment. Of these, 1,326 men and 1,578 women were included in the final analysis. The birth to age 10 factors that were controlled for were birth weight, parental social class, socio-economic disadvantage, emotional/behavioural problems, cognitive ability, and mother's educational attainment. At the multivariate level, internal locus of control and mother's interest (but not self-esteem) were significantly related to educational attainment in both men and women. Father's interest was a significant predictor of educational attainment only in women. Parent's interest was not linked to educational attainment via its impact on child's self-esteem or locus of control. Self-esteem predicted educational attainment in both genders by increasing internal locus of control, and fathers' interest predicted educational attainment in men by increasing mother's involvement. Although mothers' and fathers' interest in their children's education were not linked to educational attainment via their impact on children's self-esteem or locus of control, they were significant predictors of educational attainment especially in daughters.

The Career Locus of Control Scale for Adolescents: Further Evidence of Validity in the United States

ERIC Educational Resources Information Center

Perry, Justin C.; Liu, Xiongyi; Griffin, Grant C.

2011-01-01

This study examined the construct validity of the Career Locus of Control Scale (CLCS) among diverse urban youth within the United States (N = 308). Confirmatory factor analyses verified two of the three models as acceptable fits. Two new models were also explored. Model 5 (Internality, Luck, and Non-Control), which was one of the new models, was…

Health Locus of Control, Acculturation, and Health-Related Internet Use Among Latinas

PubMed Central

Roncancio, Angelica M.; Berenson, Abbey B.; Rahman, Mahbubur

2012-01-01

Among individuals residing in the United States, the Internet is the third most used source for obtaining health information. Little is known, however, about its use by Latinas. To understand health-related Internet use among Latinas, the authors examined it within the theoretical frameworks of health locus of control and acculturation. The authors predicted that acculturation would serve as a mediator between health locus of control and health-related Internet use, age and health-related Internet use, income and health-related Internet use, and education and health-related Internet use. Data were collected via a 25-minute self-report questionnaire. The sample consisted of 932 young (M age = 21.27 years), low-income Latinas. Using structural equation modeling, the authors observed that acculturation partially mediated the relation between health locus of control and health-related Internet use and fully mediated the relations among age, income, and Internet use. An internal health locus of control (p < .001), younger age (p < .001), and higher income (p < .001) were associated with higher levels of acculturation. Higher levels of acculturation (p < .001) and an internal health locus of control (p < .004) predicted health-related Internet use. The Internet is a powerful tool that can be used to effectively disseminate information to Latinas with limited access to health care professionals. These findings can inform the design of Internet-based health information dissemination studies targeting Latinas. PMID:22211397

Molecular Genetic Analysis of the Melanoma Regulatory locus in Xiphophorus Interspecies Hybrids

PubMed Central

Lu, Yuan; Boswell, Mikki; Boswell, William; Kneitz, Susanne; Hausmann, Michael; Klotz, Barbara; Regneri, Janine; Savage, Markita; Amores, Angel; Postlethwait, John; Warren, Wesley; Schartl, Manfred; Walter, Ronald

2018-01-01

Development of spontaneous melanoma in Xiphophorus interspecies backcross hybrid progeny, (X. hellerii × [X. maculatus Jp 163 A × X. hellerii]) is due to Mendelian segregation of a oncogene (xmrk) and a molecularly uncharacterized locus, called R(Diff), on LG5. R(Diff) is thought to suppresses the activity of xmrk in healthy X. maculatus Jp 163 A parental species that rarely develop melanoma. To better understand the molecular genetics of R(Diff), we utilized RNA-Seq to study allele-specific gene expression of spontaneous melanoma tumors and corresponding normal skin samples derived from 15 first generation backcross (BC1) hybrids and 13 fifth generation (BC5) hybrids. Allele-specific expression was determined for all genes and assigned to parental allele inheritance for each backcross hybrid individual. Results showed that genes residing in a 5.81 Mbp region on LG5 were exclusively expressed from the X. hellerii alleles in tumor-bearing BC1 hybrids. This observation indicates this region is consistently homozygous for X. hellerii alleles in tumor bearing animals, and therefore defines this region to be the R(Diff) locus. The R(Diff) locus harbors 164 gene models and includes the previously characterized R(Diff) candidate, cdkn2x. Twenty one genes in the R(Diff) region show differential expression in the tumor samples compared to normal skin tissue. These results further characterize the R(Diff) locus and suggest tumor suppression may require a multigenic region rather than a single gene variant. Differences in gene expression between tumor and normal skin tissue in this region may indicate interactions among several genes are required for backcross hybrid melanoma development. PMID:28345808

Neurolinguistic programming training, trait anxiety, and locus of control.

PubMed

Konefal, J; Duncan, R C; Reese, M A

1992-06-01

Training in the neurolinguistic programming techniques of shifting perceptual position, visual-kinesthetic dissociation, timelines, and change-history, all based on experiential cognitive processing of remembered events, leads to an increased awareness of behavioral contingencies and a more sensitive recognition of environmental cues which could serve to lower trait anxiety and increase the sense of internal control. This study reports on within-person and between-group changes in trait anxiety and locus of control as measured on the Spielberger State-Trait Anxiety Inventory and Wallston, Wallston, and DeVallis' Multiple Health Locus of Control immediately following a 21-day residential training in neurolinguistic programming. Significant with-in-person decreases in trait-anxiety scores and increases in internal locus of control scores were observed as predicted. Chance and powerful other locus of control scores were unchanged. Significant differences were noted on trait anxiety and locus of control scores between European and U.S. participants, although change scores were similar for the two groups. These findings are consistent with the hypothesis that this training may lower trait-anxiety scores and increase internal locus of control scores. A matched control group was not available, and follow-up was unfortunately not possible.

Content and organization of the human Ig VH locus: definition of three new VH families and linkage to the Ig CH locus.

PubMed Central

Berman, J E; Mellis, S J; Pollock, R; Smith, C L; Suh, H; Heinke, B; Kowal, C; Surti, U; Chess, L; Cantor, C R

1988-01-01

We present a detailed analysis of the content and organization of the human immunoglobulin VH locus. Human VH genes representing five distinct families were isolated, including novel members belonging to two out of three of the known VH gene families (VH1 and VH3) as well as members of three new families (VH4, VH5, and VH6). We report the nucleotide sequence of 21 novel human VH genes, many of which belong to the three new VH gene families. In addition, we provide a preliminary analysis of the organization of these gene segments over the full extent of the locus. We find that the five multi-segment families (VH1-5) have members interspersed over nearly the full 1500-2000 kb of the VH locus, and estimate that the entire heavy chain locus covers 2500 kb or less. Finally, we provide the first report of the physical linkage of the variable and constant loci of a human Ig gene family by demonstrating that the most proximal known human VH segments lie within 100 kb of the constant region locus. Images PMID:3396540

S locus-linked F-box genes expressed in anthers of Hordeum bulbosum.

PubMed

Kakeda, Katsuyuki

2009-09-01

Diploid Hordeum bulbosum (a wild relative of cultivated barley) exhibits a two-locus self-incompatibility (SI) system gametophytically controlled by the unlinked multiallelic loci S and Z. This unique SI system is observed in the grasses (Poaceae) including the tribe Triticeae. This paper describes the identification and characterization of two F-box genes cosegregating with the S locus in H. bulbosum, named Hordeum S locus-linked F-box 1 (HSLF1) and HSLF2, which were derived from an S (3) haplotype-specific clone (HAS175) obtained by previous AMF (AFLP-based mRNA fingerprinting) analysis. Sequence analysis showed that both genes encode similar F-box proteins with a C-terminal leucine-rich repeat (LRR) domain, which are distinct from S locus (or S haplotype-specific) F-box protein (SLF/SFB), a class of F-box proteins identified as the pollen S determinant in S-RNase-based gametophytic SI systems. A number of homologous F-box genes with an LRR domain were found in the rice genome, although the functions of the gene family are unknown. One allele of the HSLF1 gene (HSLF1-S (3)) was expressed specifically in mature anthers, whereas no expression was detected from the other two alleles examined. Although the degree of sequence polymorphism among the three HSLF1 alleles was low, a frameshift mutation was found in one of the unexpressed alleles. The HSLF2 gene showed a low level of expression with no tissue specificity as well as little sequence polymorphism among the three alleles. The multiplicity of S locus-linked F-box genes is discussed in comparison with those found in the S-RNase-based SI system.

Genome-wide association study identifies two new susceptibility loci for atopic dermatitis in the Chinese Han population.

PubMed

Sun, Liang-Dan; Xiao, Feng-Li; Li, Yang; Zhou, Wen-Ming; Tang, Hua-Yang; Tang, Xian-Fa; Zhang, Hui; Schaarschmidt, Heidi; Zuo, Xian-Bo; Foelster-Holst, Regina; He, Su-Min; Shi, Mei; Liu, Qiang; Lv, Yong-Mei; Chen, Xi-Lan; Zhu, Kun-Ju; Guo, Yi-Feng; Hu, Da-Yan; Li, Ming; Li, Min; Zhang, Yan-Hong; Zhang, Xin; Tang, Jian-Ping; Guo, Bi-Rong; Wang, Hua; Liu, Yuan; Zou, Xiao-Yan; Zhou, Fu-Sheng; Liu, Xiao-Yan; Chen, Gang; Ma, Lin; Zhang, Shu-Mei; Jiang, Ai-Ping; Zheng, Xiao-Dong; Gao, Xing-Hua; Li, Pan; Tu, Cai-Xia; Yin, Xian-Yong; Han, Xiu-Ping; Ren, Yun-Qing; Song, Shun-Peng; Lu, Zhi-Yong; Zhang, Xing-Lian; Cui, Yong; Chang, Jing; Gao, Min; Luo, Xiao-Yan; Wang, Pei-Guang; Dai, Xing; Su, Wei; Li, Hui; Shen, Chun-Pin; Liu, Sheng-Xiu; Feng, Xiao-Bo; Yang, Chun-Jun; Lin, Guo-Shu; Wang, Zai-Xing; Huang, Jian-Qing; Fan, Xing; Wang, Yan; Bao, Yi-Xiao; Yang, Sen; Liu, Jian-Jun; Franke, Andre; Weidinger, Stephan; Yao, Zhi-Rong; Zhang, Xue-Jun

2011-06-12

Atopic dermatitis is a chronic, relapsing form of inflammatory skin disorder that is affected by genetic and environmental factors. We performed a genome-wide association study of atopic dermatitis in a Chinese Han population using 1,012 affected individuals (cases) and 1,362 controls followed by a replication study in an additional 3,624 cases and 12,197 controls of Chinese Han ethnicity, as well as 1,806 cases and 3,256 controls from Germany. We identified previously undescribed susceptibility loci at 5q22.1 (TMEM232 and SLC25A46, rs7701890, P(combined) = 3.15 × 10(-9), odds ratio (OR) = 1.24) and 20q13.33 (TNFRSF6B and ZGPAT, rs6010620, P(combined) = 3.0 × 10(-8), OR = 1.17) and replicated another previously reported locus at 1q21.3 (FLG, rs3126085, P(combined) = 5.90 × 10(-12), OR = 0.82) in the Chinese sample. The 20q13.33 locus also showed evidence for association in the German sample (rs6010620, P = 2.87 × 10(-5), OR = 1.25). Our study identifies new genetic susceptibility factors and suggests previously unidentified biological pathways in atopic dermatitis.

Pseudoautosomal region in schizophrenia: linkage analysis of seven loci by sib-pair and lod-score methods.

PubMed

d'Amato, T; Waksman, G; Martinez, M; Laurent, C; Gorwood, P; Campion, D; Jay, M; Petit, C; Savoye, C; Bastard, C

1994-05-01

In a previous study, we reported a nonrandom segregation between schizophrenia and the pseudoautosomal locus DXYS14 in a sample of 33 sibships. That study has been extended by the addition of 16 new sibships from 16 different families. Data from six other loci of the pseudoautosomal region and of the immediately adjacent part of the X specific region have also been analyzed. Two methods of linkage analysis were used: the affected sibling pair (ASP) method and the lod-score method. Lod-score analyses were performed on the basis of three different models--A, B, and C--all shown to be consistent with the epidemiological data on schizophrenia. No clear evidence for linkage was obtained with any of these models. However, whatever the genetic model and the disease classification, maximum lod scores were positive with most of the markers, with the highest scores generally being obtained for the DXYS14 locus. When the ASP method was used, the earlier finding of nonrandom segregation between schizophrenia and the DXYS14 locus was still supported in this larger data set, at an increased level of statistical significance. Findings of ASP analyses were not significant for the other loci. Thus, findings obtained from analyses using the ASP method, but not the lod-score method, were consistent with the pseudoautosomal hypothesis for schizophrenia.

Mammary tumor associated Hspb1 mutation and screening of eight cat populations of the world.

PubMed

Saif, R; Awan, A R; Lyons, L; Gandolfi, B; Tayyab, M; Ellahi Babar, M; Wasim, M

2016-01-01

Current research highlights the Hspb1 based screening of eight cat populations of the world to investigate the association of newly found locus within cat mammary tumors. Total 180 cats were screened on the basis of Hspb1 4 bp deletion locus (1514-1517del4) which was observed in six mammary tumor cases in Siamese cat breed. Case-control association study revealed the non-significance with P=0.201 and an overall mutant allele frequency of 0.30 ranging from 0.20-0.40 was observed in other cat populations. Similarly, HWE was also obeyed in combined population samples with P=0.860 and found non-significant with range of 0.429-0.708 in other non-Pakistani cat populations as well. These results might be helpful to understand the association of this novel locus in a better way with large sample size of cases and may also serve as a potential marker for mammary tumor diagnosis, particularly in cats and generally in all other animal populations in comparative genetics and genomics context.

Genome-wide meta-analyses of stratified depression in Generation Scotland and UK Biobank.

PubMed

Hall, Lynsey S; Adams, Mark J; Arnau-Soler, Aleix; Clarke, Toni-Kim; Howard, David M; Zeng, Yanni; Davies, Gail; Hagenaars, Saskia P; Maria Fernandez-Pujals, Ana; Gibson, Jude; Wigmore, Eleanor M; Boutin, Thibaud S; Hayward, Caroline; Scotland, Generation; Porteous, David J; Deary, Ian J; Thomson, Pippa A; Haley, Chris S; McIntosh, Andrew M

2018-01-10

Few replicable genetic associations for Major Depressive Disorder (MDD) have been identified. Recent studies of MDD have identified common risk variants by using a broader phenotype definition in very large samples, or by reducing phenotypic and ancestral heterogeneity. We sought to ascertain whether it is more informative to maximize the sample size using data from all available cases and controls, or to use a sex or recurrent stratified subset of affected individuals. To test this, we compared heritability estimates, genetic correlation with other traits, variance explained by MDD polygenic score, and variants identified by genome-wide meta-analysis for broad and narrow MDD classifications in two large British cohorts - Generation Scotland and UK Biobank. Genome-wide meta-analysis of MDD in males yielded one genome-wide significant locus on 3p22.3, with three genes in this region (CRTAP, GLB1, and TMPPE) demonstrating a significant association in gene-based tests. Meta-analyzed MDD, recurrent MDD and female MDD yielded equivalent heritability estimates, showed no detectable difference in association with polygenic scores, and were each genetically correlated with six health-correlated traits (neuroticism, depressive symptoms, subjective well-being, MDD, a cross-disorder phenotype and Bipolar Disorder). Whilst stratified GWAS analysis revealed a genome-wide significant locus for male MDD, the lack of independent replication, and the consistent pattern of results in other MDD classifications suggests that phenotypic stratification using recurrence or sex in currently available sample sizes is currently weakly justified. Based upon existing studies and our findings, the strategy of maximizing sample sizes is likely to provide the greater gain.

A two-step process for epigenetic inheritance in Arabidopsis

PubMed Central

Blevins, Todd; Pontvianne, Frédéric; Cocklin, Ross; Podicheti, Ram; Chandrasekhara, Chinmayi; Yerneni, Satwica; Braun, Chris; Lee, Brandon; Rusch, Doug; Mockaitis, Keithanne; Tang, Haixu; Pikaard, Craig S.

2014-01-01

Summary In Arabidopsis, multisubunit RNA polymerases IV and V orchestrate RNA-directed DNA methylation (RdDM) and transcriptional silencing, but what identifies the loci to be silenced is unclear. We show that heritable silent locus identity at a specific subset of RdDM targets requires HISTONE DEACETYLASE 6 (HDA6) acting upstream of Pol IV recruitment and siRNA biogenesis. At these loci, epigenetic memory conferring silent locus identity is erased in hda6 mutants such that restoration of HDA6 activity cannot restore siRNA biogenesis or silencing. Silent locus identity is similarly lost in mutants for the cytosine maintenance methyltransferase, MET1. By contrast, pol IV or pol V mutants disrupt silencing without erasing silent locus identity, allowing restoration of Pol IV or Pol V function to restore silencing. Collectively, these observations indicate that silent locus specification and silencing are separable steps that together account for epigenetic inheritance of the silenced state. PMID:24657166

Intratypic variability of a tandem repeat locus within the DNA polymerase gene of human herpes simplex virus type 2.

PubMed

Sun, Yongjiang; Chan, Roy Kum Wah; Tan, Suat Hoon

2004-01-01

In this study, the irntratypic variability of a tandem repeat locus within the DNA polymerase (pol) gene of human herpes simplex virus type 2 (HSV2) was uncovered. The locus contained variable numbers of tandem dodecanucleotide (5'-GAC GAG GAC GGG-3') repetitive units. Our result showed that approximately 95% of analyzed HSV2 clinical isolates and the current GenBank HSV2 strains contained two copies of the repetitive units. From genital herpes specimens, three new HSV2 strains, which respectively contained 1, 3, and 4 copies of the repetitive units, were identified. This variable number of tandem repeat (VNTR) locus is absent in HSV1, and thus it also contributes to the intertypic variability of HSV1 and HSV2. The intratypic variability of the locus may be useful for HSV2 strain genotyping and this application is discussed.

A novel locus for dilated cardiomyopathy maps to canine chromosome 8.

PubMed

Werner, Petra; Raducha, Michael G; Prociuk, Ulana; Sleeper, Meg M; Van Winkle, Thomas J; Henthorn, Paula S

2008-06-01

Dilated cardiomyopathy (DCM), the most common form of cardiomyopathy, often leads to heart failure and sudden death. While a substantial proportion of DCMs are inherited, mutations responsible for the majority of DCMs remain unidentified. A genome-wide linkage study was performed to identify the locus responsible for an autosomal recessive inherited form of juvenile DCM (JDCM) in Portuguese water dogs using 16 families segregating the disease. Results link the JDCM locus to canine chromosome 8 with two-point and multipoint lod scores of 10.8 and 14, respectively. The locus maps to a 3.9-Mb region, with complete syntenic homology to human chromosome 14, that contains no genes or loci known to be involved in the development of any type of cardiomyopathy. This discovery of a DCM locus with a previously unknown etiology will provide a new gene to examine in human DCM patients and a model for testing therapeutic approaches for heart failure.

High-density genetic maps for loci involved in nuclear male sterility (NMS1) and sporophytic self-incompatibility (S-locus) in chicory (Cichorium intybus L., Asteraceae).

PubMed

Gonthier, Lucy; Blassiau, Christelle; Mörchen, Monika; Cadalen, Thierry; Poiret, Matthieu; Hendriks, Theo; Quillet, Marie-Christine

2013-08-01

High-density genetic maps were constructed for loci involved in nuclear male sterility (NMS1-locus) and sporophytic self-incompatibility (S-locus) in chicory (Cichorium intybus L.). The mapping population consisted of 389 F1' individuals derived from a cross between two plants, K28 (male-sterile) and K59 (pollen-fertile), both heterozygous at the S-locus. This F1' mapping population segregated for both male sterility (MS) and strong self-incompatibility (SI) phenotypes. Phenotyping F1' individuals for MS allowed us to map the NMS1-locus to linkage group (LG) 5, while controlled diallel and factorial crosses to identify compatible/incompatible phenotypes mapped the S-locus to LG2. To increase the density of markers around these loci, bulked segregant analysis was used. Bulks and parental plants K28 and K59 were screened using amplified fragment length polymorphism (AFLP) analysis, with a complete set of 256 primer combinations of EcoRI-ANN and MseI-CNN. A total of 31,000 fragments were generated, of which 2,350 showed polymorphism between K59 and K28. Thirteen AFLP markers were identified close to the NMS1-locus and six in the vicinity of the S-locus. From these AFLP markers, eight were transformed into sequence-characterized amplified region (SCAR) markers and of these five showed co-dominant polymorphism. The chromosomal regions containing the NMS1-locus and the S-locus were each confined to a region of 0.8 cM. In addition, we mapped genes encoding proteins similar to S-receptor kinase, the female determinant of sporophytic SI in the Brasicaceae, and also markers in the vicinity of the putative S-locus of sunflower, but none of these genes or markers mapped close to the chicory S-locus.

Ornithine aminotransferase (OAT): recombination between an X-linked OAT sequence (7.5 kb) and the Norrie disease locus.

PubMed

Ngo, J T; Bateman, J B; Spence, M A; Cortessis, V; Sparkes, R S; Kivlin, J D; Mohandas, T; Inana, G

1990-01-01

A human ornithine aminotransferase (OAT) locus has been mapped to the Xp11.2, as has the Norrie disease locus. We used a cDNA probe to investigate a 3-generation UCLA family with Norrie disease; a 4.2-kb RFLP was detected and a maximum lod score of 0.602 at zero recombination fraction was calculated. We used the same probe to study a second multigeneration family with Norrie disease from Utah. A different RFLP of 7.5 kb in size was identified and a recombinational event between the OAT locus represented by this RFLP and the disease loci was observed. Linkage analysis of these two loci in this family revealed a maximum load score of 1.88 at a recombination fraction of 0.10. Although both families have affected members with the same disease, the lod scores are reported separately because the 4.2- and 7.5-kb RFLPs may represent two different loci for the X-linked OAT.

Genetic structure of nest aggregations and drone congregations of the southeast Asian stingless bee Trigona collina.

PubMed

Cameron, E C; Franck, P; Oldroyd, B P

2004-08-01

In stingless bees, sex is determined by a single complementary sex-determining locus. This method of sex determination imposes a severe cost of inbreeding because an egg fertilized by sperm carrying the same sex allele as the egg results in a sterile diploid male. To explore how reproductive strategies may be used to avoid inbreeding in stingless bees, we studied the genetic structure of a population of 27 colonies and three drone congregations of Trigona collina in Chanthaburi, Thailand. The colonies were distributed across six nest aggregations, each aggregation located in the base of a different fig tree. Genetic analysis at eight microsatellite loci showed that colonies within aggregations were not related. Samples taken from three drone congregations showed that the males were drawn from a large number of colonies (estimated to be 132 different colonies in our largest swarm). No drone had a genotype indicating that it could have originated from the colony that it was directly outside. Combined, these results suggest that movements of drones and possibly movements of reproductive swarms among colony aggregations provide two mechanisms of inbreeding avoidance. Copyright 2004 Blackwell Publishing Ltd

Genetic Diversity and Population Structure of Leishmania infantum from Southeastern France: Evaluation Using Multi-Locus Microsatellite Typing

PubMed Central

Pomares, Christelle; Marty, Pierre; Bañuls, Anne Laure; Lemichez, Emmanuel; Pratlong, Francine; Faucher, Benoît; Jeddi, Fakhri; Moore, Sandy; Michel, Grégory; Aluru, Srikanth; Piarroux, Renaud; Hide, Mallorie

2016-01-01

In the south of France, Leishmania infantum is responsible for numerous cases of canine leishmaniasis (CanL), sporadic cases of human visceral leishmaniasis (VL) and rare cases of cutaneous and muco-cutaneous leishmaniasis (CL and MCL, respectively). Several endemic areas have been clearly identified in the south of France including the Pyrénées-Orientales, Cévennes (CE), Provence (P), Alpes-Maritimes (AM) and Corsica (CO). Within these endemic areas, the two cities of Nice (AM) and Marseille (P), which are located 150 km apart, and their surroundings, concentrate the greatest number of French autochthonous leishmaniasis cases. In this study, 270 L. infantum isolates from an extended time period (1978–2011) from four endemic areas, AM, P, CE and CO, were assessed using Multi-Locus Microsatellite Typing (MLMT). MLMT revealed a total of 121 different genotypes with 91 unique genotypes and 30 repeated genotypes. Substantial genetic diversity was found with a strong genetic differentiation between the Leishmania populations from AM and P. However, exchanges were observed between these two endemic areas in which it seems that strains spread from AM to P. The genetic differentiations in these areas suggest strong epidemiological structuring. A model-based analysis using STRUCTURE revealed two main populations: population A (consisting of samples primarily from the P and AM endemic areas with MON-1 and non-MON-1 strains) and population B consisting of only MON-1 strains essentially from the AM endemic area. For four patients, we observed several isolates from different biological samples which provided insight into disease relapse and re-infection. These findings shed light on the transmission dynamics of parasites in humans. However, further data are required to confirm this hypothesis based on a limited sample set. This study represents the most extensive population analysis of L. infantum strains using MLMT conducted in France. PMID:26808522

A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated Through Whole Genome Resequencing.

PubMed

Gao, Guangtu; Nome, Torfinn; Pearse, Devon E; Moen, Thomas; Naish, Kerry A; Thorgaard, Gary H; Lien, Sigbjørn; Palti, Yniv

2018-01-01

Single-nucleotide polymorphisms (SNPs) are highly abundant markers, which are broadly distributed in animal genomes. For rainbow trout ( Oncorhynchus mykiss ), SNP discovery has been previously done through sequencing of restriction-site associated DNA (RAD) libraries, reduced representation libraries (RRL) and RNA sequencing. Recently we have performed high coverage whole genome resequencing with 61 unrelated samples, representing a wide range of rainbow trout and steelhead populations, with 49 new samples added to 12 aquaculture samples from AquaGen (Norway) that we previously used for SNP discovery. Of the 49 new samples, 11 were double-haploid lines from Washington State University (WSU) and 38 represented wild and hatchery populations from a wide range of geographic distribution and with divergent migratory phenotypes. We then mapped the sequences to the new rainbow trout reference genome assembly (GCA_002163495.1) which is based on the Swanson YY doubled haploid line. Variant calling was conducted with FreeBayes and SAMtools mpileup , followed by filtering of SNPs based on quality score, sequence complexity, read depth on the locus, and number of genotyped samples. Results from the two variant calling programs were compared and genotypes of the double haploid samples were used for detecting and filtering putative paralogous sequence variants (PSVs) and multi-sequence variants (MSVs). Overall, 30,302,087 SNPs were identified on the rainbow trout genome 29 chromosomes and 1,139,018 on unplaced scaffolds, with 4,042,723 SNPs having high minor allele frequency (MAF > 0.25). The average SNP density on the chromosomes was one SNP per 64 bp, or 15.6 SNPs per 1 kb. Results from the phylogenetic analysis that we conducted indicate that the SNP markers contain enough population-specific polymorphisms for recovering population relationships despite the small sample size used. Intra-Population polymorphism assessment revealed high level of polymorphism and heterozygosity within each population. We also provide functional annotation based on the genome position of each SNP and evaluate the use of clonal lines for filtering of PSVs and MSVs. These SNPs form a new database, which provides an important resource for a new high density SNP array design and for other SNP genotyping platforms used for genetic and genomics studies of this iconic salmonid fish species.

Valid statistical inference methods for a case-control study with missing data.

PubMed

Tian, Guo-Liang; Zhang, Chi; Jiang, Xuejun

2018-04-01

The main objective of this paper is to derive the valid sampling distribution of the observed counts in a case-control study with missing data under the assumption of missing at random by employing the conditional sampling method and the mechanism augmentation method. The proposed sampling distribution, called the case-control sampling distribution, can be used to calculate the standard errors of the maximum likelihood estimates of parameters via the Fisher information matrix and to generate independent samples for constructing small-sample bootstrap confidence intervals. Theoretical comparisons of the new case-control sampling distribution with two existing sampling distributions exhibit a large difference. Simulations are conducted to investigate the influence of the three different sampling distributions on statistical inferences. One finding is that the conclusion by the Wald test for testing independency under the two existing sampling distributions could be completely different (even contradictory) from the Wald test for testing the equality of the success probabilities in control/case groups under the proposed distribution. A real cervical cancer data set is used to illustrate the proposed statistical methods.

Evolutionary method for finding communities in bipartite networks.

PubMed

Zhan, Weihua; Zhang, Zhongzhi; Guan, Jihong; Zhou, Shuigeng

2011-06-01

An important step in unveiling the relation between network structure and dynamics defined on networks is to detect communities, and numerous methods have been developed separately to identify community structure in different classes of networks, such as unipartite networks, bipartite networks, and directed networks. Here, we show that the finding of communities in such networks can be unified in a general framework-detection of community structure in bipartite networks. Moreover, we propose an evolutionary method for efficiently identifying communities in bipartite networks. To this end, we show that both unipartite and directed networks can be represented as bipartite networks, and their modularity is completely consistent with that for bipartite networks, the detection of modular structure on which can be reformulated as modularity maximization. To optimize the bipartite modularity, we develop a modified adaptive genetic algorithm (MAGA), which is shown to be especially efficient for community structure detection. The high efficiency of the MAGA is based on the following three improvements we make. First, we introduce a different measure for the informativeness of a locus instead of the standard deviation, which can exactly determine which loci mutate. This measure is the bias between the distribution of a locus over the current population and the uniform distribution of the locus, i.e., the Kullback-Leibler divergence between them. Second, we develop a reassignment technique for differentiating the informative state a locus has attained from the random state in the initial phase. Third, we present a modified mutation rule which by incorporating related operations can guarantee the convergence of the MAGA to the global optimum and can speed up the convergence process. Experimental results show that the MAGA outperforms existing methods in terms of modularity for both bipartite and unipartite networks.

Stratified randomization controls better for batch effects in 450K methylation analysis: a cautionary tale.

PubMed

Buhule, Olive D; Minster, Ryan L; Hawley, Nicola L; Medvedovic, Mario; Sun, Guangyun; Viali, Satupaitea; Deka, Ranjan; McGarvey, Stephen T; Weeks, Daniel E

2014-01-01

Batch effects in DNA methylation microarray experiments can lead to spurious results if not properly handled during the plating of samples. Two pilot studies examining the association of DNA methylation patterns across the genome with obesity in Samoan men were investigated for chip- and row-specific batch effects. For each study, the DNA of 46 obese men and 46 lean men were assayed using Illumina's Infinium HumanMethylation450 BeadChip. In the first study (Sample One), samples from obese and lean subjects were examined on separate chips. In the second study (Sample Two), the samples were balanced on the chips by lean/obese status, age group, and census region. We used methylumi, watermelon, and limma R packages, as well as ComBat, to analyze the data. Principal component analysis and linear regression were, respectively, employed to identify the top principal components and to test for their association with the batches and lean/obese status. To identify differentially methylated positions (DMPs) between obese and lean males at each locus, we used a moderated t-test. Chip effects were effectively removed from Sample Two but not Sample One. In addition, dramatic differences were observed between the two sets of DMP results. After "removing" batch effects with ComBat, Sample One had 94,191 probes differentially methylated at a q-value threshold of 0.05 while Sample Two had zero differentially methylated probes. The disparate results from Sample One and Sample Two likely arise due to the confounding of lean/obese status with chip and row batch effects. Even the best possible statistical adjustments for batch effects may not completely remove them. Proper study design is vital for guarding against spurious findings due to such effects.

Stratified randomization controls better for batch effects in 450K methylation analysis: a cautionary tale

PubMed Central

Buhule, Olive D.; Minster, Ryan L.; Hawley, Nicola L.; Medvedovic, Mario; Sun, Guangyun; Viali, Satupaitea; Deka, Ranjan; McGarvey, Stephen T.; Weeks, Daniel E.

2014-01-01

Background: Batch effects in DNA methylation microarray experiments can lead to spurious results if not properly handled during the plating of samples. Methods: Two pilot studies examining the association of DNA methylation patterns across the genome with obesity in Samoan men were investigated for chip- and row-specific batch effects. For each study, the DNA of 46 obese men and 46 lean men were assayed using Illumina's Infinium HumanMethylation450 BeadChip. In the first study (Sample One), samples from obese and lean subjects were examined on separate chips. In the second study (Sample Two), the samples were balanced on the chips by lean/obese status, age group, and census region. We used methylumi, watermelon, and limma R packages, as well as ComBat, to analyze the data. Principal component analysis and linear regression were, respectively, employed to identify the top principal components and to test for their association with the batches and lean/obese status. To identify differentially methylated positions (DMPs) between obese and lean males at each locus, we used a moderated t-test. Results: Chip effects were effectively removed from Sample Two but not Sample One. In addition, dramatic differences were observed between the two sets of DMP results. After “removing” batch effects with ComBat, Sample One had 94,191 probes differentially methylated at a q-value threshold of 0.05 while Sample Two had zero differentially methylated probes. The disparate results from Sample One and Sample Two likely arise due to the confounding of lean/obese status with chip and row batch effects. Conclusion: Even the best possible statistical adjustments for batch effects may not completely remove them. Proper study design is vital for guarding against spurious findings due to such effects. PMID:25352862

Locus of Control & Motivation Strategies for Learning Questionnaire: Predictors of Student Success on the ATI Comprehensive Predictor Exam & NCLEX-RN Examination

ERIC Educational Resources Information Center

Carpenter, Jane H.

2011-01-01

The two purposes of this study were to determine whether locus of control (LOC) was predictive of how a student would perform on the ATI Comprehensive Predictor Exam and the NCLEX-RN, and if the Motivated Strategies for Learning Questionnaire (MSLQ) provided information that would help determine predictors of success on these two exams. The study…

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.

Nine microsatellite loci developed from the octocoral, Paragorgia arborea

USGS Publications Warehouse

Coykendall, D. Katharine; Morrison, Cheryl L.

2015-01-01

Paragorgia arborea, or bubblegum coral, occurs in continental slope habitats worldwide, which are increasingly threatened by human activities such as energy development and fisheries practices. From 101 putative loci screened, nine microsatellite markers were developed from samples taken from Baltimore canyon in the western North Atlantic Ocean. The number of alleles ranged from two to thirteen per locus and each displayed equilibrium. These nuclear resources will help further research on population connectivity in threatened coral species where mitochondrial markers are known to lack fine-scale genetic diversity.

The distribution of intra-genomically variable dinoflagellate symbionts at Lord Howe Island, Australia

NASA Astrophysics Data System (ADS)

Wilkinson, Shaun P.; Pontasch, Stefanie; Fisher, Paul L.; Davy, Simon K.

2016-06-01

The symbiotic dinoflagellates of corals and other marine invertebrates ( Symbiodinium) are essential to the development of shallow-water coral reefs. This genus contains considerable genetic diversity and a corresponding range of physiological and ecological traits. Most genetic variation arises through the accumulation of somatic mutations that arise during asexual reproduction. Yet growing evidence suggests that occasional sexual reproductive events also occur within, and perhaps between, Symbiodinium lineages, further contributing to the pool of genetic variation available for evolutionary adaptation. Intra-genomic variation can therefore arise from both sexual and asexual reproductive processes, making it difficult to discern its underlying causes and consequences. We used quantitative PCR targeting the ITS2 locus to estimate proportions of genetically homogeneous symbionts and intra-genomically variable Symbiodinium (IGV Symbiodinium) in the reef-building coral Pocillopora damicornis at Lord Howe Island, Australia. We then sampled colonies through time and at a variety of spatial scales to find out whether the distribution of these symbionts followed patterns consistent with niche partitioning. Estimated ratios of homogeneous to IGV Symbiodinium varied between colonies within sites (metres to tens of metres) and between sites separated by hundreds to thousands of metres, but remained stable within colonies through time. Symbiont ratios followed a temperature gradient, with the local thermal maximum emerging as a negative predictor for the estimated proportional abundance of IGV Symbiodinium. While this pattern may result from fine-scale spatial population structure, it is consistent with an increased susceptibility to thermal stress, suggesting that the evolutionary processes that generate IGV (such as inter-lineage recombination and the accumulation of somatic mutations at the ITS2 locus) may have important implications for the fitness of the symbiont and that of the coral host.

Resurrection of Indian Ocean humbug damselfish, Dascyllus abudafur (Forsskål) from synonymy with its Pacific Ocean sibling, Dascyllus aruanus (L.).

PubMed

Borsa, Philippe; Sembiring, Andrianus; Fauvelot, Cécile; Chen, Wei-Jen

2014-12-01

Previous phylogeographic studies of the humbug damselfish, a widespread Indo-West Pacific coral reef fish, have revealed a split of two main mitochondrial lineages distributed on either side of the Indo-Pacific barrier. This has been interpreted as the result of vicariance. It has been hypothesized that reproductive barriers might currently limit gene flow between humbug damselfish populations from the Indian Ocean and the Pacific Ocean. In this study, we review the published phylogeographic information to update the distribution of the two main mitochondrial lineages of humbug damselfish. The Indian lineage was distributed from the Red Sea to the eastern extremity of the Sunda Shelf while the Pacific lineage, which diverged from the former by 0.6% net nucleotide divergence and diagnostic substitutions at three nucleotide sites at the cytochrome b locus, was distributed east and north of the Sunda Shelf. The two forms, which are also genetically distinct at nuclear loci, were also characterized by distinct pigmentation patterns. We argue that the two forms represent geminate species. Epithet aruanus Linnaeus is maintained for the Pacific Ocean humbug damselfish while epithet abudafur (Forsskål) is here resurrected for the Indian Ocean humbug damselfish. Future studies should focus on the population genetic structure of the transition zone between Dascyllus abudafur and D. aruanus. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Meiotic drive influences the outcome of sexually antagonistic selection at a linked locus.

PubMed

Patten, M M

2014-11-01

Most meiotic drivers, such as the t-haplotype in Mus and the segregation distorter (SD) in Drosophila, act in a sex-specific manner, gaining a transmission advantage through one sex although suffering only the fitness costs associated with the driver in the other. Their inheritance is thus more likely through one of the two sexes, a property they share with sexually antagonistic alleles. Previous theory has shown that pairs of linked loci segregating for sexually antagonistic alleles are more likely to remain polymorphic and that linkage disequilibrium accrues between them. I probe this similarity between drive and sexual antagonism and examine the evolution of chromosomes experiencing these selection pressures simultaneously. Reminiscent of previous theory, I find that: the opportunity for polymorphism increases for a sexually antagonistic locus that is physically linked to a driving locus; the opportunity for polymorphism at a driving locus also increases when linked to a sexually antagonistic locus; and stable linkage disequilibrium accompanies any polymorphic equilibrium. Additionally, I find that drive at a linked locus favours the fixation of sexually antagonistic alleles that benefit the sex in which drive occurs. Further, I show that under certain conditions reduced recombination between these two loci is selectively favoured. These theoretical results provide clear, testable predictions about the nature of sexually antagonistic variation on driving chromosomes and have implications for the evolution of genomic architecture. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Effects of complex life cycles on genetic diversity: cyclical parthenogenesis.

PubMed

Rouger, R; Reichel, K; Malrieu, F; Masson, J P; Stoeckel, S

2016-11-01

Neutral patterns of population genetic diversity in species with complex life cycles are difficult to anticipate. Cyclical parthenogenesis (CP), in which organisms undergo several rounds of clonal reproduction followed by a sexual event, is one such life cycle. Many species, including crop pests (aphids), human parasites (trematodes) or models used in evolutionary science (Daphnia), are cyclical parthenogens. It is therefore crucial to understand the impact of such a life cycle on neutral genetic diversity. In this paper, we describe distributions of genetic diversity under conditions of CP with various clonal phase lengths. Using a Markov chain model of CP for a single locus and individual-based simulations for two loci, our analysis first demonstrates that strong departures from full sexuality are observed after only a few generations of clonality. The convergence towards predictions made under conditions of full clonality during the clonal phase depends on the balance between mutations and genetic drift. Second, the sexual event of CP usually resets the genetic diversity at a single locus towards predictions made under full sexuality. However, this single recombination event is insufficient to reshuffle gametic phases towards full-sexuality predictions. Finally, for similar levels of clonality, CP and acyclic partial clonality (wherein a fixed proportion of individuals are clonally produced within each generation) differentially affect the distribution of genetic diversity. Overall, this work provides solid predictions of neutral genetic diversity that may serve as a null model in detecting the action of common evolutionary or demographic processes in cyclical parthenogens (for example, selection or bottlenecks).

Linkage analyses in Darier disease (DD) and Halley-Halley disease (HHD): Fine mapping of the DD locus on chromosome 12q and rejection of the hypothesis that HHD is allelic to DD

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

Richard, G.; Wright, A.R.; Compton, J.G.

1994-09-01

DD and HHD are rare autosomal dominant genodermatoses. These disorders of cornification share some clinical and histologic features and for many years were thought to be variants of the same disease. DD presents as hyperkeratotic papules and plaques, usually in a seborrheic distribution; rarely, blisters can occur. Mucous membranes and nails may also be involved. Skin involvement in HHD includes erythematous and scaly plaques, and vesicular or crusted lesions, often in intertriginous areas. Both diseases have age-dependent penetrance and are characterized histologically by a focal loss of cell adhesion in the suprabasal epidermis leading to lacunaes (acantholysis) and premature keratinizationmore » (dyskeratosis). We analyzed linkage of DD in ten families with markers in 12q23-q24.1, the region to which it has been mapped. Detailed genotype analysis of recombinant chromosomes in our families, along with previously reported data, refine the location of the DD gene to about a 4 cM interval flanked by the loci D12S129 and D12S105. We have excluded two genes in 12q22-q24, PLA2A and PAH, as candidate loci for DD. Three other gene loci (PPP1C, PMCH and PMCA1) mapping in 12q21-q24, remain potential candidates. The region containing the DD gene is an obvious candidate location to test for HHD. We investigated four multigeneration families with HHD for linkage to the DD gene locus using several tightly linked microsatellite markers. Obligate recombination with each marker tested was observed, and the HHD locus was excluded from about 37 cM around the DD locus, proving that DD and HHD are not allelic disorders.« less

The IGF2 Locus

USDA-ARS?s Scientific Manuscript database

Insulin-like growth factor 2 (IGF2) is a peptide hormone regulating various cellular processes such as proliferation and apoptosis. IGF2 is vital to embryo development. The IGF2 locus covers approximately 150-kb genomic region on human chromosome 11, containing two imprinted genes, IGF2 and H19, sha...

Genetic architecture and evolution of the S locus supergene in Primula vulgaris.

PubMed

Li, Jinhong; Cocker, Jonathan M; Wright, Jonathan; Webster, Margaret A; McMullan, Mark; Dyer, Sarah; Swarbreck, David; Caccamo, Mario; Oosterhout, Cock van; Gilmartin, Philip M

2016-12-02

Darwin's studies on heterostyly in Primula described two floral morphs, pin and thrum, with reciprocal anther and stigma heights that promote insect-mediated cross-pollination. This key innovation evolved independently in several angiosperm families. Subsequent studies on heterostyly in Primula contributed to the foundation of modern genetic theory and the neo-Darwinian synthesis. The established genetic model for Primula heterostyly involves a diallelic S locus comprising several genes, with rare recombination events that result in self-fertile homostyle flowers with anthers and stigma at the same height. Here we reveal the S locus supergene as a tightly linked cluster of thrum-specific genes that are absent in pins. We show that thrums are hemizygous not heterozygous for the S locus, which suggests that homostyles do not arise by recombination between S locus haplotypes as previously proposed. Duplication of a floral homeotic gene 51.7 million years (Myr) ago, followed by its neofunctionalization, created the current S locus assemblage which led to floral heteromorphy in Primula. Our findings provide new insights into the structure, function and evolution of this archetypal supergene.

Determining the linkage of disease-resistance genes to molecular markers: the LOD-SCORE method revisited with regard to necessary sample sizes.

PubMed

Hühn, M

1995-05-01

Some approaches to molecular marker-assisted linkage detection for a dominant disease-resistance trait based on a segregating F2 population are discussed. Analysis of two-point linkage is carried out by the traditional measure of maximum lod score. It depends on (1) the maximum-likelihood estimate of the recombination fraction between the marker and the disease-resistance gene locus, (2) the observed absolute frequencies, and (3) the unknown number of tested individuals. If one replaces the absolute frequencies by expressions depending on the unknown sample size and the maximum-likelihood estimate of recombination value, the conventional rule for significant linkage (maximum lod score exceeds a given linkage threshold) can be resolved for the sample size. For each sub-population used for linkage analysis [susceptible (= recessive) individuals, resistant (= dominant) individuals, complete F2] this approach gives a lower bound for the necessary number of individuals required for the detection of significant two-point linkage by the lod-score method.

Model Identification and FE Simulations: Effect of Different Yield Loci and Hardening Laws in Sheet Forming

NASA Astrophysics Data System (ADS)

Flores, P.; Duchêne, L.; Lelotte, T.; Bouffioux, C.; El Houdaigui, F.; Van Bael, A.; He, S.; Duflou, J.; Habraken, A. M.

2005-08-01

The bi-axial experimental equipment developed by Flores enables to perform Baushinger shear tests and successive or simultaneous simple shear tests and plane-strain tests. Such experiments and classical tensile tests investigate the material behavior in order to identify the yield locus and the hardening models. With tests performed on two steel grades, the methods applied to identify classical yield surfaces such as Hill or Hosford ones as well as isotropic Swift type hardening or kinematic Armstrong-Frederick hardening models are explained. Comparison with the Taylor-Bishop-Hill yield locus is also provided. The effect of both yield locus and hardening model choice will be presented for two applications: Single Point Incremental Forming (SPIF) and a cup deep drawing.

Genotyping and association analysis of HLA-B61 in Japanese.

PubMed

Lin, L; Tokunaga, K; Ogawa, A; Ishikawa, Y; Kashiwase, K; Akaza, T; Kuwata, S; Tadokoro, K; Juji, T

1993-06-01

The distribution of HLA-B61-related alleles, B*4002-B*4006, was examined in the Japanese population by using PCR-SSO and PCR-RFLP methods. About half of the B61-positive individuals possessed B*4002 and the remaining half possessed B*4006. In addition, these two major B61 alleles were separately associated with different HLA-C alleles: B*4002 exhibited a strong linkage disequilibrium with Cw10, whereas B*4006 was strongly associated with C blank and DR9. Amino acid residues that contribute to the serologic epitopes of the B61 group and their relationships with other HLA-B locus antigens are discussed.

Prospective Genotyping of Mycobacterium tuberculosis from Fresh Clinical Samples

PubMed Central

Bidovec-Stojkovič, Urška; Seme, Katja; Žolnir-Dovč, Manca; Supply, Philip

2014-01-01

Shorter time-to-result is key for improving molecular-guided epidemiological investigation of tuberculosis (TB) cases. We performed a prospective study to evaluate the use of standardized MIRU-VNTR (mycobacterial interspersed repetitive-unit-variable-number tandem-repeat) typing of Mycobacterium tuberculosis directly on 79 fresh clinical samples from 26 TB patients consecutively enrolled over a 17-month period. Overall, complete 24-locus types were obtained for 18 out of the 26 (69.2%) patients and 14 of the 16 grade 3+ and grade 2+ samples (87.5%). The degree of completion of the genotypes obtained significantly correlated with smear microscopy grade both for 26 first samples (p = 0.0003) and for 53 follow-up samples (p = 0.002). For 20 of the 26 patients for whom complete or even incomplete M. tuberculosis isolate genotypes were obtained, typing applied to the clinical samples allowed the same unambiguous conclusions regarding case clustering or uniqueness as those that could have been drawn based on the corresponding cultured isolates. Standard 24 locus MIRU-VNTR typing of M. tuberculosis can be applied directly to fresh clinical samples, with typeability depending on the bacterial load in the sample. PMID:25313883

Genetic variation and gene expression across multiple tissues and developmental stages in a non-human primate

PubMed Central

Jasinska, Anna J.; Zelaya, Ivette; Service, Susan K.; Peterson, Christine B.; Cantor, Rita M.; Choi, Oi-Wa; DeYoung, Joseph; Eskin, Eleazar; Fairbanks, Lynn A.; Fears, Scott; Furterer, Allison E.; Huang, Yu S.; Ramensky, Vasily; Schmitt, Christopher A.; Svardal, Hannes; Jorgensen, Matthew J.; Kaplan, Jay R.; Villar, Diego; Aken, Bronwen L.; Flicek, Paul; Nag, Rishi; Wong, Emily S.; Blangero, John; Dyer, Thomas D.; Bogomolov, Marina; Benjamini, Yoav; Weinstock, George M.; Dewar, Ken; Sabatti, Chiara; Wilson, Richard K.; Jentsch, J. David; Warren, Wesley; Coppola, Giovanni; Woods, Roger P.; Freimer, Nelson B.

2017-01-01

By analyzing multi-tissue gene expression and genome-wide genetic variation data in samples from a vervet monkey pedigree, we generated a transcriptome resource and produced the first catalogue of expression quantitative trait loci (eQTLs) in a non-human primate model. This catalogue contains more genome-wide significant eQTLs, per sample, than comparable human resources, and reveals sex and age-related expression patterns. Findings include a master regulatory locus that likely plays a role in immune function, and a locus regulating hippocampal long non-coding RNAs (lncRNAs), whose expression correlates with hippocampal volume. This resource will facilitate genetic investigation of quantitative traits, including brain and behavioral phenotypes relevant to neuropsychiatric disorders. PMID:29083405

Genetic heterogeneity in Finnish hereditary prostate cancer using ordered subset analysis

PubMed Central

Simpson, Claire L; Cropp, Cheryl D; Wahlfors, Tiina; George, Asha; Jones, MaryPat S; Harper, Ursula; Ponciano-Jackson, Damaris; Tammela, Teuvo; Schleutker, Johanna; Bailey-Wilson, Joan E

2013-01-01

Prostate cancer (PrCa) is the most common male cancer in developed countries and the second most common cause of cancer death after lung cancer. We recently reported a genome-wide linkage scan in 69 Finnish hereditary PrCa (HPC) families, which replicated the HPC9 locus on 17q21-q22 and identified a locus on 2q37. The aim of this study was to identify and to detect other loci linked to HPC. Here we used ordered subset analysis (OSA), conditioned on nonparametric linkage to these loci to detect other loci linked to HPC in subsets of families, but not the overall sample. We analyzed the families based on their evidence for linkage to chromosome 2, chromosome 17 and a maximum score using the strongest evidence of linkage from either of the two loci. Significant linkage to a 5-cM linkage interval with a peak OSA nonparametric allele-sharing LOD score of 4.876 on Xq26.3-q27 (ΔLOD=3.193, empirical P=0.009) was observed in a subset of 41 families weakly linked to 2q37, overlapping the HPCX1 locus. Two peaks that were novel to the analysis combining linkage evidence from both primary loci were identified; 18q12.1-q12.2 (OSA LOD=2.541, ΔLOD=1.651, P=0.03) and 22q11.1-q11.21 (OSA LOD=2.395, ΔLOD=2.36, P=0.006), which is close to HPC6. Using OSA allows us to find additional loci linked to HPC in subsets of families, and underlines the complex genetic heterogeneity of HPC even in highly aggregated families. PMID:22948022

Multi-locus sequence typing of Salmonella enterica serovar Typhimurium isolates from wild birds in northern England suggests host-adapted strain.

PubMed

Hughes, L A; Wigley, P; Bennett, M; Chantrey, J; Williams, N

2010-10-01

Recent studies have suggested that Salmonella Typhimurium strains associated with mortality in UK garden birds are significantly different from strains that cause disease in humans and livestock and that wild bird strains may be host adapted. However, without further genomic characterization of these strains, it is not possible to determine whether they are host adapted. The aim of this study was to characterize a representative sample of Salm. Typhimurium strains detected in wild garden birds using multi-locus sequence typing (MLST)to investigate evolutionary relationships between them. Multi-locus sequence typing was performed on nine Salm. Typhimurium strains isolated from wild garden birds. Two sequence types were identified, the most common of which was ST568. Examination of the public Salmonella enterica MLST database revealed that only three other ST568 isolates had been cultured from a human in Scotland. Two further isolates of Salm. Typhimurium were determined to be ST19. Results of MLST analysis suggest that there is a predominant strain of Salm. Typhimurium circulating among garden bird populations in the United Kingdom, which is rarely detected in other species, supporting the hypothesis that this strain is host adapted. Host-pathogen evolution is often assumed to lead to pathogens becoming less virulent to avoid the death of their host; however, infection with ST568 led to high mortality rates among the wild birds examined, which were all found dead at wild bird-feeding stations. We hypothesize that by attracting unnaturally high densities of birds, wild bird-feeding stations may facilitate the transmission of ST568 between wild birds, therefore reducing the evolutionary cost of this pathogen killing its host, resulting in a host-adapted strain with increased virulence.

Ancient roots for polymorphism at the HLA-DQ. alpha. locus in primates

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

Gyllensten, U.B.; Erlich, H.A.

1989-12-01

The genes encoding the human histocompatibility antigens (HLA) exhibit a remarkable degree of polymorphism as revealed by immunologic and molecular analyses. This extensive sequence polymorphism either may have been generated during the lifetime of the human species or could have arisen before speciation and been maintained in the contemporary human population by selection or, possibly, by genetic drift. These two hypotheses were examined using the polymerase chain reaction method to amplify polymorphic sequences from the DQ{alpha} locus, as well as the DX{alpha} locus, an homologous but nonexpressed locus, in a series of primates that diverged at known times. In general,more » the amino acid sequence of a specific human DQ{alpha} allelic type is more closely related to its chimpanzee or gorilla counterpart than to other human DQ{alpha} alleles. Phylogenetic analysis of the silent nucleotide position changes shows that the similarity of allelic types between species is due to common ancestry rather than convergent evolution. Thus, most of the polymorphism at the DQ{alpha} locus in the human species was already present at least 5 million years ago in the ancestral species that gave rise to the chimpanzee, gorilla, and human lineages. However, one of the DQ{alpha} alleles may have arisen after speciation by recombination between two ancestral alleles.« less

Distribution of lod scores in oligogenic linkage analysis.

PubMed

Williams, J T; North, K E; Martin, L J; Comuzzie, A G; Göring, H H; Blangero, J

2001-01-01

In variance component oligogenic linkage analysis it can happen that the residual additive genetic variance bounds to zero when estimating the effect of the ith quantitative trait locus. Using quantitative trait Q1 from the Genetic Analysis Workshop 12 simulated general population data, we compare the observed lod scores from oligogenic linkage analysis with the empirical lod score distribution under a null model of no linkage. We find that zero residual additive genetic variance in the null model alters the usual distribution of the likelihood-ratio statistic.

The UCLA Design Diversity Experiment (DEDIX) system: A distributed testbed for multiple-version software

NASA Technical Reports Server (NTRS)

Avizienis, A.; Gunningberg, P.; Kelly, J. P. J.; Strigini, L.; Traverse, P. J.; Tso, K. S.; Voges, U.

1986-01-01

To establish a long-term research facility for experimental investigations of design diversity as a means of achieving fault-tolerant systems, a distributed testbed for multiple-version software was designed. It is part of a local network, which utilizes the Locus distributed operating system to operate a set of 20 VAX 11/750 computers. It is used in experiments to measure the efficacy of design diversity and to investigate reliability increases under large-scale, controlled experimental conditions.

Genetic diversity of Staphylococcus aureus in Buruli ulcer.

PubMed

Amissah, Nana Ama; Glasner, Corinna; Ablordey, Anthony; Tetteh, Caitlin S; Kotey, Nana Konama; Prah, Isaac; van der Werf, Tjip S; Rossen, John W; van Dijl, Jan Maarten; Stienstra, Ymkje

2015-02-01

Buruli ulcer (BU) is a necrotizing skin disease caused by Mycobacterium ulcerans. Previous studies have shown that wounds of BU patients are colonized with M. ulcerans and several other microorganisms, including Staphylococcus aureus, which may interfere with wound healing. The present study was therefore aimed at investigating the diversity and topography of S. aureus colonizing BU patients during treatment. We investigated the presence, diversity, and spatio-temporal distribution of S. aureus in 30 confirmed BU patients from Ghana during treatment. S. aureus was isolated from nose and wound swabs, and by replica plating of wound dressings collected bi-weekly from patients. S. aureus isolates were characterized by multiple-locus variable number tandem repeat fingerprinting (MLVF) and spa-typing, and antibiotic susceptibility was tested. Nineteen (63%) of the 30 BU patients tested positive for S. aureus at least once during the sampling period, yielding 407 S. aureus isolates. Detailed analysis of 91 isolates grouped these isolates into 13 MLVF clusters and 13 spa-types. Five (26%) S. aureus-positive BU patients carried the same S. aureus genotype in their anterior nares and wounds. S. aureus isolates from the wounds of seven (37%) patients were distributed over two different MLVF clusters. Wounds of three (16%) patients were colonized with isolates belonging to two different genotypes at the same time, and five (26%) patients were colonized with different S. aureus types over time. Five (17%) of the 30 included BU patients tested positive for methicillin-resistant S. aureus (MRSA). The present study showed that the wounds of many BU patients were contaminated with S. aureus, and that many BU patients from the different communities carried the same S. aureus genotype during treatment. This calls for improved wound care and hygiene.

The WWW as a research medium: an illustrative survey on paranormal belief.

PubMed

Göritz, A S; Schumacher, J

2000-06-01

Data collected with a short World Wide Web (WWW) survey on paranormal belief, age, sex, locus of control, extraversion, emotional and physical well-being, and mood were compared with findings from recent literature while controlling for effects of self-selection. Each variable was measured with one item. The sample comprised 342 women, 648 men, and 8 participants of unknown sex, of whom 76.7% were self-selected and 23.3% did not select themselves. There was a weak but, given the large sample, significant effect of self-selection regarding paranormal belief (rpb 932 = .08) but no relationships for paranormal belief and the examined variables. In the entire sample, statistically significant correlations ranging from .13 to .07 between paranormal belief and female sex, scores on external locus of control, good mood, extraversion, and emotional well-being corresponded with previous offline results.

Forensic discrimination of vaginal epithelia by DNA methylation analysis through pyrosequencing.

PubMed

Antunes, Joana; Silva, Deborah S B S; Balamurugan, Kuppareddi; Duncan, George; Alho, Clarice S; McCord, Bruce

2016-10-01

The accurate identification of body fluids from crime scenes can aid in the discrimination between criminal and innocent intent. This research aimed to determine if the levels of DNA methylation in the locus PFN3A could be used to discriminate vaginal epithelia from other body fluids. In this work we bisulfite-modified and amplified DNA samples from blood, saliva, semen, and vaginal epithelia using primers for PFN3A. Through pyrosequencing we were able to show that vaginal epithelia present distinct methylation levels when compared to other body fluids. Mixtures of different body fluids present methylation values that correlate with single-source body fluid samples and the primers for PFN3A are specific for primates. This report successfully demonstrated that the analysis of methylation in the PFN3A locus can be used for vaginal epithelia discrimination in forensic samples. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular polymorphisms of the ABO locus as informative markers of ancestry in Central Argentina.

PubMed

Tavella, María Pía; García, Angelina; Pauro, Maia; Demarchi, Darío A; Nores, Rodrigo

2017-07-08

The aim of this study was to investigate the distribution of molecular polymorphisms of the ABO gene in four population samples from the province of Córdoba, in Central Argentina, and to compare them with other worldwide populations. A total of 110 buccal swab samples from autochthonous individuals of Córdoba were typified. Molecular characterization of the allelic variants was performed by the analysis of exons 6 and 7 of the ABO gene using PCR-RFLP analysis. Additionally, the Native American AIM O1v542 was characterized by direct sequencing. The four Córdoba populations did not show significant geographic structure, although the frequency of the O1v542 haplotype, detected in all the populations studied, ranged from 0.019 to 0.222. The principal component analysis based on O allele distribution showed that the populations from Córdoba clustered close to the admixed populations of Santiago and Mexico City, and at intermediate distances between European and Native American populations, while being distant from the African population. The results demonstrate that the analysis of the ABO system constitutes a useful tool for the study of the genetic structure and evolutionary history of human populations, reflecting accurately the relative contribution of parental continental contribution to the gene pool of admixed populations. © 2017 Wiley Periodicals, Inc.

The unusual S locus of Leavenworthia is composed of two sets of paralogous loci.

PubMed

Chantha, Sier-Ching; Herman, Adam C; Castric, Vincent; Vekemans, Xavier; Marande, William; Schoen, Daniel J

2017-12-01

The Leavenworthia self-incompatibility locus (S locus) consists of paralogs (Lal2, SCRL) of the canonical Brassicaceae S locus genes (SRK, SCR), and is situated in a genomic position that differs from the ancestral one in the Brassicaceae. Unexpectedly, in a small number of Leavenworthia alabamica plants examined, sequences closely resembling exon 1 of SRK have been found, but the function of these has remained unclear. BAC cloning and expression analyses were employed to characterize these SRK-like sequences. An SRK-positive Bacterial Artificial Chromosome clone was found to contain complete SRK and SCR sequences located close by one another in the derived genomic position of the Leavenworthia S locus, and in place of the more typical Lal2 and SCRL sequences. These sequences are expressed in stigmas and anthers, respectively, and crossing data show that the SRK/SCR haplotype is functional in self-incompatibility. Population surveys indicate that < 5% of Leavenworthia S loci possess such alleles. An ancestral translocation or recombination event involving SRK/SCR and Lal2/SCRL likely occurred, together with neofunctionalization of Lal2/SCRL, and both haplotype groups now function as Leavenworthia S locus alleles. These findings suggest that S locus alleles can have distinctly different evolutionary origins. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

EsrE-A yigP Locus-Encoded Transcript-Is a 3′ UTR sRNA Involved in the Respiratory Chain of E. coli

PubMed Central

Xia, Hui; Yang, Xichen; Tang, Qiongwei; Ye, Jiang; Wu, Haizhen; Zhang, Huizhan

2017-01-01

The yigP locus is widely conserved among γ-proteobacteria. Mutation of the yigP locus impacts aerobic growth of Gram-negative bacteria. However, the underlying mechanism of how the yigP locus influences aerobic growth remains largely unknown. Here, we demonstrated that the yigP locus in Escherichia coli encodes two transcripts; the mRNA of ubiquinone biosynthesis protein, UbiJ, and the 3′ untranslated region small regulatory RNA (sRNA), EsrE. EsrE is an independent transcript that is transcribed using an internal promoter of the yigP locus. Surprisingly, we found that both the EsrE sRNA and UbiJ protein were required for Q8 biosynthesis, and were sufficient to rescue the growth defect ascribed to deletion of the yigP locus. Moreover, our data showed that EsrE targeted multiple mRNAs involved in several cellular processes including murein biosynthesis and the tricarboxylic acid cycle. Among these targets, sdhD mRNA that encodes one subunit of succinate dehydrogenase (SDH), was significantly activated. Our findings provided an insight into the important function of EsrE in bacterial adaptation to various environments, as well as coordinating different aspects of bacterial physiology. PMID:28900423

Structure and expression of the attacin genes in Hyalophora cecropia.

PubMed

Sun, S C; Lindström, I; Lee, J Y; Faye, I

1991-02-26

To study the regulation of the immune genes in insects, we have cloned and sequenced the attacin gene locus of the giant silk moth Hyalophora cecropia. The locus contains one acidic and one basic attacin gene as well as two pseudogenes, which are remnants of basic attacin genes. A small insertion element was found within the locus. The two functional attacin genes are transcribed in opposite directions and have two introns inserted at homologous positions. A common sequence, GGGGATTCCT, is found at nucleotide position -48 in the acidic gene and at nucleotide position -58 in the basic gene. Interestingly, this decanucleotide is similar to the consensus of the NF-k B-binding site. Expression studies revealed that both attacins are strongly induced by phorbol 12-myristate 13-acetate, lipopolysaccharide and bacteria. However, only the acidic attacin gene showed a clear response to injury.

RELATIONSHIP OF ASSESS SELF-ESTEEM AND LOCUS OF CONTROL WITH QUALITY OF LIFE DURING TREATMENT STAGES IN PATIENTS REFERRING TO DRUG ADDICTION REHABILITATION CENTERS

PubMed Central

Heidari, Mohammad; Ghodusi, Mansureh

2016-01-01

Objective: Thus, the present research was carried out aimed at determining the relationship between self-esteem and locus of control and quality of life during treatment stages in the patients referring to drug addiction rehabilitation centers of Borujen city, Iran. Methods: The current study was a sectional research of descriptive correlation type. The research sample was 150 individuals of patients referring to addiction rehabilitation centers of Borujen city. For data gathering, Rosenberg Self-esteem Scale, Rotter’s Locus of Control Scale, and SF36 Quality of Life Questionnaire were used. Following collection of questionnaires, the data were analyzed using SPSS/16 software. Results: According to the results, in the 12th day of treatment, 96 patients exhibited moderate self-esteem, 102 patients had internal locus of control, and the score of their overall quality of life was 40.43±12.71. Furthermore, Pearson’s correlation coefficient indicated that a significant and positive relationship was observed between locus of control and quality of life during different treatment stages. Conclusion: It seems that quality of life improves during addiction treatment stages due to improvement of personality traits including locus of control and self-esteem. Therefore, consultation methods as a very crucial priority in addiction rehabilitation centers shall be taken into account by the health sector authorities and managers and can play an essential role in enhancing quality of life. PMID:27698598

Two genetic markers closely linked to adult polycystic kidney disease on chromosome 16.

PubMed Central

Reeders, S T; Breuning, M H; Corney, G; Jeremiah, S J; Meera Khan, P; Davies, K E; Hopkinson, D A; Pearson, P L; Weatherall, D J

1986-01-01

The genetic locus for autosomal dominant adult polycystic kidney disease was recently assigned to chromosome 16 by the finding of genetic linkage to the alpha globin gene cluster. Further study showed that the phosphoglycolate phosphatase locus is also closely linked to both the locus for adult polycystic kidney disease and the alpha globin gene cluster. These findings have important implications for the prenatal and presymptomatic diagnosis of adult polycystic kidney disease and for a better understanding of its pathogenesis. Images FIG 1 PMID:3008903

Population genetic structure of clinical and environmental isolates of Blastomyces dermatitidis, Based on 27 Polymorphic Microsatellite Markers

USGS Publications Warehouse

Meece, J.K.; Anderson, J.L.; Fisher, M.C.; Henk, D.A.; Sloss, Brian L.; Reed, K.D.

2011-01-01

Blastomyces dermatitidis, a thermally dimorphic fungus, is the etiologic agent of North American blastomycosis. Clinical presentation is varied, ranging from silent infections to fulminant respiratory disease and dissemination to skin and other sites. Exploration of the population genetic structure of B. dermatitidis would improve our knowledge regarding variation in virulence phenotypes, geographic distribution, and difference in host specificity. The objective of this study was to develop and test a panel of microsatellite markers to delineate the population genetic structure within a group of clinical and environmental isolates of B. dermatitidis. We developed 27 microsatellite markers and genotyped B. dermatitidis isolates from various hosts and environmental sources (n = 112). Assembly of a neighbor-joining tree of allele-sharing distance revealed two genetically distinct groups, separated by a deep node. Bayesian admixture analysis showed that two populations were statistically supported. Principal coordinate analysis also reinforced support for two genetic groups, with the primary axis explaining 61.41% of the genetic variability. Group 1 isolates average 1.8 alleles/locus, whereas group 2 isolates are highly polymorphic, averaging 8.2 alleles/locus. In this data set, alleles at three loci are unshared between the two groups and appear diagnostic. The mating type of individual isolates was determined by PCR. Both mating type-specific genes, the HMG and ??-box domains, were represented in each of the genetic groups, with slightly more isolates having the HMG allele. One interpretation of this study is that the species currently designated B. dermatitidis includes a cryptic subspecies or perhaps a separate species. ?? 2011, American Society for Microbiology.

Population genetic structure of clinical and environmental isolates of Blastomyces dermatitidis based on 27 polymorphic microsatellite markers

USGS Publications Warehouse

Meece, Jennifer K.; Anderson, Jennifer L.; Fisher, Matthew C.; Henk, Daniel A.; Sloss, Brian L.; Reed, Kurt D.

2011-01-01

Blastomyces dermatitidis, a thermally dimorphic fungus, is the etiologic agent of North American blastomycosis. Clinical presentation is varied, ranging from silent infections to fulminant respiratory disease and dissemination to skin and other sites. Exploration of the population genetic structure of B. dermatitidis would improve our knowledge regarding variation in virulence phenotypes, geographic distribution, and difference in host specificity. The objective of this study was to develop and test a panel of microsatellite markers to delineate the population genetic structure within a group of clinical and environmental isolates of B. dermatitidis. We developed 27 microsatellite markers and genotyped B. dermatitidis isolates from various hosts and environmental sources (n=112). Assembly of a neighbor-joining tree of allele-sharing distance revealed two genetically distinct groups, separated by a deep node. Bayesian admixture analysis showed that two populations were statistically supported. Principal coordinate analysis also reinforced support for two genetic groups, with the primary axis explaining 61.41% of the genetic variability. Group 1 isolates average 1.8 alleles/locus, whereas group 2 isolates are highly polymorphic, averaging 8.2 alleles/locus. In this data set, alleles at three loci are unshared between the two groups and appear diagnostic. The mating type of individual isolates was determined by PCR. Both mating type-specific genes, the HMG and α-box domains, were represented in each of the genetic groups, with slightly more isolates having the HMG allele. One interpretation of this study is that the species currently designated B. dermatitidis includes a cryptic subspecies or perhaps a separate species.

Evaluation of optimized bronchoalveolar lavage sampling designs for characterization of pulmonary drug distribution.

PubMed

Clewe, Oskar; Karlsson, Mats O; Simonsson, Ulrika S H

2015-12-01

Bronchoalveolar lavage (BAL) is a pulmonary sampling technique for characterization of drug concentrations in epithelial lining fluid and alveolar cells. Two hypothetical drugs with different pulmonary distribution rates (fast and slow) were considered. An optimized BAL sampling design was generated assuming no previous information regarding the pulmonary distribution (rate and extent) and with a maximum of two samples per subject. Simulations were performed to evaluate the impact of the number of samples per subject (1 or 2) and the sample size on the relative bias and relative root mean square error of the parameter estimates (rate and extent of pulmonary distribution). The optimized BAL sampling design depends on a characterized plasma concentration time profile, a population plasma pharmacokinetic model, the limit of quantification (LOQ) of the BAL method and involves only two BAL sample time points, one early and one late. The early sample should be taken as early as possible, where concentrations in the BAL fluid ≥ LOQ. The second sample should be taken at a time point in the declining part of the plasma curve, where the plasma concentration is equivalent to the plasma concentration in the early sample. Using a previously described general pulmonary distribution model linked to a plasma population pharmacokinetic model, simulated data using the final BAL sampling design enabled characterization of both the rate and extent of pulmonary distribution. The optimized BAL sampling design enables characterization of both the rate and extent of the pulmonary distribution for both fast and slowly equilibrating drugs.

Material Hardship and Internal Locus of Control Over the Prevention of Child Obesity in Low-Income Hispanic Pregnant Women.

PubMed

Gross, Rachel S; Mendelsohn, Alan L; Gross, Michelle B; Scheinmann, Roberta; Messito, Mary Jo

2016-07-01

To determine the relations between household material hardships and having a low internal locus of control over the prevention of child obesity in low-income Hispanic pregnant women. We performed a cross-sectional analysis of baseline data collected during a third trimester prenatal visit from women participating in the Starting Early Study, a randomized controlled trial to test the efficacy of a primary care-based family-centered early child obesity prevention intervention. Using multiple logistic regression analyses, we determined whether 4 domains of material hardship (food insecurity, difficulty paying bills, housing disrepair, neighborhood stress), considered individually and also cumulatively, were associated with having a low internal locus of control over the prevention of child obesity. The sample included 559 low-income Hispanic pregnant women, with 60% having experienced at least 1 hardship. Food insecurity was independently associated with a low internal locus of control over the prevention of child obesity (adjusted odds ratio, 2.38; 95% confidence interval, 1.50-3.77), controlling for other hardships and confounders. Experiencing a greater number of material hardships was associated in a dose-dependent relationship with an increased odds of having a low internal locus of control. Prenatal material hardships, in particular food insecurity, were associated with having a lower prenatal internal locus of control over the prevention of child obesity. Longitudinal follow-up of this cohort is needed to determine how relations between material hardships and having a low internal locus of control will ultimately affect infant feeding practices and child weight trajectories. Copyright © 2016 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.

Health locus of control in patients undergoing coronary artery surgery - changes and associated outcomes: a seven-year cohort study.

PubMed

Rideout, Andrew; Tolmie, Elizabeth; Lindsay, Grace

2017-01-01

Health locus of control is a measure of an individual's beliefs in factors that are thought to determine health experiences. Scores are generated and form a graduated linear scale from external to internal control, with respect to their views on health causality. Health locus of control has been considered to be a relatively stable entity. However, it is not clear if this status changes in the advent of serious health challenges, such as coronary artery bypass graft surgery. The aim of this study is to explore the variability of health locus of control and its association with postoperative health in this context. In a longitudinal cohort study of patients undergoing coronary artery bypass graft surgery, a purposive sample ( n=215) were recruited from the waiting list and followed up postoperatively, at approximately one year and seven years later. Patients undergoing coronary artery bypass graft surgery demonstrated marked fluctuations in health locus of control in their peri-operative and rehabilitative phases. Mean health locus of control became more external (often associated with poorer outcomes) peri-operatively, and more internal (generally associated with better health outcomes) in the rehabilitative period. Health locus of control scores were shown to be changeable during a major health care intervention, with possible consequences for patient outcomes and care needs. The significant health belief upheaval demonstrated in this cohort should be considered in assessing patients preoperatively, and managed as part of the patients' clinical journey by both acute and rehabilitation staff. It is likely to have particular importance in individualised assessment and management of future prevention advice for patients.

Mutagenicity in emissions from coal- and oil-fired boilers.

PubMed Central

Alfheim, I; Bergström, J G; Jenssen, D; Møller, M

1983-01-01

The mutagenicity of emission samples from three oil-fired and four coal-fired boilers have been compared by using the Salmonella/microsome assay. Very little or no mutagenic activity was observed in samples from five of these boilers. The sample from one oil-fired boiler showed mutagenic activity of about 500 revertants/MJ, and the sample from a coal-fired fluidized bed combustor had an activity of 58,000 revertants/MJ measured with strain TA 98 in the absence of metabolic activation. All samples contained substances that were cytotoxic to the test bacteria, thus making it difficult to obtain linear dose-response curves. Mutagenic activity at low levels may remain undetected due to this toxicity of the samples. Samples with mutagenic activity below the detection limit in the Salmonella test have also been tested for forward mutations at the HGPRT locus in V79 hamster cells. Weak mutagenic effects were detected in two of the samples, whereas the sample from one oil-fired boiler remained negative. In this test, as well as in the Salmonella test, a strong cytotoxic effect could be observed with all samples. PMID:6825617

The doublesex gene integrates multi-locus complementary sex determination signals in the Japanese ant, Vollenhovia emeryi.

PubMed

Miyakawa, Misato Okamoto; Tsuchida, Koji; Miyakawa, Hitoshi

2018-03-01

A female diploid, male haploid sex determination system (haplodiploidy) is found in hymenopteran taxa, such as ants, wasps, bees and sawflies. In this system, a single, complementary sex-determination (sl-CSD) locus functions as the primary sex-determination signal. In the taxa that has evolved this system, females and males are heterozygous and hemi/homozygous at the CSD locus, respectively. While the sl-CSD system enables females to alter sex ratios in the nest, it carries a high cost in terms of inbreeding, as individuals that are homozygous at the CSD locus become sterile diploid males. To counter this risk, some of hymenopteran species have evolved a multi-locus CSD (ml-CSD) system, which effectively reduces the proportion of sterile males. However, the mechanism by which these multiple primary signals are integrated and how they affect the terminal sex-differentiation signal of the molecular cascade have not yet been clarified. To resolve these questions, we examined the molecular cascade in the Japanese ant Vollenhovia emeryi, which we previously confirmed has two CSD loci. Here, we showed that the sex-determination gene, doublesex (dsx), which is highly conserved among phylogenetically distant taxa, is responsible for integrating two CSD signals in V. emeryi. After identifying and characterizing dsx, genotypes containing two CSD loci and splicing patterns of dsx were found to correspond to the sexual phenotype, suggesting that two primary signals are integrated into dsx. These findings will facilitate future molecular and functional studies of the sex determination cascade in V. emeryi, and shed light on the evolution and diversification of sex determination systems in insects. Copyright © 2018 Elsevier Ltd. All rights reserved.

Localizing multiple X chromosome-linked retinitis pigmentosa loci using multilocus homogeneity tests

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

Ott, J.; Terwilliger, J.D.; Bhattacharya, S.

1990-01-01

Multilocus linkage analysis of 62 family pedigrees with X chromosome-linked retinitis pigmentosa (XLRP) was undertaken to determine the presence of possible multiple disease loci and to reliability estimate their map location. Multilocus homogeneity tests furnish convincing evidence for the presence of two XLRP loci, the likelihood ratio being 6.4 {times} 10{sup 9}:1 in a favor of two versus a single XLRP locus and gave accurate estimates for their map location. In 60-75% of the families, location of an XLRP gene was estimated at 1 centimorgan distal to OTC, and in 25-40% of the families, an XLRP locus was located halfwaymore » between DXS14 (p58-1) and DXZ1 (Xcen), with an estimated recombination fraction of 25% between the two XLRP loci. There is also good evidence for third XLRP locus, midway between DXS28 (C7) and DXS164 (pERT87), supported by a likelihood ratio of 293:1 for three versus two XLRP loci.« less

Investigation into the performance of different models for predicting stutter.

PubMed

Bright, Jo-Anne; Curran, James M; Buckleton, John S

2013-07-01

In this paper we have examined five possible models for the behaviour of the stutter ratio, SR. These were two log-normal models, two gamma models, and a two-component normal mixture model. A two-component normal mixture model was chosen with different behaviours of variance; at each locus SR was described with two distributions, both with the same mean. The distributions have difference variances: one for the majority of the observations and a second for the less well-behaved ones. We apply each model to a set of known single source Identifiler™, NGM SElect™ and PowerPlex(®) 21 DNA profiles to show the applicability of our findings to different data sets. SR determined from the single source profiles were compared to the calculated SR after application of the models. The model performance was tested by calculating the log-likelihoods and comparing the difference in Akaike information criterion (AIC). The two-component normal mixture model systematically outperformed all others, despite the increase in the number of parameters. This model, as well as performing well statistically, has intuitive appeal for forensic biologists and could be implemented in an expert system with a continuous method for DNA interpretation. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Association between the GABA(A) receptor alpha5 subunit gene locus (GABRA5) and bipolar affective disorder.

PubMed

Papadimitriou, G N; Dikeos, D G; Karadima, G; Avramopoulos, D; Daskalopoulou, E G; Vassilopoulos, D; Stefanis, C N

1998-02-07

Genetic factors seem to play an important role in the pathogenesis of affective disorder. The candidate gene strategies are being used, among others, to identify the genes conferring vulnerability to the disease. The genes coding for the receptors of gamma-aminobutyric acid (GABA) have been proposed as candidates for affective disorder, since the GABA neurotransmitter system has been implicated in the pathogenesis of the illness. We examined the possible genetic association between the GABA(A) receptor alpha5 subunit gene locus (GABRA5) on chromosome 15 and affective disorder, in 48 bipolar patients (BP), 40 unipolar patients (UP), and 50 healthy individuals, age- and sex-matched to the patients. All patients and controls were unrelated Greeks. Diagnoses were made after direct interviews according to the DSM-IV and ICD-10 criteria. For the genotyping, a dinucleotide (CA) repeat marker was used. The polymerase chain reaction (PCR) products found were nine alleles with lengths between 272 and 290 base pairs (bp). The distribution of allelic frequencies of the GABRA5 locus differed significantly between BP patients and controls with the 282-bp allele found to be associated with BP affective disorder, while no such difference was observed between the groups of UP patients and controls nor between the two patient groups. The presence or absence of the 282-bp allele in the genotype of BP patients was not shown to influence the age of onset and the overall clinical severity, but was found to be associated with a preponderance of manic over depressive episodes in the course of the illness.

Amplification of DNA from preserved specimens shows blowflies were preadapted for the rapid evolution of insecticide resistance

PubMed Central

Hartley, C. J.; Newcomb, R. D.; Russell, R. J.; Yong, C. G.; Stevens, J. R.; Yeates, D. K.; La Salle, J.; Oakeshott, J. G.

2006-01-01

Mutations of esterase 3 confer two forms of organophosphate resistance on contemporary Australasian Lucilia cuprina. One form, called diazinon resistance, is slightly more effective against commonly used insecticides and is now more prevalent than the other form, called malathion resistance. We report here that the single amino acid replacement associated with diazinon resistance and two replacements associated with malathion resistance also occur in esterase 3 in the sibling species Lucilia sericata, suggesting convergent evolution around a finite set of resistance options. We also find parallels between the species in the geographic distributions of the polymorphisms: In both cases, the diazinon-resistance change is absent or rare outside Australasia where insecticide pressure is lower, whereas the changes associated with malathion resistance are widespread. Furthermore, PCR analysis of pinned specimens of Australasian L. cuprina collected before the release of organophosphate insecticides reveals no cases of the diazinon-resistance change but several cases of those associated with malathion resistance. Thus, the early outbreak of resistance in this species can be explained by the preexistence of mutant alleles encoding malathion resistance. The pinned specimen analysis also shows much higher genetic diversity at the locus before organophosphate use, suggesting that the subsequent sweep of diazinon resistance in Australasia has compromised the scope for the locus to respond further to the ongoing challenge of the insecticides. PMID:16723400

Meta-analysis of Parkinson's disease: identification of a novel locus, RIT2.

PubMed

Pankratz, Nathan; Beecham, Gary W; DeStefano, Anita L; Dawson, Ted M; Doheny, Kimberly F; Factor, Stewart A; Hamza, Taye H; Hung, Albert Y; Hyman, Bradley T; Ivinson, Adrian J; Krainc, Dmitri; Latourelle, Jeanne C; Clark, Lorraine N; Marder, Karen; Martin, Eden R; Mayeux, Richard; Ross, Owen A; Scherzer, Clemens R; Simon, David K; Tanner, Caroline; Vance, Jeffery M; Wszolek, Zbigniew K; Zabetian, Cyrus P; Myers, Richard H; Payami, Haydeh; Scott, William K; Foroud, Tatiana

2012-03-01

Genome-wide association (GWAS) methods have identified genes contributing to Parkinson's disease (PD); we sought to identify additional genes associated with PD susceptibility. A 2-stage design was used. First, individual level genotypic data from 5 recent PD GWAS (Discovery Sample: 4,238 PD cases and 4,239 controls) were combined. Following imputation, a logistic regression model was employed in each dataset to test for association with PD susceptibility and results from each dataset were meta-analyzed. Second, 768 single-nucleotide polymorphisms (SNPs) were genotyped in an independent Replication Sample (3,738 cases and 2,111 controls). Genome-wide significance was reached for SNPs in SNCA (rs356165; G: odds ratio [OR]=1.37; p=9.3×10(-21)), MAPT (rs242559; C: OR=0.78; p=1.5×10(-10)), GAK/DGKQ (rs11248051; T: OR=1.35; p=8.2×10(-9)/rs11248060; T: OR=1.35; p=2.0×10(-9)), and the human leukocyte antigen (HLA) region (rs3129882; A: OR=0.83; p=1.2×10(-8)), which were previously reported. The Replication Sample confirmed the associations with SNCA, MAPT, and the HLA region and also with GBA (E326K; OR=1.71; p=5×10(-8) Combined Sample) (N370; OR=3.08; p=7×10(-5) Replication sample). A novel PD susceptibility locus, RIT2, on chromosome 18 (rs12456492; p=5×10(-5) Discovery Sample; p=1.52×10(-7) Replication sample; p=2×10(-10) Combined Sample) was replicated. Conditional analyses within each of the replicated regions identified distinct SNP associations within GBA and SNCA, suggesting that there may be multiple risk alleles within these genes. We identified a novel PD susceptibility locus, RIT2, replicated several previously identified loci, and identified more than 1 risk allele within SNCA and GBA. Copyright © 2012 American Neurological Association.

Multiple signals at the extended 8p23 locus are associated with susceptibility to systemic lupus erythematosus.

PubMed

Demirci, F Yesim; Wang, Xingbin; Morris, David L; Feingold, Eleanor; Bernatsky, Sasha; Pineau, Christian; Clarke, Ann; Ramsey-Goldman, Rosalind; Manzi, Susan; Vyse, Timothy J; Kamboh, M I

2017-06-01

A major systemic lupus erythematosus (SLE) susceptibility locus lies within a common inversion polymorphism region (encompassing 3.8 - 4.5  Mb) located at 8p23. Initially implicated genes included FAM167A-BLK and XKR6 , of which BLK received major attention due to its known role in B-cell biology. Recently, additional SLE risk carried in non-inverted background was also reported. In this case -control study, we further investigated the 'extended' 8p23 locus (~ 4  Mb) where we observed multiple SLE signals and assessed these signals for their relation to the inversion affecting this region. The study involved a North American discovery data set ( ~ 1200  subjects) and a replication data set (> 10 000  subjects) comprising European-descent individuals. Meta-analysis of 8p23 SNPs, with p < 0.05 in both data sets, identified 51 genome-wide significant SNPs (p < 5.0 × 10 -8 ). While most of these SNPs were related to previously implicated signals ( XKR6-FAM167A-BLK subregion), our results also revealed two 'new' SLE signals, including SGK223-CLDN23-MFHAS1 (6.06 × 10 -9 ≤ meta p ≤ 4.88 × 10 -8 ) and CTSB (meta p = 4.87 × 10 -8 ) subregions that are located > 2 Mb upstream and ~ 0.3  Mb downstream from previously reported signals. Functional assessment of relevant SNPs indicated putative cis -effects on the expression of various genes at 8p23. Additional analyses in discovery sample, where the inversion genotypes were inferred, replicated the association of non-inverted status with SLE risk and suggested that a number of SLE risk alleles are predominantly carried in non-inverted background. Our results implicate multiple (known+novel) SLE signals/genes at the extended 8p23 locus, beyond previously reported signals/genes, and suggest that this broad locus contributes to SLE risk through the effects of multiple genes/pathways. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

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

Evidence of red sensitive photoreceptors in Pygopleurus israelitus (Glaphyridae: Coleoptera) and its implications for beetle pollination in the southeast Mediterranean.

PubMed

Martínez-Harms, J; Vorobyev, M; Schorn, J; Shmida, A; Keasar, T; Homberg, U; Schmeling, F; Menzel, R

2012-06-01

A very well-documented case of flower-beetle interaction is the association in the Mediterranean region between red bowl-shaped flowers and beetles of the family Glaphyridae. The present study examines the visual mechanisms by which Pygopleurus israelitus (Glaphyridae: Scarabaeoidea: Coleoptera) would perceive the colors of flowers they visit by characterizing the spectral sensitivity of its photoreceptors. Our measurements revealed the presence of three types of photoreceptors, maximally sensitive in the UV, green and red areas of the spectrum. Using color vision space diagrams, we calculated the distribution of beetle-visited flower colors in the glaphyrid and honeybee color space and evaluated whether chromatic discrimination differs between the two types of pollinators. Respective color loci in the beetle color space are located on one side of the locus for green foliage background, whereas in the honeybee the flower color loci surround the locus occupied by green foliage. Our results represent the first evidence of a red sensitive photoreceptor in a flower-visiting coleopteran species, highlighting Glaphyridae as an interesting model group to study the role of pollinators in flower color evolution.

[The significance of the relationship between external/internal locus of control and adolescent substance use in behavioral medicine].

PubMed

Pikó, Bettina; Kovács, Eszter; Kriston, Pálma

2011-02-27

Prevention and treatment of the addictions are key public health priorities in modern society. In medical practice, in relation to the biochemical processes, mapping the addiction-prone personality traits, like external/internal locus of control are getting more and more attention. Individuals with high level on internal locus of control, for example, tend to take care of their health behavior; the lack of it, on the other hand, may worsen the effectiveness of stress release which may increase the likelihood of turning to substance use. The main goal of the present study was to investigate the relationship between adolescent substance use (both lifetime prevalence and the actual substance user status) and external/internal locus of control). The data collection of the questionnaire survey was going on among 656 high school students in Szeged (age range between 14-21 years, mean = 16.5 years, S.D. = 1.5 years of age, 49.1% of the sample was female). Associations between indicators of substance use (as dependent variables) and scale points of external/internal locus of control (as independent variables) were assessed using odds ratios calculated by logistic regression analyses, whereas gender was used as a controlling variable. Among boys, scale points of external, among girls, those of internal locus of control showed higher values. External locus of control increased, whereas internal locus of control decreased the risk of substance use, however, the relative role of external/internal locus of control was different according to the type of substance use and the prevalence values. In terms of smoking, lifetime prevalence, whereas in terms of marijuana use, the actual user status was influenced. In addition, while the latter one was also affected by gender, it did not play a role at all in the previous one. All these findings suggest that behavioral control may play a particularly important role in prevention of adolescent substance use. For developing this, methods of cognitive therapy would be effective to be completed with autogenic relaxation training as well.

DXYS156: a multi-purpose short tandem repeat locus for determination of sex, paternal and maternal geographic origins and DNA fingerprinting.

PubMed

Calì, Francesco; Forster, P; Kersting, Christian; Mirisola, Mario G; D'Anna, Rosalba; De Leo, Giacomo; Romano, Valentino

2002-06-01

In forensic science and in legal medicine Y chromosomal typing is indispensable for sex determination, for paternity testing in the absence of the father and for distinguishing males in multiple rape cases. Another potential application is the estimation of paternal geographic origin or family name from a crime stain to narrow down the range of suspects and thus reduce costs of mass screenings. However, Y typing alone cannot provide a sufficiently resolved DNA fingerprint as required for court convictions. Thus, there is a dilemma whether or not to sacrifice valuable material for the sake of extensive Y chromosomal investigations when stain DNA is limited (typically allowing only few PCR amplifications). We here describe a Y-chromosome-specific nucleotide insertion in the duplicate short tandem repeat (STR) locus DXYS156 which allows us to distinguish males from females as does the commonly used amelogenin system, but with the advantage that this locus is multi-allelic, thus substantially contributing towards DNA fingerprinting of a sample and furthermore enabling the detection of sample contamination. Yet another bonus is that both the X and the Y copies of DXYS156 have alleles specific to different parts of the world, offering separate estimates of maternal and paternal descent of that sample. We therefore recommend the inclusion of DXYS156 in standard multiplexing kits for forensic, archaeological and genealogical applications.

Linkage and association studies identify a novel locus for Alzheimer disease at 7q36 in a Dutch population-based sample.

PubMed

Rademakers, Rosa; Cruts, Marc; Sleegers, Kristel; Dermaut, Bart; Theuns, Jessie; Aulchenko, Yurii; Weckx, Stefan; De Pooter, Tim; Van den Broeck, Marleen; Corsmit, Ellen; De Rijk, Peter; Del-Favero, Jurgen; van Swieten, John; van Duijn, Cornelia M; Van Broeckhoven, Christine

2005-10-01

We obtained conclusive linkage of Alzheimer disease (AD) with a candidate region of 19.7 cM at 7q36 in an extended multiplex family, family 1270, ascertained in a population-based study of early-onset AD in the northern Netherlands. Single-nucleotide polymorphism and haplotype association analyses of a Dutch patient-control sample further supported the linkage at 7q36. In addition, we identified a shared haplotype at 7q36 between family 1270 and three of six multiplex AD-affected families from the same geographical region, which is indicative of a founder effect and defines a priority region of 9.3 cM. Mutation analysis of coding exons of 29 candidate genes identified one linked synonymous mutation, g.38030G-->C in exon 10, that affected codon 626 of the PAX transactivation domain interacting protein gene (PAXIP1). It remains to be determined whether PAXIP1 has a functional role in the expression of AD in family 1270 or whether another mutation at this locus explains the observed linkage and sharing. Together, our linkage data from the informative family 1270 and the association data in the population-based early-onset AD patient-control sample strongly support the identification of a novel AD locus at 7q36 and re-emphasize the genetic heterogeneity of AD.

Identification, genetic localization, and allelic diversity of selectively amplified microsatellite polymorphic loci in lettuce and wild relatives (Lactuca spp.).

PubMed

Witsenboer, H; Michelmore, R W; Vogel, J

1997-12-01

Selectively amplified microsatellite polymorphic locus (SAMPL) analysis is a method of amplifying microsatellite loci using generic PCR primers. SAMPL analysis uses one AFLP primer in combination with a primer complementary to microsatellite sequences. SAMPL primers based on compound microsatellite sequences provided the clearest amplification patterns. We explored the potential of SAMPL analysis in lettuce to detect PCR-based codominant microsatellite markers. Fifty-eight SAMPLs were identified and placed on the genetic map. Seventeen were codominant. SAMPLs were dispersed with RFLP markers on 11 of the 12 main linkage groups in lettuce, indicating that they have a similar genomic distribution. Some but not all fragments amplified by SAMPL analysis were confirmed to contain microsatellite sequences by Southern hybridization. Forty-five cultivars of lettuce and five wild species of Lactuca were analyzed to determine the allelic diversity for codominant SAMPLs. From 3 to 11 putative alleles were found for each SAMPL; 2-6 alleles were found within Lactuca sativa and 1-3 alleles were found among the crisphead genotypes, the most genetically homogeneous plant type of L. sativa. This allelic diversity is greater than that found for RFLP markers. Numerous new alleles were observed in the wild species; however, there were frequent null alleles. Therefore, SAMPL analysis is more applicable to intraspecific than to interspecific comparisons. A phenetic analysis based on SAMPLs resulted in a dendrogram similar to those based on RFLP and AFLP markers.

Mutation screening of patients with Alzheimer disease identifies APP locus duplication in a Swedish patient

PubMed Central

2011-01-01

Background Missense mutations in three different genes encoding amyloid-β precursor protein, presenilin 1 and presenilin 2 are recognized to cause familial early-onset Alzheimer disease. Also duplications of the amyloid precursor protein gene have been shown to cause the disease. At the Dept. of Geriatric Medicine, Karolinska University Hospital, Sweden, patients are referred for mutation screening for the identification of nucleotide variations and for determining copy-number of the APP locus. Methods We combined the method of microsatellite marker genotyping with a quantitative real-time PCR analysis to detect duplications in patients with Alzheimer disease. Results In 22 DNA samples from individuals diagnosed with clinical Alzheimer disease, we identified one patient carrying a duplication on chromosome 21 which included the APP locus. Further mapping of the chromosomal region by array-comparative genome hybridization showed that the duplication spanned a maximal region of 1.09 Mb. Conclusions This is the first report of an APP duplication in a Swedish Alzheimer patient and describes the use of quantitative real-time PCR as a tool for determining copy-number of the APP locus. PMID:22044463

Mutation screening of patients with Alzheimer disease identifies APP locus duplication in a Swedish patient.

PubMed

Thonberg, Håkan; Fallström, Marie; Björkström, Jenny; Schoumans, Jacqueline; Nennesmo, Inger; Graff, Caroline

2011-11-01

Missense mutations in three different genes encoding amyloid-β precursor protein, presenilin 1 and presenilin 2 are recognized to cause familial early-onset Alzheimer disease. Also duplications of the amyloid precursor protein gene have been shown to cause the disease. At the Dept. of Geriatric Medicine, Karolinska University Hospital, Sweden, patients are referred for mutation screening for the identification of nucleotide variations and for determining copy-number of the APP locus. We combined the method of microsatellite marker genotyping with a quantitative real-time PCR analysis to detect duplications in patients with Alzheimer disease. In 22 DNA samples from individuals diagnosed with clinical Alzheimer disease, we identified one patient carrying a duplication on chromosome 21 which included the APP locus. Further mapping of the chromosomal region by array-comparative genome hybridization showed that the duplication spanned a maximal region of 1.09 Mb. This is the first report of an APP duplication in a Swedish Alzheimer patient and describes the use of quantitative real-time PCR as a tool for determining copy-number of the APP locus.

The effect of educational intervention on prevention of postpartum depression: an application of health locus of control.

PubMed

Moshki, Mahdi; Baloochi Beydokhti, Tahereh; Cheravi, Khadijeh

2014-08-01

To assess the effectiveness of application of health locus of control in pregnant women for prevention of postpartum depression in Iran. Nearly 10-15% of women suffer postnatal depression by the end of the second week after delivery, which creates problems in caring for the child that may affect child's future learning and concentration. Pre-post experimental design. Two hundred and thirty volunteer women were randomly divided into experimental and control groups. The data collection tools included a demographic questionnaire, the Multidimensional Health Locus of Control Scale and the Edinburg Depression Scale. Based on the associations found in the pretest, intervention programme was planned and carried out in the focused group discussion method. Data were collected after the end of scheduled sessions, immediately and one month later. The data were analysed with SPSS-16 using statistical methods including anova, chi-square test, Student's t-test and paired t-test. Chance health locus of control significantly reduced and internal health locus of control significantly increased, immediately after intervention. Also, a month after intervention, a significant difference was observed between the two groups in reducing postpartum depression. The planned participatory intervention led to empowerment and increased awareness and internalisation of health control beliefs and less tendency towards external health control beliefs, especially chance, improvement in general health leading to improved psychological health for prevention of postpartum depression in mothers. Clinicians might assess chance and internal health locus of control to identify the women at risk of developing depression during their pregnancy and to develop prevention and treatment plans. © 2013 John Wiley & Sons Ltd.

Selfing, Local Mate Competition, and Reinforcement.

PubMed

Rausher, Mark D

2017-02-01

Reinforcement can contribute to speciation by increasing the strength of prezygotic isolating mechanisms. Theoretical analyses over the past two decades have demonstrated that conditions for reinforcement are not unduly restrictive, and empirical investigations have documented over a dozen likely cases, indicating that it may be a reasonably common phenomenon in nature. Largely uncharacterized, however, is the diversity of biological scenarios that can create the reduced hybrid fitness that drives reinforcement. Here I examine one such scenario-the evolution of the "selfing syndrome" (a suite of characters including reductions in flower size and in nectar, pollen, and scent production) in highly selfing plant species. Using a four-locus model, where the loci are (1) a discrimination locus, (2) a target-of-discimination locus, (3) a pollen-production locus, and (4) a selfing-rate locus, I determine the conditions under which this syndrome can favor reinforcement, an increase in discrimination through change at locus 1, in an outcrossing species that experiences gene flow from a highly selfing species. In the absence of both linkage disequilibrium between loci and pollen discounting, reinforcement can occur, but only in a very small fraction of the parameter combinations examined. Moderate linkage ([Formula: see text]) between one pair of loci increases this fraction moderately, depending on which two loci are linked. Pollen discounting (a reduction in pollen exported to other plants due to increased selfing), by contrast, can increase the fraction of parameter combinations that result in reinforcement substantially. The evolution of reduced pollen production in highly selfing species thus facilitates reinforcement, especially if substantial pollen discounting is associated with selfing.

Deregulated HOX genes in ameloblastomas are located in physical contiguity to keratin genes.

PubMed

Schiavo, Giulia; D'Antò, Vincenzo; Cantile, Monica; Procino, Alfredo; Di Giovanni, Stefano; Valletta, Rossella; Terracciano, Luigi; Baumhoer, Daniel; Jundt, Gernot; Cillo, Clemente

2011-11-01

The expression of the HOX gene network in mid-stage human tooth development mostly concerns the epithelial tooth germ compartment and involves the C and D HOX loci. To further dissect the HOX gene implication with tooth epithelium differentiation we compared the expression of the whole HOX network in human ameloblastomas, as paradigm of epithelial odontogenic tumors, with tooth germs. We identified two ameloblastoma molecular types with respectively low and high number of active HOX C genes. The highly expressing HOX C gene ameloblastomas were characterized by a strong keratinized phenotype. Locus C HOX genes are located on chromosome 12q13-15 in physical contiguity with one of the two keratin gene clusters included in the human genome. The most posterior HOX C gene, HOX C13, is capable to interact with hair keratin genes located on the other keratin gene cluster in physical contiguity with the HOX B locus on chromosome 17q21-22. Inside the HOX C locus, a 2.2 kb ncRNA (HOTAIR) able to repress transcription, in cis, along the entire HOX C locus and, in trans, at the posterior region of the HOX D locus has recently been identified. Interestingly both loci are deregulated in ameloblastomas. Our finding support an important role of the HOX network in characterizing the epithelial tooth compartment. Furthermore, the physical contiguity between locus C HOX and keratin genes in normal tooth epithelium and their deregulation in the neoplastic counterparts suggest they may act on the same mechanism potentially involved with epithelial tumorigenesis. Copyright © 2011 Wiley Periodicals, Inc.

A Novel Locus For Dilated Cardiomyopathy Maps to Canine Chromosome 8

PubMed Central

Werner, Petra; Raducha, Michael G.; Prociuk, Ulana; Sleeper, Meg M.; Henthorn, Paula S.

2008-01-01

Dilated cardiomyopathy (DCM), the most common form of cardiomyopathy, often leads to heart failure and sudden death. While a substantial proportion of DCMs are inherited, mutations responsible for the majority of DCMs remain unidentified. A genome-wide linkage study was performed to identify the locus responsible for an autosomal recessive inherited form of juvenile DCM (JDCM) in Portuguese water dogs using 16 families segregating the disease. Results link the JDCM locus to canine chromosome 8 with two-point and multipoint LOD scores of 10.8 and 14, respectively. The locus maps to a 3.9 Mb region, with complete syntenic homology to human chromosome 14, that contains no genes or loci known to be involved in the development of any type of cardiomyopathy. This discovery of a DCM locus with a previously unknown etiology will provide a new gene to examine in human DCM patients and a model for testing therapeutic approaches for heart failure. PMID:18442891

Evolution of recombination rates in a multi-locus, haploid-selection, symmetric-viability model.

PubMed

Chasnov, J R; Ye, Felix Xiaofeng

2013-02-01

A fast algorithm for computing multi-locus recombination is extended to include a recombination-modifier locus. This algorithm and a linear stability analysis is used to investigate the evolution of recombination rates in a multi-locus, haploid-selection, symmetric-viability model for which stable equilibria have recently been determined. When the starting equilibrium is symmetric with two selected loci, we show analytically that modifier alleles that reduce recombination always invade. When the starting equilibrium is monomorphic, and there is a fixed nonzero recombination rate between the modifier locus and the selected loci, we determine analytical conditions for which a modifier allele can invade. In particular, we show that a gap exists between the recombination rates of modifiers that can invade and the recombination rate that specifies the lower stability boundary of the monomorphic equilibrium. A numerical investigation shows that a similar gap exists in a weakened form when the starting equilibrium is fully polymorphic but asymmetric. Copyright © 2012 Elsevier Inc. All rights reserved.

Job Satisfaction and Locus of Control in an Academic Setting

ERIC Educational Resources Information Center

Stachowiak, Bonni J.

2010-01-01

This study explored any relationships that existed between faculty members' locus of control and job satisfaction at a small, private, faith-based university. Two demographic variables were also analyzed in the findings: number of years teaching in higher education and tenure status. The job satisfaction instrument used was the Job in General…

Inventory and Expressive Measures of Locus of Control and Academic Performance: A 5-Year Outcome Study

ERIC Educational Resources Information Center

Otten, Mark W.

1977-01-01

Rotter's Internal External Locus of Control Scale and Ezekiel's Personal Future Autobiography were administered to 45 freshmen and 45 graduate students. Although the two tests had negative nonsignificant correlations, both tests were positively correlated with academic achievement (specifically, graduation within five years) for the internal locus…

Age-Dependent and Age-Independent Measures of Locus of Control.

ERIC Educational Resources Information Center

Sherman, Lawrence W.; Hofmann, Richard

Using a longitudinal data set obtained from 169 pre-adolescent children between the ages of 8 and 13 years, this study statistically divided locus of control into two independent components. The first component was noted as "age-dependent" (AD) and was determined by predicted values generated by regressing children's ages onto their…

Induction of mutations by bismuth-212 alpha particles at two genetic loci in human B-lymphoblasts.

PubMed

Metting, N F; Palayoor, S T; Macklis, R M; Atcher, R W; Liber, H L; Little, J B

1992-12-01

The human lymphoblast cell line TK6 was exposed to the alpha-particle-emitting radon daughter 212Bi by adding DTPA-chelated 212Bi directly to the cell suspension. Cytotoxicity and mutagenicity at two genetic loci were measured, and the molecular nature of mutant clones was studied by Southern blot analysis. Induced mutant fractions were 2.5 x 10(-5)/Gy at the hprt locus and 3.75 x 10(-5)/Gy at the tk locus. Molecular analysis of HPRT- mutant DNAs showed a high frequency (69%) of clones with partial or full deletions of the hprt gene among radiation-induced mutants compared with spontaneous mutants (31%). Chi-squared analyses of mutational spectra show a significant difference (P < or = 0.005) between spontaneous mutants and alpha-particle-induced mutants. Comparison with published studies of accelerator-produced heavy-ion exposures of TK6 cells indicates that the induction of mutations at the hprt locus, and perhaps a subset of mutations at the tk locus, is a simple linear function of particle fluence regardless of the ion species or its LET.

A new polymorphic pepsinogen locus (Pg-2) in the rat (Rattus norvegicus).

PubMed

Hamada, S; Yamada, J; Bender, K; Adams, M

1987-07-01

Only two types of pepsinogens, which are products of the Pg-1 locus, are present in rat urine. In gastric mucosa, however, additional pepsinogen isozymes are expressed. We have found a polymorphism for rat gastric mucosa pepsinogen using agarose gel electrophoresis. Some inbred rat strains expressed a pepsinogen band, while others did not. The trait was found to be controlled by a single autosomal locus. We tentatively designated the locus as Pg-2 with two alleles, Pg-2a for the one controlling presence of the band and Pg-2o for the one controlling absence. Linkage analysis using BN and TM strains revealed that Pg-2 was closely linked to Pg-1 (3.7 +/- 1.8 cM), and that it did not belong to LG I (Hbb and p), LG II (Acon-1 and Mup-1), LG IV (Hao-1 and Svp-1), LG V (Es-1 and Es-3), LG VI (Gc and h), LG IX (RT1), LG X (Fh and Pep-3), nor a LG containing Ahd-2 (as yet undetermined).

Advanced UXO Discrimination using Magnetometry: Understanding Remanent Magnetization

DTIC Science & Technology

2009-09-01

moments of steel samples. The MRIP comprises six three-component fluxgate magnetometers symmetrically distributed around a rotating sample holder. Samples...comprises six three- component fluxgate magnetometers symmetrically distributed around a rotating sample holder. Samples are placed on the holder... fluxgate magnetometers symmetrically distributed around a rotating sample holder. Samples are placed on the holder and are slowly spun through two

Two Different Secondary Metabolism Gene Clusters Occupied the Same Ancestral Locus in Fungal Dermatophytes of the Arthrodermataceae

PubMed Central

Zhang, Han; Rokas, Antonis; Slot, Jason C.

2012-01-01

Background Dermatophyte fungi of the family Arthrodermataceae (Eurotiomycetes) colonize keratinized tissue, such as skin, frequently causing superficial mycoses in humans and other mammals, reptiles, and birds. Competition with native microflora likely underlies the propensity of these dermatophytes to produce a diversity of antibiotics and compounds for scavenging iron, which is extremely scarce, as well as the presence of an unusually large number of putative secondary metabolism gene clusters, most of which contain non-ribosomal peptide synthetases (NRPS), in their genomes. To better understand the historical origins and diversification of NRPS-containing gene clusters we examined the evolution of a variable locus (VL) that exists in one of three alternative conformations among the genomes of seven dermatophyte species. Results The first conformation of the VL (termed VLA) contains only 539 base pairs of sequence and lacks protein-coding genes, whereas the other two conformations (termed VLB and VLC) span 36 Kb and 27 Kb and contain 12 and 10 genes, respectively. Interestingly, both VLB and VLC appear to contain distinct secondary metabolism gene clusters; VLB contains a NRPS gene as well as four porphyrin metabolism genes never found to be physically linked in the genomes of 128 other fungal species, whereas VLC also contains a NRPS gene as well as several others typically found associated with secondary metabolism gene clusters. Phylogenetic evidence suggests that the VL locus was present in the ancestor of all seven species achieving its present distribution through subsequent differential losses or retentions of specific conformations. Conclusions We propose that the existence of variable loci, similar to the one we studied, in fungal genomes could potentially explain the dramatic differences in secondary metabolic diversity between closely related species of filamentous fungi, and contribute to host adaptation and the generation of metabolic diversity. PMID:22860027

Nucleotide variation at the dopa decarboxylase (Ddc) gene in natural populations of Drosophila melanogaster.

PubMed

Tatarenkov, Andrey; Ayala, Francisco J

2007-08-01

We studied nucleotide sequence variation at the gene coding for dopa decarboxylase (Ddc) in seven populations of Drosophila melanogaster. Strength and pattern of linkage disequilibrium are somewhat distinct in the extensively sampled Spanish and Raleigh populations. In the Spanish population, a few sites are in strong positive association, whereas a large number of sites in the Raleigh population are associated nonrandomly but the association is not strong. Linkage disequilibrium analysis shows presence of two groups of haplotypes in the populations, each of which is fairly diverged, suggesting epistasis or inversion polymorphism. There is evidence of two forms of natural selection acting on Ddc. The McDonald-Kreitman test indicates a deficit of fixed amino acid differences between D. melanogaster and D. simulans, which may be due to negative selection. An excess of derived alleles at high frequency, significant according to the H-test, is consistent with the effect of hitchhiking. The hitchhiking may have been caused by directional selection downstream of the locus studied, as suggested by a gradual decrease of the polymorphism-to-divergence ratio. Altogether, the Ddc locus exhibits a complicated pattern of variation apparently due to several evolutionary forces. Such a complex pattern may be a result of an unusually high density of functionally important genes.

Photometric calibration of the COMBO-17 survey with the Softassign Procrustes Matching method

NASA Astrophysics Data System (ADS)

Sheikhbahaee, Z.; Nakajima, R.; Erben, T.; Schneider, P.; Hildebrandt, H.; Becker, A. C.

2017-11-01

Accurate photometric calibration of optical data is crucial for photometric redshift estimation. We present the Softassign Procrustes Matching (SPM) method to improve the colour calibration upon the commonly used Stellar Locus Regression (SLR) method for the COMBO-17 survey. Our colour calibration approach can be categorised as a point-set matching method, which is frequently used in medical imaging and pattern recognition. We attain a photometric redshift precision Δz/(1 + zs) of better than 2 per cent. Our method is based on aligning the stellar locus of the uncalibrated stars to that of a spectroscopic sample of the Sloan Digital Sky Survey standard stars. We achieve our goal by finding a correspondence matrix between the two point-sets and applying the matrix to estimate the appropriate translations in multidimensional colour space. The SPM method is able to find the translation between two point-sets, despite the existence of noise and incompleteness of the common structures in the sets, as long as there is a distinct structure in at least one of the colour-colour pairs. We demonstrate the precision of our colour calibration method with a mock catalogue. The SPM colour calibration code is publicly available at https://neuronphysics@bitbucket.org/neuronphysics/spm.git.

Genetic variability among populations of Lutzomyia (Psathyromyia) shannoni (Dyar 1929) (Diptera: Psychodidae: Phlebotominae) in Colombia.

PubMed

Cárdenas, E; Munstermann, L E; Martínez, O; Corredor, D; Ferro, C

2001-02-01

Polyacrylamide gel electrophoresis was used to elucidate genetic variation at 13 isozyme loci among forest populations of Lutzomyia shannoni from three widely separated locations in Colombia: Palambí (Nariño Department), Cimitarra (Santander Department) and Chinácota (Norte de Santander Department). These samples were compared with a laboratory colony originating from the Magdalena Valley in Central Colombia. The mean heterozygosity ranged from 16 to 22%, with 2.1 to 2.6 alleles detected per locus. Nei's genetic distances among populations were low, ranging from 0.011 to 0.049. The estimated number of migrants (Nm=3.8) based on Wright's F-Statistic, F ST, indicated low levels of gene flow among Lu. shannoni forest populations. This low level of migration indicates that the spread of stomatitis virus occurs via infected host, not by infected insect. In the colony sample of 79 individuals, the Gpi locus was homozygotic (0.62/0.62) in all females and heterozygotic (0.62/0.72) in all males. Although this phenomenon is probably a consequence of colonization, it indicates that Gpi is linked to a sex determining locus.

Physical mapping of a pollen modifier locus controlling self-incompatibility in apricot and synteny analysis within the Rosaceae.

PubMed

Zuriaga, Elena; Molina, Laura; Badenes, María Luisa; Romero, Carlos

2012-06-01

S-locus products (S-RNase and F-box proteins) are essential for the gametophytic self-incompatibility (GSI) specific recognition in Prunus. However, accumulated genetic evidence suggests that other S-locus unlinked factors are also required for GSI. For instance, GSI breakdown was associated with a pollen-part mutation unlinked to the S-locus in the apricot (Prunus armeniaca L.) cv. 'Canino'. Fine-mapping of this mutated modifier gene (M-locus) and the synteny analysis of the M-locus within the Rosaceae are here reported. A segregation distortion loci mapping strategy, based on a selectively genotyped population, was used to map the M-locus. In addition, a bacterial artificial chromosome (BAC) contig was constructed for this region using overlapping oligonucleotides probes, and BAC-end sequences (BES) were blasted against Rosaceae genomes to perform micro-synteny analysis. The M-locus was mapped to the distal part of chr.3 flanked by two SSR markers within an interval of 1.8 cM corresponding to ~364 Kb in the peach (Prunus persica L. Batsch) genome. In the integrated genetic-physical map of this region, BES were mapped against the peach scaffold_3 and BACs were anchored to the apricot map. Micro-syntenic blocks were detected in apple (Malus × domestica Borkh.) LG17/9 and strawberry (Fragaria vesca L.) FG6 chromosomes. The M-locus fine-scale mapping provides a solid basis for self-compatibility marker-assisted selection and for positional cloning of the underlying gene, a necessary goal to elucidate the pollen rejection mechanism in Prunus. In a wider context, the syntenic regions identified in peach, apple and strawberry might be useful to interpret GSI evolution in Rosaceae.

Comparative population genetics of a mimicry locus among hybridizing Heliconius butterfly species.

PubMed

Chamberlain, N L; Hill, R I; Baxter, S W; Jiggins, C D; Kronforst, M R

2011-09-01

The comimetic Heliconius butterfly species pair, H. erato and H. melpomene, appear to use a conserved Mendelian switch locus to generate their matching red wing patterns. Here we investigate whether H. cydno and H. pachinus, species closely related to H. melpomene, use this same switch locus to generate their highly divergent red and brown color pattern elements. Using an F2 intercross between H. cydno and H. pachinus, we first map the genomic positions of two novel red/brown wing pattern elements; the G locus, which controls the presence of red vs brown at the base of the ventral wings, and the Br locus, which controls the presence vs absence of a brown oval pattern on the ventral hind wing. The results reveal that the G locus is tightly linked to markers in the genomic interval that controls red wing pattern elements of H. erato and H. melpomene. Br is on the same linkage group but approximately 26 cM away. Next, we analyze fine-scale patterns of genetic differentiation and linkage disequilibrium throughout the G locus candidate interval in H. cydno, H. pachinus and H. melpomene, and find evidence for elevated differentiation between H. cydno and H. pachinus, but no localized signature of association. Overall, these results indicate that the G locus maps to the same interval as the locus controlling red patterning in H. melpomene and H. erato. This, in turn, suggests that the genes controlling red pattern elements may be homologous across Heliconius, supporting the hypothesis that Heliconius butterflies use a limited suite of conserved genetic switch loci to generate both convergent and divergent wing patterns.

TECHNICAL ADVANCES: Effects of genotyping protocols on success and errors in identifying individual river otters (Lontra canadensis) from their faeces.

PubMed

Hansen, Heidi; Ben-David, Merav; McDonald, David B

2008-03-01

In noninvasive genetic sampling, when genotyping error rates are high and recapture rates are low, misidentification of individuals can lead to overestimation of population size. Thus, estimating genotyping errors is imperative. Nonetheless, conducting multiple polymerase chain reactions (PCRs) at multiple loci is time-consuming and costly. To address the controversy regarding the minimum number of PCRs required for obtaining a consensus genotype, we compared consumer-style the performance of two genotyping protocols (multiple-tubes and 'comparative method') in respect to genotyping success and error rates. Our results from 48 faecal samples of river otters (Lontra canadensis) collected in Wyoming in 2003, and from blood samples of five captive river otters amplified with four different primers, suggest that use of the comparative genotyping protocol can minimize the number of PCRs per locus. For all but five samples at one locus, the same consensus genotypes were reached with fewer PCRs and with reduced error rates with this protocol compared to the multiple-tubes method. This finding is reassuring because genotyping errors can occur at relatively high rates even in tissues such as blood and hair. In addition, we found that loci that amplify readily and yield consensus genotypes, may still exhibit high error rates (7-32%) and that amplification with different primers resulted in different types and rates of error. Thus, assigning a genotype based on a single PCR for several loci could result in misidentification of individuals. We recommend that programs designed to statistically assign consensus genotypes should be modified to allow the different treatment of heterozygotes and homozygotes intrinsic to the comparative method. © 2007 The Authors.

FaRXf1: a locus conferring resistance to angular leaf spot caused by Xanthomonas fragariae in octoploid strawberry.

PubMed

Roach, Jack A; Verma, Sujeet; Peres, Natalia A; Jamieson, Andrew R; van de Weg, W Eric; Bink, Marco C A M; Bassil, Nahla V; Lee, Seonghee; Whitaker, Vance M

2016-06-01

Angular leaf spot is a devastating bacterial disease of strawberry. Resistance from two wild accessions is highly heritable and controlled by a major locus on linkage group 6D. Angular leaf spot caused by Xanthomonas fragariae is the only major bacterial disease of cultivated strawberry (Fragaria ×ananassa). While this disease may cause reductions of up to 8 % of marketable yield in Florida winter annual production, no resistant cultivars have been commercialized. Wild accessions US4808 and US4809 were previously identified as resistant to the four genetic clades of X. fragariae, and introgression of the trait into commercial quality perennial-type germplasm was initiated. Previous reports indicated high heritability for the trait but proposed both single-locus and multi-locus inheritance models. The objective of this study was to determine the mode of inheritance of resistance, to identify causal loci, and to begin introgression of resistance into Florida-adapted germplasm. Resistance was observed in two years of field trials with inoculated plants that assayed four full-sib families descended from US4808 to US4809. Resistance segregated 1:1 in all families indicating control by a dominant allele at a single locus. Using a selective genotyping approach with the IStraw90 Axiom(®) SNP array and pedigree-based QTL detection, a single major-effect QTL was identified in two full-sib families, one descended from each resistant accession. High-resolution melt curve analysis validated the presence of the QTL in separate populations. The QTL was delimited to the 33.1-33.6 Mbp (F. vesca vesca v1.1 reference) and 34.8-35.3 Mbp (F. vesca bracteata v2.0 reference) regions of linkage group 6D for both resistance sources and was designated FaRXf1. Characterization of this locus will facilitate marker-assisted selection toward the development of resistant cultivars.

Empower Me? Yes, Please, But in My Way: Different Patterns of Experiencing Empowerment in Patients with Chronic Conditions.

PubMed

Suárez Vázquez, Ana; Del Río Lanza, Ana Belén; Suárez Álvarez, Leticia; Vázquez Casielles, Rodolfo

2017-07-01

Empowerment is a widely used word within the realm of health care. This is especially true in the case of patients living with a chronic illness, who may be active participants and learn to manage their disease, irrespective of their desires or preferences. This article focuses on the empowering experience of patients with chronic conditions. We have built on earlier research that explains the factors that mediate communication between health care professionals and patients: patient participation, patient impact, meaning, health care professionals' information provision, health care professionals' emotional support, health care professionals' attentive listening, health care professionals' trust, and patient collaboration. We propose a new model for detecting types of patients who differ in the way they live their empowering experience. Using survey data from a sample of 181 patients of hemophilia, we found two types of patients: patients with an inner locus of empowerment and patients with an outer locus of empowerment. We conclude by discussing different strategies for fostering the sense of power in each of these types of patients.

Linkage of autosomal recessive primary congenital glaucoma to the GLC3A locus in Roms (Gypsies) from Slovakia.

PubMed

Plásilová, M; Feráková, E; Kádasi, L; Poláková, H; Gerinec, A; Ott, J; Ferák, V

1998-01-01

The autosomal recessive form of primary congenital glaucoma (gene symbol GLC3) has been recently mapped to two different loci, GLC3A (at 2p21), and GLC3B (at 1p36), respectively, on families of Turkish and Saudi Arabian provenance. This disorder is known to occur with an extremely high incidence in Roms (Gypsies) in Slovakia. We performed a standard linkage analysis on a sample of 7 Slovak Gypsy families comprising 18 affected members, and found significant linkage with four STR markers from the chromosomal region of 2p21 (D2S1788, D2S1346, D2S2328, and D2S1356), without heterogeneity. This finding demonstrates that in the Rom population of Slovakia, primary congenital glaucoma is due to the locus GLC3A, and consequently, to the mutation(s) in the cytochrome P4501B1 gene, which has been recently identified as the principal cause of the disease. Roms represent the third population, in which the disorder has been mapped to GLC3A.

[Multiple-locus variable number tandem repeat analysis of Bordetella pertussis strains collected in the Czech Republic in 1967-2015: spread of a variant adapted to the population with a high vaccination coverage].

PubMed

Lžičařová, D; Zavadilová, J; Musílek, M; Jandová, Z; Křížová, P; Fabiánová, K

To perform multiple-locus variable number tandem repeat analysis (MLVA) of B. pertussis strains from the collection of the National Reference Laboratory for Diphtheria and Pertussis (NRL/DIPE), National Institute of Public Health (NIPH), Prague. The study strains were isolated from clinical specimens collected mostly in the Czech Republic over a nearly 50-year period from 1967 to 2015 (June). The isolates from three periods characterized by different vaccination strategies and trends in pertussis are compared for genetic diversity and distribution of MLVA types (MT). Based on the results obtained, the suitability for use of MLVA in the analysis of epidemic outbreaks of B. pertussis in the Czech Republic is considered. DNA samples extracted from B. pertussis strains included in the present study were examined by MLVA using the standard protocol. Data were processed by means of the eBURST algorithm and the calculation of the Simpson diversity index (DI) was used for the statistical analysis. Data were analyzed as a whole and also separately for strains from the three periods: 1967-1980, 1990-2007, and 2008-2015 (June). Fourteen different MT were detected in the study strains, with three of them not being reported before. The most common MTs were MT27 and MT29. MT29 was predominant in 1967-1980 while MT27 was the most prevalent in 1990-2007 and 2008-2015 (June). The DI was the lowest (0.49) in 2008-2015 (June), and comparably higher DIs were calculated for the two previous periods (i.e. 0.667 for 1967-1980 and 0.654 for 1990-2007). MLVA revealed a decrease in genetic diversity and shifts in MT distribution of B. pertussis strains isolated from clinical specimens in the Czech Republic from 1967 to 2015 (June). These shifts in the Czech Republic can be characterized as a progressive increase in global MTs at the expense of the locally unique ones. The most common MT, similarly to other geographical areas with long-term high vaccination coverage, is MT27. The results of MLVA of 136 B. pertussis strains can provide a background for using this method in molecular epidemiological analysis of smaller groups of strains.

The autosomal dominant familial exudative vitreoretinopathy locus maps on 11q and is closely linked to D11S533

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

Li, Yuen; Schwinger, D.; Gal, A.

1992-10-01

Autosomal dominant familial exudative vitreoretinopathy (adFEVR) is a hereditary disorder characterized by the incomplete vascularization of the peripheral retina. The primary biochemical defect in adFEVR is unknown. The adFEVR locus has tentatively been assigned to 11q by linkage studies. The authors report the results of an extended multipoint linkage analysis of two families with adFEVR by using five markers (INT2, D11S533, D11S527, D11S35, and CD3D) from 11q13-q23. Pairwise linkage data obtained in the two families were rather similar and hence have not provided evidence for genetic heterogeneity. The highest compiled two-point lod score (3.67, at a recombination fraction of .07)more » was obtained for the disease locus versus D11S533. Multipoint analyses showed that the adFEVR locus maps most likely, with a maximum location score of over 20, between D11S533/D11S526 and D11S35, at recombination rates of .147 and .104, respectively. Close linkage without recombination (maximum lod score 11.26) has been found between D11S533 and D11S526. 15 refs., 3 figs., 4 tabs.« less

Erythrocyte phosphofructokinase in rat strains with genetically determined differences in 2,3-diphosphoglycerate levels.

PubMed

Noble, N A; Tanaka, K R

1981-02-01

We have studied the erythrocyte enzyme phosphofructokinase (PFK) from two strains of Long-Evans rats with genetically determined differences in erythrocyte 2,3-diphosphoglycerate (DPG) levels. The DPG difference is due to two alleles at one locus. With one probable exception, the genotype at this locus is always associated with the hemoglobin (Hb) electrophoretic phenotype, due to a polymorphism at the III beta-globin locus. The enzyme PFK has been implicated in the DPG difference because glycolytic intermediate levels suggest that this enzyme has a higher in vivo activity in High-DPG strain rats, although the total PFK activity does not differ. We report here that partially purified erythrocyte PFK from Low-DPG strain cells is inhibited significantly more at physiological levels of DPG (P less than 0.01) than PFK from High-DPG strain erythrocytes. Citrate and adenosine triphosphate also inhibit the Low-DPG enzyme more than the High-DPG enzyme. Therefore, a structurally different PFK, with a greater sensitivity to inhibitors, may explain the lower DPG and ATP levels observed in Low-DPG strain animals. These data support a two-locus (Hb and PFK) hypothesis and provide a gene marker to study the underlying genetic and physiologic relationships of these loci.

An efficient Bayesian meta-analysis approach for studying cross-phenotype genetic associations

PubMed Central

Majumdar, Arunabha; Haldar, Tanushree; Bhattacharya, Sourabh; Witte, John S.

2018-01-01

Simultaneous analysis of genetic associations with multiple phenotypes may reveal shared genetic susceptibility across traits (pleiotropy). For a locus exhibiting overall pleiotropy, it is important to identify which specific traits underlie this association. We propose a Bayesian meta-analysis approach (termed CPBayes) that uses summary-level data across multiple phenotypes to simultaneously measure the evidence of aggregate-level pleiotropic association and estimate an optimal subset of traits associated with the risk locus. This method uses a unified Bayesian statistical framework based on a spike and slab prior. CPBayes performs a fully Bayesian analysis by employing the Markov Chain Monte Carlo (MCMC) technique Gibbs sampling. It takes into account heterogeneity in the size and direction of the genetic effects across traits. It can be applied to both cohort data and separate studies of multiple traits having overlapping or non-overlapping subjects. Simulations show that CPBayes can produce higher accuracy in the selection of associated traits underlying a pleiotropic signal than the subset-based meta-analysis ASSET. We used CPBayes to undertake a genome-wide pleiotropic association study of 22 traits in the large Kaiser GERA cohort and detected six independent pleiotropic loci associated with at least two phenotypes. This includes a locus at chromosomal region 1q24.2 which exhibits an association simultaneously with the risk of five different diseases: Dermatophytosis, Hemorrhoids, Iron Deficiency, Osteoporosis and Peripheral Vascular Disease. We provide an R-package ‘CPBayes’ implementing the proposed method. PMID:29432419

A New Perspective on Polyploid Fragaria (Strawberry) Genome Composition Based on Large-Scale, Multi-Locus Phylogenetic Analysis.

PubMed

Yang, Yilong; Davis, Thomas M

2017-12-01

The subgenomic compositions of the octoploid (2n = 8× = 56) strawberry (Fragaria) species, including the economically important cultivated species Fragaria x ananassa, have been a topic of long-standing interest. Phylogenomic approaches utilizing next-generation sequencing technologies offer a new window into species relationships and the subgenomic compositions of polyploids. We have conducted a large-scale phylogenetic analysis of Fragaria (strawberry) species using the Fluidigm Access Array system and 454 sequencing platform. About 24 single-copy or low-copy nuclear genes distributed across the genome were amplified and sequenced from 96 genomic DNA samples representing 16 Fragaria species from diploid (2×) to decaploid (10×), including the most extensive sampling of octoploid taxa yet reported. Individual gene trees were constructed by different tree-building methods. Mosaic genomic structures of diploid Fragaria species consisting of sequences at different phylogenetic positions were observed. Our findings support the presence in octoploid species of genetic signatures from at least five diploid ancestors (F. vesca, F. iinumae, F. bucharica, F. viridis, and at least one additional allele contributor of unknown identity), and questions the extent to which distinct subgenomes are preserved over evolutionary time in the allopolyploid Fragaria species. In addition, our data support divergence between the two wild octoploid species, F. virginiana and F. chiloensis. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Taenia solium, Taenia saginata, Taenia asiatica, their hybrids and other helminthic infections occurring in a neglected tropical diseases' highly endemic area in Lao PDR

PubMed Central

Sato, Megumi; Yanagida, Tetsuya; Waikagul, Jitra; Pongvongsa, Tiengkham; Sako, Yasuhito; Sanguankiat, Surapol; Yoonuan, Tipparayat; Kounnavang, Sengchanh; Kawai, Satoru; Ito, Akira; Okamoto, Munehiro; Moji, Kazuhiko

2018-01-01

Most part of Southeast Asia is considered endemic for human-infecting Taenia tapeworms; Taenia solium, T. saginata, and T. asiatica. However, until now there was no report of the occurrence of human cases of T. asiatica in Lao PDR. This study, conducted in Savannakhet Province, Lao PDR, microscopically examined a total of 470 fecal samples by Kato Katz method and found 86% of people harboring at least one helminth. Hookworms were detected in 56% of the samples besides Opisthorchis like eggs (42%), Trichuris trichiura (27%), Ascaris spp. (14%), and Taenia spp. (4%) eggs. Serology for cysticercosis showed 6.8% positives with results varying from 3% to 14.3% in Ethnic School students and Kalouk Kao village respectively. Species-specific PCR targeting mitochondrial DNA (mtDNA) of 28 tapeworms, recovered from 16 patients, revealed T. solium (n = 2), T. saginata (n = 21), and T. asiatica (n = 5). Two patients were confirmed to be coinfected with T. saginata and T. asiatica, indicating the endemicity of the 3 human Taenia in Lao PDR. However, nucleotide sequencing of a nuclear DNA gene, DNA polymerase delta (pold) revealed that all the tapeworms identified as T. asiatica using mtDNA had T. saginata type allele at pold locus, demonstrating that they are not “pure T. asiatica” but the hybrid descendants between the two species, confirming the wide distribution of hybrids of T. saginata/ T. asiatica in Southeast Asia. The high prevalence of several helminthic NTDs in east Savannakhet area even with conventional control measures indicates the importance to establish wide and multifaceted health programs to sustainably improve the quality of life of the populations living in these communities. PMID:29420601

Diverse Burkholderia Species Isolated from Soils in the Southern United States with No Evidence of B. pseudomallei.

PubMed

Hall, Carina M; Busch, Joseph D; Shippy, Kenzie; Allender, Christopher J; Kaestli, Mirjam; Mayo, Mark; Sahl, Jason W; Schupp, James M; Colman, Rebecca E; Keim, Paul; Currie, Bart J; Wagner, David M

2015-01-01

The global distribution of the soil-dwelling bacterium Burkholderia pseudomallei, causative agent of melioidosis, is poorly understood. We used established culturing methods developed for B. pseudomallei to isolate Burkholderia species from soil collected at 18 sampling sites in three states in the southern United States (Arizona (n = 4), Florida (n = 7), and Louisiana (n = 7)). Using multi-locus sequence typing (MLST) of seven genes, we identified 35 Burkholderia isolates from these soil samples. All species belonged to the B. cepacia complex (Bcc), including B. cenocepacia, B. cepacia, B. contaminans, B. diffusa, B. metallica, B. seminalis, B. vietnamiensis and two unnamed members of the Bcc. The MLST analysis provided a high level of resolution among and within these species. Despite previous clinical cases within the U.S. involving B. pseudomallei and its close phylogenetic relatives, we did not isolate any of these taxa. The Bcc contains a number of opportunistic pathogens that cause infections in cystic fibrosis patients. Interestingly, we found that B. vietnamiensis was present in soil from all three states, suggesting it may be a common component in southern U.S. soils. Most of the Burkholderia isolates collected in this study were from Florida (30/35; 86%), which may be due to the combination of relatively moist, sandy, and acidic soils found there compared to the other two states. We also investigated one MLST gene, recA, for its ability to identify species within Burkholderia. A 365bp fragment of recA recovered nearly the same species-level identification as MLST, thus demonstrating its cost effective utility when conducting environmental surveys for Burkholderia. Although we did not find B. pseudomallei, our findings document that other diverse Burkholderia species are present in soils in the southern United States.

Investigating the genetic diversity of Echinococcus granulosus sensu stricto with new microsatellites.

PubMed

Umhang, Gérald; Grenouillet, Frédéric; Bastid, Vanessa; M'Rad, Selim; Valot, Benoît; Oudni-M'Rad, Myriam; Babba, Hamouda; Boué, Franck

2018-06-18

Cystic echinococcosis is a zoonotic disease with worldwide distribution caused by the larval stage of the Cestode parasite Echinococcus granulosus sensu lato. Due to the predominance or even the exclusive presence of E. granulosus sensu stricto (s.s.) among E. granulosus species in many areas, the genetic diversity needs to be further investigated at the species level to better understand the inter- and intra-focus epidemiological features. Short sequences of mitochondrial or nuclear genes generally lack or have limited discriminatory power, hindering the detection of polymorphisms to reflect geographically based peculiarities and/or any history of infection. A high discriminatory power can only be reached by sequencing complete or near complete mitogenomes or relatively long nuclear sequences, which is time-consuming and onerous. To overcome this issue, a systematic research for single-locus microsatellites was performed on the nuclear genome of E. granulosus s.s. in order to investigate its intra-species genetic diversity. Two microsatellites, EgSca6 and EgSca11, were selected and characterized. The test of a panel of 75 cystic echinococcosis samples revealed a very high discrimination index of 0.824 for EgSca6, 0.987 for EgSca11, and 0.994 when multiplexing both microsatellites. Testing cystic echinococcosis samples from both liver and lungs in five sheep revealed that these two microsatellites appear to be of particular interest for investigating genetic diversity at the intra-individual host level. As this method has many advantages compared to classical sequencing, the availability of other targets means that it is potentially possible to constitute a panel facilitating large-scale molecular epidemiology studies for E. granulosus s.l.

Diverse Burkholderia Species Isolated from Soils in the Southern United States with No Evidence of B. pseudomallei

PubMed Central

Hall, Carina M.; Busch, Joseph D.; Shippy, Kenzie; Allender, Christopher J.; Kaestli, Mirjam; Mayo, Mark; Sahl, Jason W.; Schupp, James M.; Colman, Rebecca E.; Keim, Paul; Currie, Bart J.; Wagner, David M.

2015-01-01

The global distribution of the soil-dwelling bacterium Burkholderia pseudomallei, causative agent of melioidosis, is poorly understood. We used established culturing methods developed for B. pseudomallei to isolate Burkholderia species from soil collected at 18 sampling sites in three states in the southern United States (Arizona (n = 4), Florida (n = 7), and Louisiana (n = 7)). Using multi-locus sequence typing (MLST) of seven genes, we identified 35 Burkholderia isolates from these soil samples. All species belonged to the B. cepacia complex (Bcc), including B. cenocepacia, B. cepacia, B. contaminans, B. diffusa, B. metallica, B. seminalis, B. vietnamiensis and two unnamed members of the Bcc. The MLST analysis provided a high level of resolution among and within these species. Despite previous clinical cases within the U.S. involving B. pseudomallei and its close phylogenetic relatives, we did not isolate any of these taxa. The Bcc contains a number of opportunistic pathogens that cause infections in cystic fibrosis patients. Interestingly, we found that B. vietnamiensis was present in soil from all three states, suggesting it may be a common component in southern U.S. soils. Most of the Burkholderia isolates collected in this study were from Florida (30/35; 86%), which may be due to the combination of relatively moist, sandy, and acidic soils found there compared to the other two states. We also investigated one MLST gene, recA, for its ability to identify species within Burkholderia. A 365bp fragment of recA recovered nearly the same species-level identification as MLST, thus demonstrating its cost effective utility when conducting environmental surveys for Burkholderia. Although we did not find B. pseudomallei, our findings document that other diverse Burkholderia species are present in soils in the southern United States. PMID:26600238

Effects of chromatic image statistics on illumination induced color differences.

PubMed

Lucassen, Marcel P; Gevers, Theo; Gijsenij, Arjan; Dekker, Niels

2013-09-01

We measure the color fidelity of visual scenes that are rendered under different (simulated) illuminants and shown on a calibrated LCD display. Observers make triad illuminant comparisons involving the renderings from two chromatic test illuminants and one achromatic reference illuminant shown simultaneously. Four chromatic test illuminants are used: two along the daylight locus (yellow and blue), and two perpendicular to it (red and green). The observers select the rendering having the best color fidelity, thereby indirectly judging which of the two test illuminants induces the smallest color differences compared to the reference. Both multicolor test scenes and natural scenes are studied. The multicolor scenes are synthesized and represent ellipsoidal distributions in CIELAB chromaticity space having the same mean chromaticity but different chromatic orientations. We show that, for those distributions, color fidelity is best when the vector of the illuminant change (pointing from neutral to chromatic) is parallel to the major axis of the scene's chromatic distribution. For our selection of natural scenes, which generally have much broader chromatic distributions, we measure a higher color fidelity for the yellow and blue illuminants than for red and green. Scrambled versions of the natural images are also studied to exclude possible semantic effects. We quantitatively predict the average observer response (i.e., the illuminant probability) with four types of models, differing in the extent to which they incorporate information processing by the visual system. Results show different levels of performance for the models, and different levels for the multicolor scenes and the natural scenes. Overall, models based on the scene averaged color difference have the best performance. We discuss how color constancy algorithms may be improved by exploiting knowledge of the chromatic distribution of the visual scene.

Somatic INK4a-ARF locus mutations: a significant mechanism of gene inactivation in squamous cell carcinomas of the head and neck.

PubMed

Poi, M J; Yen, T; Li, J; Song, H; Lang, J C; Schuller, D E; Pearl, D K; Casto, B C; Tsai, M D; Weghorst, C M

2001-01-01

The INK4a-ARF locus is located on human chromosome 9p21 and is known to encode two functionally distinct tumor-suppressor genes. The p16(INK4a) (p16) tumor-suppressor gene product is a negative regulator of cyclin-dependent kinases 4 and 6, which in turn positively regulate progression of mammalian cells through the cell cycle. The p14(ARF) tumor-suppressor gene product specifically interacts with human double minute 2, leading to the subsequent stabilization of p53 and G(1) arrest. Previous investigations analyzing the p16 gene in squamous cell carcinomas of the head and neck (SCCHNs) have suggested the predominate inactivating events to be homozygous gene deletions and hypermethylation of the p16 promoter. Somatic mutational inactivation of p16 has been reported to be low (0-10%, with a combined incidence of 25 of 279, or 9%) and to play only a minor role in the development of SCCHN. The present study examined whether this particular mechanism of INK4a/ARF inactivation, specifically somatic mutation, has been underestimated in SCCHN by determining the mutational status of the p16 and p14(ARF) genes in 100 primary SCCHNs with the use of polymerase chain reaction technology and a highly sensitive, nonradioactive modification of single-stranded conformational polymorphism (SSCP) analysis termed "cold" SSCP. Exons 1alpha, 1beta, and 2 of INK4a/ARF were amplified using intron-based primers or a combination of intron- and exon-based primers. A total of 27 SCCHNs (27%) exhibited sequence alterations in this locus, 22 (22%) of which were somatic sequence alterations and five (5%) of which were a single polymorphism in codon 148. Of the 22 somatic alterations, 20 (91%) directly or indirectly involved exon 2, and two (9%) were located within exon 1alpha. No mutations were found in exon 1beta. All 22 somatic mutations would be expected to yield altered p16 proteins, but only 15 of them should affect p14(ARF) proteins. Specific somatic alterations included microdeletions or insertions (nine of 22, 41%), a microrearrangement (one of 22, 5%), and single nucleotide substitutions (12 of 22, 56%). In addition, we analyzed the functional characteristics of seven unique mutant p16 proteins identified in this study by assessing their ability to inhibit cyclin-dependent kinase 4 activity. Six of the seven mutant proteins tested exhibited reduced function compared with wild-type p16, ranging from minor decreases of function (twofold to eightfold) in four samples to total loss of function (29- to 38-fold decrease) in two other samples. Overall, somatic mutation of the INK4a/ARF tumor suppressor locus, resulting in functionally deficient p16 and possibly p14(ARF) proteins, seems to be a prevalent event in the development of SCCHN. Mol. Carcinog. 30:26-36, 2001. Copyright 2001 Wiley-Liss, Inc.

Social and cultural influences among Mexican border entrepreneurs.

PubMed

Díaz Bretones, Francisco; Cappello, Héctor M; Garcia, Pedro A

2009-06-01

Social and cultural conditions (including U.S. border and inland influence, role models within the family, and educational background) which affect locus of control and achievement motivation among Mexican entrepreneurs were explored among 64 selected entrepreneurs in two Mexican towns, one on the Mexico-U.S. border, the other located inland. Analyses showed that the border subsample scored higher on External locus of control; however, in both subsamples the father was an important element in the locus of control variable and the entrepreneur status. No statistically significant mean difference was noted for achievement motivation. Practical applications and limitations are discussed.

Contribution for an African autosomic STR database (AmpF/STR Identifiler and Powerplex 16 System) and a report on genotypic variations.

PubMed

Alves, Cíntia; Gusmão, Leonor; Damasceno, Albertino; Soares, Benilde; Amorim, António

2004-01-28

Allele frequencies, together with some parameters of forensic interest, for 17 STRs included in the AmpF/STR Identifiler (CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, TH01, TPO and VWA) and Powerplex 16 System (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, Penta D, Penta E, TH01, TPO and VWA) were estimated from a sample of 135-144 unrelated individuals from Mozambique. No deviations from Hardy-Weinberg equilibrium were observed with the exception of the FGA locus (using the Bonferroni correction for the number of loci analysed, the departure observed at this locus was not significant). Comparative analyses between our population data and other African databases, namely Promega's African-Americans, AB Applied Biosystems African-Americans and two other population samples from Mozambique and Guiné Bissau, are presented and discussed. Genotype inconsistencies between both commercial kits (for D16S539 and D8S1179) and other genotypic variations (three-banded allele patterns for TPO) are also reported.

Development of microsatellite markers for Anadenanthera colubrina (Leguminosae), a neotropical tree species.

PubMed

Feres, Juliana Massimino; Monteiro, Mariza; Zucchi, Maria I; Pinheiro, José B; Mestriner, Moacyr A; Alzate-Marin, Ana Lilia

2012-04-01

We developed and characterized nuclear microsatellite markers for Anadenanthera colubrina, a tropical tree species widely distributed in South America. Leaf samples of mature A. colubrina trees, popularly called "angico," were collected from an area that is greatly impacted by agricultural practices in the region of Ribeirão Preto in São Paulo State in southeastern Brazil. Twenty simple sequence repeat (SSR) markers were developed, 14 of which had polymorphic loci. A total of 96 alleles were detected with an average of 6.86 alleles per polymorphic locus. The expected heterozygosity, calculated at polymorphic loci, ranged from 0.18 to 0.83. Finally, we demonstrated that 18 loci were cross-amplified in A. peregrina. A total of 14 polymorphic markers suggest a high potential for genetic diversity, gene flow, and mating system analyses in A. colubrina.

Attitude towards littering as a mediator of the relationship between personality attributes and responsible environmental behavior

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

Ojedokun, Oluyinka, E-mail: yinkaoje2004@yahoo.com

Highlights: > Independently, altruism and locus of control contributed significantly toward attitude towards littering. > Altruism and locus of control jointly contributed significantly to attitude towards littering. > The results further show a significant joint influence of altruism and locus of control on REB. > The independent contributions reveal that altruism and locus of control contribute significantly to REB. > Attitude towards littering mediates the relationship between locus of control and REB. - Abstract: The study tested whether attitude towards littering mediates the relationship between personality attributes (altruism and locus of control) and responsible environmental behavior (REB) among some residentsmore » of Ibadan metropolis, Nigeria. Using multistage sampling technique, measures of each construct were administered to 1360 participants. Results reveal significant independent and joint influence of personality attributes on attitude towards littering and responsible environmental behavior, respectively. Attitude towards littering also mediates the relationship between personality characteristics and REB. These findings imply that individuals who possess certain desirable personality characteristics and who have unfavorable attitude towards littering have more tendencies to engage in pro-environmental behavior. Therefore, stakeholders who have waste management as their priority should incorporate this information when guidelines for public education and litter prevention programs are being developed. It is suggested that psychologists should be involved in designing of litter prevention strategies. This will ensure the inclusion of behavioral issues in such strategies. An integrated approach to litter prevention that combines empowerment, cognitive, social, and technical solutions is recommended as the most effective tool of tackling the litter problem among residents of Ibadan metropolis.« less

Identification and Characterization of Genomic Amplifications in Ovarian Serous Carcinoma

DTIC Science & Technology

2008-01-01

lower cost. As a result, we have analyzed more than 40 affinity purified ovarian serous tumors and our results demonstrated that CCNE1, Notch3 , Rsf-1...serous tumors. In addition, we have further characterized the biological functions of the two of the commonly amplified genes, Notch3 and Rsf-1, in...analyses, we have focused on two of the most frequently amplified regions, 11q13.2 (Rsf-1 locus) and 19p13 ( Notch3 locus), for detailed mapping and

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.

STBase: One Million Species Trees for Comparative Biology

PubMed Central

McMahon, Michelle M.; Deepak, Akshay; Fernández-Baca, David; Boss, Darren; Sanderson, Michael J.

2015-01-01

Comprehensively sampled phylogenetic trees provide the most compelling foundations for strong inferences in comparative evolutionary biology. Mismatches are common, however, between the taxa for which comparative data are available and the taxa sampled by published phylogenetic analyses. Moreover, many published phylogenies are gene trees, which cannot always be adapted immediately for species level comparisons because of discordance, gene duplication, and other confounding biological processes. A new database, STBase, lets comparative biologists quickly retrieve species level phylogenetic hypotheses in response to a query list of species names. The database consists of 1 million single- and multi-locus data sets, each with a confidence set of 1000 putative species trees, computed from GenBank sequence data for 413,000 eukaryotic taxa. Two bodies of theoretical work are leveraged to aid in the assembly of multi-locus concatenated data sets for species tree construction. First, multiply labeled gene trees are pruned to conflict-free singly-labeled species-level trees that can be combined between loci. Second, impacts of missing data in multi-locus data sets are ameliorated by assembling only decisive data sets. Data sets overlapping with the user’s query are ranked using a scheme that depends on user-provided weights for tree quality and for taxonomic overlap of the tree with the query. Retrieval times are independent of the size of the database, typically a few seconds. Tree quality is assessed by a real-time evaluation of bootstrap support on just the overlapping subtree. Associated sequence alignments, tree files and metadata can be downloaded for subsequent analysis. STBase provides a tool for comparative biologists interested in exploiting the most relevant sequence data available for the taxa of interest. It may also serve as a prototype for future species tree oriented databases and as a resource for assembly of larger species phylogenies from precomputed trees. PMID:25679219

Complex segregation analysis of blood pressure and heart rate measured before and after a 20-week endurance exercise training program: the HERITAGE Family Study.

PubMed

An, P; Rice, T; Pérusse, L; Borecki, I B; Gagnon, J; Leon, A S; Skinner, J S; Wilmore, J H; Bouchard, C; Rao, D C

2000-05-01

Complex segregation analysis of baseline resting blood pressure (BP) and heart rate (HR) and their responses to training (post-training minus baseline) were performed in a sample of 482 individuals from 99 white families who participated in the HERITAGE Family Study. Resting BP and HR were measured at baseline and after a 20-week training program. Baseline resting BP and HR were age-adjusted and age-BMI-adjusted, and the responses to training were age-adjusted and age-baseline-adjusted, within four gender-by-generation groups. This study also analyzed the responses to training in two subsets of families: (1) the so-called "high" subsample, 45 families (216 individuals) with at least one member whose baseline resting BP is in the high end of the normal BP range (the upper 95th percentile: systolic BP [SBP] > or = 135 or diastolic BP [DBP] > or = 80 mm Hg); and (2) the so-called "nonhigh" subsample, the 54 remaining families (266 individuals). Baseline resting SBP was influenced by a multifactorial component (23%), which was independent of body mass index (BMI). Baseline resting DBP was influenced by a putative recessive locus, which accounted for 31% of the variance. In addition to the major gene effect, which may impact BMI as well, baseline resting DBP was also influenced by a multifactorial component (29%). Baseline resting HR was influenced by a putative dominant locus independent of BMI, which accounted for 31% of the variance. For the responses to training, no familiality was found in the whole sample or in the nonhigh subsample. However, in the high subsample, resting SBP response to training was influenced by a putative recessive locus, which accounted for 44% of the variance. No familiality was found for resting DBP response to training. Resting HR response to training was influenced by a major effect (accounting for 35% of the variance), with an ambiguous transmission from parents to offspring.

[HL-A antigen distribution in duodenal ulcer patients].

PubMed

Ilieva, P; Minev, M; Etŭrska, M

1980-01-01

The incidence of HLA-antigens was studied in 405 patients with clinically, roentgenologically and gastroscopically confirmed ulcer of duodenum and in 1085 controls, healthy subjects. Increased incidence of both antigens from locus B was established among the patients: HLA-B17 and HLA-BW21. A reduction of HLA-A3 incidence was found from the antigens of locus A. In the determination of incidence of HLA antigenes, depending on blood grouping ABO both of patients and healthy subjects, it was established that antigen HLA-A3 is less frequent in the patients with blood group B, whereas antigen HLA-B12 is found more often among the patients with blood group A.

Epidemiological evidence for the role of the haemoglobin receptor, HmbR, in meningococcal virulence

PubMed Central

Harrison, Odile B.; Evans, Nicholas J.; Blair, Jessica M.; Grimes, Holly S.; Tinsley, Colin R.; Nassif, Xavier; Kriz, Paula; Ure, Roisin; Gray, Steve J.; Derrick, Jeremy P.; Maiden, Martin C.J.; Feavers, Ian M.

2009-01-01

The distribution of the haemoglobin receptor gene (hmbR) was investigated in disease and carried Neisseria meningitidis isolates revealing that the gene occurred at a significantly higher frequency in disease isolates compared to those obtained from carriage. Where hmbR was absent, the locus was occupied by the cassettes exl2 or exl3, or with a “pseudo hmbR” gene designated exl4. The hmbR locus in published N. meningitidis genomes, as well as N. gonorrhoeae and N. lactamica ST-640, exhibited characteristics of a pathogenicity island. These data are consistent with a role for the hmbR gene in meningococcal disease. PMID:19476432