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1

Clinical Significance of the CCR5delta32 Allele in Hepatitis C  

PubMed Central

Background The CCR5 receptor, expressed on Th1 cells, may influence clinical outcomes of HCV infection. We explored a possible link between a CCR5 32-base deletion (CCR5delta32), resulting in the expression of a non-functioning receptor, and clinical outcomes of HCV infection. Methods CCR5 and HCV-related phenotypes were analysed in 1,290 chronically infected patients and 160 patients with spontaneous clearance. Results Carriage of the CCR5delta32 allele was observed in 11% of spontaneous clearers compared to 17% of chronically infected patients (OR?=?0.59, 95% CI interval 0.35–0.99, P?=?0.047). Carriage of this allele also tended to be observed more frequently among patients with liver inflammation (19%) compared to those without inflammation (15%, OR?=?1.38, 95% CI interval 0.99–1.95, P?=?0.06). The CCR5delta32 was not associated with sustained virological response (P?=?0.6), fibrosis stage (P?=?0.8), or fibrosis progression rate (P?=?0.4). Conclusions The CCR5delta32 allele appears to be associated with a decreased rate of spontaneous HCV eradication, but not with hepatitis progression or response to antiviral therapy. PMID:25191700

Morard, Isabelle; Clément, Sophie; Calmy, Alexandra; Mangia, Alessandra; Cerny, Andrea; De Gottardi, Andrea; Gorgievski, Meri; Heim, Markus; Malinverni, Raffaele; Moradpour, Darius; Müllhaupt, Beat; Semela, David; Pascarella, Stéphanie; Bochud, Pierre-Yves; Negro, Franco

2014-01-01

2

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

PubMed Central

Background In Europe, the north-south downhill cline frequency of the chemokine receptor CCR5 allele with a 32-bp deletion (CCR5-?32) raises interesting questions for evolutionary biologists. We had suggested first that, in the past, the European colonizers, principally Romans, might have been instrumental of a progressively decrease of the frequencies southwards. Indeed, statistical analyses suggested strong negative correlations between the allele frequency and historical parameters including the colonization dates by Mediterranean civilisations. The gene flows from colonizers to native populations were extremely low but colonizers are responsible of the spread of several diseases suggesting that the dissemination of parasites in naive populations could have induced a breakdown rupture of the fragile pathocenosis changing the balance among diseases. The new equilibrium state has been reached through a negative selection of the null allele. Results Most of the human diseases are zoonoses and cat might have been instrumental in the decrease of the allele frequency, because its diffusion through Europe was a gradual process, due principally to Romans; and that several cat zoonoses could be transmitted to man. The possible implication of a feline lentivirus (FIV) which does not use CCR5 as co-receptor is discussed. This virus can infect primate cells in vitro and induces clinical signs in macaque. Moreover, most of the historical regions with null or low frequency of CCR5-?32 allele coincide with historical range of the wild felid species which harbor species-specific FIVs. Conclusion We proposed the hypothesis that the actual European CCR5 allelic frequencies are the result of a negative selection due to a disease spreading. A cat zoonosis, could be the most plausible hypothesis. Future studies could provide if CCR5 can play an antimicrobial role in FIV pathogenesis. Moreover, studies of ancient DNA could provide more evidences regarding the implications of zoonoses in the actual CCR5-?32 distribution. PMID:18925940

Faure, Eric

2008-01-01

3

Dating the origin of the CCR5-Delta32 AIDS-resistance allele by the coalescence of haplotypes.  

PubMed Central

The CCR5-Delta32 deletion obliterates the CCR5 chemokine and the human immunodeficiency virus (HIV)-1 coreceptor on lymphoid cells, leading to strong resistance against HIV-1 infection and AIDS. A genotype survey of 4,166 individuals revealed a cline of CCR5-Delta32 allele frequencies of 0%-14% across Eurasia, whereas the variant is absent among native African, American Indian, and East Asian ethnic groups. Haplotype analysis of 192 Caucasian chromosomes revealed strong linkage disequilibrium between CCR5 and two microsatellite loci. By use of coalescence theory to interpret modern haplotype genealogy, we estimate the origin of the CCR5-Delta32-containing ancestral haplotype to be approximately 700 years ago, with an estimated range of 275-1,875 years. The geographic cline of CCR5-Delta32 frequencies and its recent emergence are consistent with a historic strong selective event (e.g. , an epidemic of a pathogen that, like HIV-1, utilizes CCR5), driving its frequency upward in ancestral Caucasian populations. PMID:9585595

Stephens, J C; Reich, D E; Goldstein, D B; Shin, H D; Smith, M W; Carrington, M; Winkler, C; Huttley, G A; Allikmets, R; Schriml, L; Gerrard, B; Malasky, M; Ramos, M D; Morlot, S; Tzetis, M; Oddoux, C; di Giovine, F S; Nasioulas, G; Chandler, D; Aseev, M; Hanson, M; Kalaydjieva, L; Glavac, D; Gasparini, P; Kanavakis, E; Claustres, M; Kambouris, M; Ostrer, H; Duff, G; Baranov, V; Sibul, H; Metspalu, A; Goldman, D; Martin, N; Duffy, D; Schmidtke, J; Estivill, X; O'Brien, S J; Dean, M

1998-01-01

4

The case for selection at CCR5-Delta32.  

PubMed

The C-C chemokine receptor 5, 32 base-pair deletion (CCR5-Delta32) allele confers strong resistance to infection by the AIDS virus HIV. Previous studies have suggested that CCR5-Delta32 arose within the past 1,000 y and rose to its present high frequency (5%-14%) in Europe as a result of strong positive selection, perhaps by such selective agents as the bubonic plague or smallpox during the Middle Ages. This hypothesis was based on several lines of evidence, including the absence of the allele outside of Europe and long-range linkage disequilibrium at the locus. We reevaluated this evidence with the benefit of much denser genetic maps and extensive control data. We find that the pattern of genetic variation at CCR5-Delta32 does not stand out as exceptional relative to other loci across the genome. Moreover using newer genetic maps, we estimated that the CCR5-Delta32 allele is likely to have arisen more than 5,000 y ago. While such results can not rule out the possibility that some selection may have occurred at C-C chemokine receptor 5 (CCR5), they imply that the pattern of genetic variation seen at CCR5-Delta32 is consistent with neutral evolution. More broadly, the results have general implications for the design of future studies to detect the signs of positive selection in the human genome. PMID:16248677

Sabeti, Pardis C; Walsh, Emily; Schaffner, Steve F; Varilly, Patrick; Fry, Ben; Hutcheson, Holli B; Cullen, Mike; Mikkelsen, Tarjei S; Roy, Jessica; Patterson, Nick; Cooper, Richard; Reich, David; Altshuler, David; O'Brien, Stephen; Lander, Eric S

2005-11-01

5

"Ground truth" for selection on CCR5-Delta32.  

PubMed

A much-celebrated story of positive selection in the human genome is the 32-bp deletion in the chemokine receptor CCR5, a variant that confers resistance to AIDS. This variant was postulated to be a relatively recent response to plague or smallpox. New research shows that the frequency of CCR5-Delta32 in Bronze Age samples is similar to that seen today, pushing the observed age of the allele back to at least 3000 and possibly 5000 years ago. Interestingly, the extent of heterozygosity, differentiation across populations and linkage disequilibrium in the CCR5 region is not dissimilar to other human genomic regions, challenging claims of recent positive selection. PMID:16678299

Hedrick, Philip W; Verrelli, Brian C

2006-06-01

6

Homozygous and Heterozygous CCR5-(DELTA)32 Genotypes Are Associated With Resistance to HIV Infection (Epidemiology)  

Microsoft Academic Search

Objective: To investigate evidence for resistance to HIV-1 infection associated with the heterozygous genotype CCR5 -+\\/(DELTA)32 and with the homozygous genotype CCR5-(DELTA)32\\/(DELTA)32, which results in a nonfunctional CCR5 receptor. Design: Cohort study of initially HIV-seronegative high-risk individuals from eight different cities. Enrollment data were analyzed to investigate the association of demographic factors and risk behaviors with CCR5 genotypes on the

Michael Marmor; Haynes W. Sheppard; Deborah Donnell

7

Resistance to human immunodeficiency virus type 1 (HIV-1) generated by lentivirus vector-mediated delivery of the CCR5{Delta}32 gene despite detectable expression of the HIV-1 co-receptors.  

PubMed

It has previously been demonstrated that there are two distinct mechanisms for genetic resistance to human immunodeficiency virus type 1 (HIV-1) conferred by the CCR5Delta32 gene: the loss of wild-type CCR5 surface expression and the generation of CCR5Delta32 protein, which interacts with CXCR4. To analyse the protective effects of long-term expression of the CCR5Delta32 protein, recombinant lentiviral vectors were used to deliver the CCR5Delta32 gene into human cell lines and primary peripheral blood mononuclear cells that had been immortalized by human T-cell leukemia virus type 1. Blasticidin S-resistant cell lines expressing the lentivirus-encoded CCR5Delta32 showed a significant reduction in HIV-1 Env-mediated fusion assays. It was shown that CD4(+) T lymphocytes expressing the lentivirus-encoded CCR5Delta32 gene were highly resistant to infection by a primary but not by a laboratory-adapted X4 strain, suggesting different infectivity requirements. In contrast to previous studies that analysed the CCR5Delta32 protective effects in a transient expression system, this study showed that long-term expression of CCR5Delta32 conferred resistance to HIV-1 despite cell-surface expression of the HIV co-receptors. The results suggest an additional unknown mechanism for generating the CCR5Delta32 resistance phenotype and support the hypothesis that the CCR5Delta32 protein acts as an HIV-suppressive factor by altering the stoichiometry of the molecules involved in HIV-1 entry. The lentiviral-CCR5Delta32 vectors offer a method of generating HIV-resistant cells by delivery of the CCR5Delta32 gene that may be useful for stem cell- or T-cell-based gene therapy for HIV-1 infection. PMID:18796731

Jin, Qingwen; Marsh, Jon; Cornetta, Kenneth; Alkhatib, Ghalib

2008-10-01

8

A comparison of type 2 diabetes risk allele load between African Americans and European Americans.  

PubMed

The prevalence of type 2 diabetes (T2D) is greater in populations of African descent compared to European-descent populations. Genetic risk factors may underlie the disparity in disease prevalence. Genome-wide association studies (GWAS) have identified >60 common genetic variants that contribute to T2D risk in populations of European, Asian, African and Hispanic descent. These studies have not comprehensively examined population differences in cumulative risk allele load. To investigate the relationship between risk allele load and T2D risk, 46 T2D single nucleotide polymorphisms (SNPs) in 43 loci from GWAS in European, Asian, and African-derived populations were genotyped in 1,990 African Americans (n = 963 T2D cases, n = 1,027 controls) and 1,644 European Americans (n = 719 T2D cases, n = 925 controls) ascertained and recruited using a common protocol in the southeast United States. A genetic risk score (GRS) was constructed from the cumulative risk alleles for each individual. In African American subjects, risk allele frequencies ranged from 0.024 to 0.964. Risk alleles from 26 SNPs demonstrated directional consistency with previous studies, and 3 SNPs from ADAMTS9, TCF7L2, and ZFAND6 showed nominal evidence of association (p < 0.05). African American individuals carried 38-67 (53.7 ± 4.0, mean ± SD) risk alleles. In European American subjects, risk allele frequencies ranged from 0.084 to 0.996. Risk alleles from 36 SNPs demonstrated directional consistency, and 10 SNPs from BCL11A, PSMD6, ADAMTS9, ZFAND3, ANK1, CDKN2A/B, TCF7L2, PRC1, FTO, and BCAR1 showed evidence of association (p < 0.05). European American individuals carried 38-65 (50.9 ± 4.4) risk alleles. African Americans have a significantly greater burden of 2.8 risk alleles (p = 3.97 × 10(-89)) compared to European Americans. However, GRS modeling showed that cumulative risk allele load was associated with risk of T2D in European Americans, but only marginally in African Americans. This result suggests that there are ethnic-specific differences in genetic architecture underlying T2D, and that these differences complicate our understanding of how risk allele load impacts disease susceptibility. PMID:25273842

Keaton, Jacob M; Cooke Bailey, Jessica N; Palmer, Nicholette D; Freedman, Barry I; Langefeld, Carl D; Ng, Maggie C Y; Bowden, Donald W

2014-12-01

9

Distinguishing species of European sturgeons Acipenser spp. using microsatellite allele sequences.  

PubMed

Five microsatellite markers were analysed and their alleles were sequenced for the three sturgeon species that lived in western Europe: the European sturgeon Acipenser sturio, the Atlantic sturgeon Acipenser oxyrinchus and the Adriatic sturgeon Acipenser naccarii. A total of 94 different allele sequences were obtained. Fixed mutations in the flanking regions or in the core repeat of microsatellites provided a clear distinction between the different species. Comparison of allele sequences also provided some insights into microsatellites and the evolution of Acipenser species. These nuclear markers can be used to solve species determination problems, and combined with mitochondrial markers, will be useful to identify introgression and hybridization among the three species. Moreover, because they are short and with a limited allele size range, they are particularly suited for analysis of museum specimens or archaeological remains. PMID:21235556

Chassaing, O; Hänni, C; Berrebi, P

2011-01-01

10

Genotypic and Allelic Variability in CYP19A1 among Populations of African and European Ancestry.  

PubMed

CYP19A1 facilitates the bioconversion of estrogens from androgens. CYP19A1 intron single nucleotide polymorphisms (SNPs) may alter mRNA splicing, resulting in altered CYP19A1 activity, and potentially influencing disease susceptibility. Genetic studies of CYP19A1 SNPs have been well documented in populations of European ancestry; however, studies in populations of African ancestry are limited. In the present study, ten 'candidate' intronic SNPs in CYP19A1 from 125 African Americans (AA) and 277 European Americans (EA) were genotyped and their frequencies compared. Allele frequencies were also compared with HapMap and ASW 1000 Genomes populations. We observed significant differences in the minor allele frequencies between AA and EA in six of the ten SNPs including rs10459592 (p<0.0001), rs12908960 (p<0.0001), rs1902584 (p = 0.016), rs2470144 (p<0.0001), rs1961177 (p<0.0001), and rs6493497 (p = 0.003). While there were no significant differences in allele frequencies between EA and CEU in the HapMap population, a 1.2- to 19-fold difference in allele frequency for rs10459592 (p = 0.004), rs12908960 (p = 0.0006), rs1902584 (p<0.0001), rs2470144 (p = 0.0006), rs1961177 (p<0.0001), and rs6493497 (p = 0.0092) was observed between AA and the Yoruba (YRI) population. Linkage disequilibrium (LD) blocks and haplotype clusters that is unique to the EA population but not AA was also observed. In summary, we demonstrate that differences in the allele frequencies of CYP19A1 intron SNPs are not consistent between populations of African and European ancestry. Thus, investigations into whether CYP19A1 intron SNPs contribute to variations in cancer incidence, outcomes and pharmacological response seen in populations of different ancestry may prove beneficial. PMID:25647083

Starlard-Davenport, Athena; Orloff, Mohammed S; Dhakal, Ishwori; Penney, Rosalind B; Kadlubar, Susan A

2015-01-01

11

Genotypic and Allelic Variability in CYP19A1 among Populations of African and European Ancestry  

PubMed Central

CYP19A1 facilitates the bioconversion of estrogens from androgens. CYP19A1 intron single nucleotide polymorphisms (SNPs) may alter mRNA splicing, resulting in altered CYP19A1 activity, and potentially influencing disease susceptibility. Genetic studies of CYP19A1 SNPs have been well documented in populations of European ancestry; however, studies in populations of African ancestry are limited. In the present study, ten ‘candidate’ intronic SNPs in CYP19A1 from 125 African Americans (AA) and 277 European Americans (EA) were genotyped and their frequencies compared. Allele frequencies were also compared with HapMap and ASW 1000 Genomes populations. We observed significant differences in the minor allele frequencies between AA and EA in six of the ten SNPs including rs10459592 (p<0.0001), rs12908960 (p<0.0001), rs1902584 (p = 0.016), rs2470144 (p<0.0001), rs1961177 (p<0.0001), and rs6493497 (p = 0.003). While there were no significant differences in allele frequencies between EA and CEU in the HapMap population, a 1.2- to 19-fold difference in allele frequency for rs10459592 (p = 0.004), rs12908960 (p = 0.0006), rs1902584 (p<0.0001), rs2470144 (p = 0.0006), rs1961177 (p<0.0001), and rs6493497 (p = 0.0092) was observed between AA and the Yoruba (YRI) population. Linkage disequilibrium (LD) blocks and haplotype clusters that is unique to the EA population but not AA was also observed. In summary, we demonstrate that differences in the allele frequencies of CYP19A1 intron SNPs are not consistent between populations of African and European ancestry. Thus, investigations into whether CYP19A1 intron SNPs contribute to variations in cancer incidence, outcomes and pharmacological response seen in populations of different ancestry may prove beneficial. PMID:25647083

Starlard-Davenport, Athena; Orloff, Mohammed S.; Dhakal, Ishwori; Penney, Rosalind B.; Kadlubar, Susan A.

2015-01-01

12

Diverging trends between heterozygosity and allelic richness during postglacial colonization in the European beech.  

PubMed Central

Variation at 12 polymorphic isozyme loci was studied in the European beech on the basis of an extensive sample of 389 populations distributed throughout the species range. Special emphasis was given to the analysis of the pattern of geographic variation on the basis of two contrasting measures of genetic diversity, gene diversity (H) and allelic richness, and to their relationship. Measures of allelic richness were corrected for variation in sample size by using the rarefaction method. As expected, maximum allelic richness was found in the southeastern part of the range (southern Italy and the Balkans), where beech was confined during the last ice age. Surprisingly, H was lower in refugia than in recently colonized regions, resulting in a negative correlation between the two diversity measures. The decrease of allelic richness and the simultaneous increase of H during postglacial recolonization was attributed to several processes that differentially affect the two diversity parameters, such as bottlenecks due to long-distance founding events, selection during population establishment, and increased gene flow at low population densities. PMID:11139519

Comps, B; Gömöry, D; Letouzey, J; Thiébaut, B; Petit, R J

2001-01-01

13

Conserved KIR Allele-Level Haplotypes Are Altered by Microvariation in Individuals with European Ancestry  

PubMed Central

Natural killer cell immunoglobulin-like receptor (KIR) haplotype-specific DNA fragments were sequenced to identify centromeric and telomeric allele level haplotype structures and their frequencies from 76 unrelated individuals with European ancestry. Analysis was simplified by redefining the 5’ boundary of the centromeric KIR gene cluster to include only exons 7-9 of KIR3DL3. Three consensus allele level haplotypes were identified for a centromeric gene presence/absence structure designated as Cen-A1. KIR3DL3*00201 (ex 7-9)—KIR2DL3*001—KIR2DL1*00302 was the most frequent (37.5%) centromeric structure. Single consensus haplotypes were observed for haplotype structures Cen-B1 and Cen-B2. Six Tel-A1 and two Tel-B1 consensus haplotypes were observed; the most prevalent (23.0%) was KIR2DL4*00102—KIR3DL1*002—KIR2DS4*00101—KIR3DL2*002. A small number of nucleotide substitutions (?3) in the coding regions of the functional KIR genes created microvariants of the consensus haplotypes. Eight less common haplotype structures were also detected. Four carried hybrid genes formed during gene deletion events, two carried an insertion with a 2DL5/3DP1 fusion gene, and two included a very large insertion. These data show that the KIR gene complex is composed of a limited number of conserved allele level centromeric and telomeric haplotypes that have diversified by mutation, recombination within a locus, and unequal crossing over. PMID:21796155

Hou, Lihua; Chen, Minghua; Ng, Jennifer; Hurley, Carolyn Katovich

2012-01-01

14

[Geographical variation of allele frequencies at the LDH-A* locus in the arctic grayling Thymallus arcticus Pall. and in the European grayling Thymallus arcticus L].  

PubMed

The allele frequencies of LDH-A* locus were studied in the population of Siberian grayling from the Kozhym River (Pechora basin) and in the population of European grayling from Pechora, Mezen', and Vym' rivers (Northern Dvina basin). In samples of both species (n = 134), three LDH-A phenotypes have been identified in total, which proved to be under the control of two alleles: LDH-A*100 and LDH-A*50. The alternative alleles of LDH-A* locus were identified in the populations of Siberian grayling from Kozhym River and in the population of European grayling from the same river and other Pechora tributaries, namely, LDH-A*100 and LDH-A*50 in the Siberian and the European grayling, respectively. However, in the European grayling populations from the Mezen' and Vym' rivers, both alleles occur at the frequencies of the rare LDH-A*100 allele of 0.143 and 0.222, respectively. According to the published data, the frequency of LDH-A*100 allele increases in the European grayling populations of northwestern (Finland) and southern (France) rivers, reaching 0.872 and 1.000 in Rhone and Loire, respectively, i.e., the values characteristic of the Siberian grayling populations. PMID:15575515

Shubin, P N; Efimtseva, é A; shubin, Iu P; Chelpanova, T I

2004-10-01

15

The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent  

PubMed Central

Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of SLC24A5 accounts for lighter skin in Europeans but not in East Asians. A previous genome-wide association study carried out in a heterogeneous sample of UK immigrants of South Asian descent suggested that this gene also contributes significantly to skin pigmentation variation among South Asians. In the present study, we have quantitatively assessed skin pigmentation for a largely homogeneous cohort of 1228 individuals from the Southern region of the Indian subcontinent. Our data confirm significant association of rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic variation in the cohort studied. Our extensive survey of the polymorphism in 1573 individuals from 54 ethnic populations across the Indian subcontinent reveals wide presence of the derived-A allele, although the frequencies vary substantially among populations. We also show that the geospatial pattern of this allele is complex, but most importantly, reflects strong influence of language, geography and demographic history of the populations. Sequencing 11.74 kb of SLC24A5 in 95 individuals worldwide reveals that the rs1426654-A alleles in South Asian and West Eurasian populations are monophyletic and occur on the background of a common haplotype that is characterized by low genetic diversity. We date the coalescence of the light skin associated allele at 22–28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India. PMID:24244186

Möls, Märt; Hill, Sarah; Tamang, Rakesh; Chaubey, Gyaneshwer; Goto, Rie; Ho, Simon Y. W.; Gallego Romero, Irene; Crivellaro, Federica; Hudjashov, Georgi; Rai, Niraj; Metspalu, Mait; Mascie-Taylor, C. G. Nicholas; Pitchappan, Ramasamy; Singh, Lalji; Mirazon-Lahr, Marta; Thangaraj, Kumarasamy; Villems, Richard; Kivisild, Toomas

2013-01-01

16

Shared and independent colorectal cancer risk alleles in TGF?-related genes in African and European Americans.  

PubMed

Genome-wide association studies (GWAS) in colorectal cancer (CRC) identified five regions near transforming growth factor ?-related genes BMP4, GREM1, CDH1, SMAD7 and RPHN2. The true risk alleles remain to be identified in these regions, and their role in CRC risk in non-European populations has been understudied. Our previous work noted significant genetic heterogeneity between African Americans (AAs) and European Americans (EAs) for single nucleotide polymorphisms (SNPs) identified in GWAS. We hypothesized that associations may not have been replicated in AAs due to differential or independent genetic structures. In order to test this hypothesis, we genotyped 195 tagging SNPs across these five gene regions in 1194 CRC cases (795 AAs and 399 EAs) and 1352 controls (985 AAs and 367 EAs). Imputation was performed, and association testing of genotyped and imputed SNPs included ancestry, age and sex as covariates. In two of the five genes originally associated with CRC, we found evidence for association in AAs including rs1862748 in CDH1 (OR(Add) = 0.82, P = 0.02) and in GREM1 the SNPs rs10318 (OR(Rec) = 60.1, P = 0.01), rs11632715 (OR(Rec) = 2.36; P = 0.004) and rs12902616 (OR(Rec) = 1.28, P = 0.005), the latter which is in linkage disequilibrium with the previously identified SNP rs4779584. Testing more broadly for associations in these gene regions in AAs, we noted three statistically significant association peaks in GREM1 and RHPN2 that were not identified in EAs. We conclude that some CRC risk alleles are shared between EAs and AAs and others are population specific. PMID:24753543

Kupfer, Sonia S; Skol, Andrew D; Hong, Ellie; Ludvik, Anton; Kittles, Rick A; Keku, Temitope O; Sandler, Robert S; Ellis, Nathan A

2014-09-01

17

Geographical Variation of Allele Frequencies at the LDH-A* Locus in the Arctic Grayling Thymallus arcticus Pall. and in the European Grayling Thymallus thymallus L  

Microsoft Academic Search

The allele frequencies of LDH-A* locus were studied in the populations of Siberian grayling from the Kozhym River (Pechora basin) and in the population of European grayling from Pechora, Mezen', and Vym' rivers (Northern Dvina basin). In samples of both species (n = 134), three LDH-A phenotypes have been identified in total, which proved to be under the control of

P. N. Shubin; E. A. Efimtzeva; Yu. P. Shubin; T. I. Chelpanova

2004-01-01

18

The ITGAV rs3738919-C allele is associated with rheumatoid arthritis in the European Caucasian population: a family-based study  

PubMed Central

The integrin ?v?3, whose ?v subunit is encoded by the ITGAV gene, plays a key role in angiogenesis. Hyperangiogenesis is involved in rheumatoid arthritis (RA) and the ITGAV gene is located in 2q31, one of the suggested RA susceptibility loci. Our aim was to test the ITGAV gene for association and linkage to RA in a family-based study from the European Caucasian population. Two single nucleotide polymorphisms were genotyped by PCR-restriction fragment length polymorphism in 100 French Caucasian RA trio families (one RA patient and both parents), 100 other French families and 265 European families available for replication. The genetic analyses for association and linkage were performed using the comparison of allelic frequencies (affected family-based controls), the transmission disequilibrium test, and the genotype relative risk. We observed a significant RA association for the C allele of rs3738919 in the first sample (affected family-based controls, RA index cases 66.5% versus controls 56.7%; P = 0.04). The second sample showed the same trend, and the third sample again showed a significant RA association. When all sets were combined, the association was confirmed (affected family-based controls, RA index cases 64.6% versus controls 58.1%; P = 0.005). The rs3738919-C allele was also linked to RA (transmission disequilibrium test, 56.5% versus50% of transmission; P = 0.009) and the C-allele-containing genotype was more frequent in RA index cases than in controls (RA index cases 372 versus controls 339; P = 0.002, odds ratio = 1.94, 95% confidence interval = 1.3–2.9). The rs3738919-C allele of the ITGAV gene is associated with RA in the European Caucasian population, suggesting ITGAV as a new minor RA susceptibility gene. PMID:17615072

Jacq, Laurent; Garnier, Sophie; Dieudé, Philippe; Michou, Laëtitia; Pierlot, Céline; Migliorini, Paola; Balsa, Alejandro; Westhovens, René; Barrera, Pilar; Alves, Helena; Vaz, Carlos; Fernandes, Manuela; Pascual-Salcedo, Dora; Bombardieri, Stefano; Dequeker, Jan; Radstake, Timothy R; Van Riel, Piet; van de Putte, Leo; Lopes-Vaz, Antonio; Glikmans, Elodie; Barbet, Sandra; Lasbleiz, Sandra; Lemaire, Isabelle; Quillet, Patrick; Hilliquin, Pascal; Teixeira, Vitor Hugo; Petit-Teixeira, Elisabeth; Mbarek, Hamdi; Prum, Bernard; Bardin, Thomas; Cornélis, François

2007-01-01

19

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

PubMed

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

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

2009-12-01

20

Influence of the CXCL1 rs4074 A Allele on Alcohol Induced Cirrhosis and HCC in Patients of European Descent  

PubMed Central

Background and Aims CXCL1 (CXC chemokine-ligand-1) is a ligand for CXC chemokine receptor 2 expressed on hepatic stellate cells (HSC). Thus, CXCL1 might contribute to HSC activation and fibrogenesis. In the present study, we investigated the influence of the CXCL1 rs4074 polymorphism on the occurrence of alcohol induced liver cirrhosis and hepatocellular carcinoma (HCC). Methods The study involved 458 patients with alcoholic cirrhosis (170 with HCC), 115 alcoholics without liver disease and 342 healthy controls. All subjects were genotyped for the CXCL1 rs4074 polymorphism and CXCL1 serum levels of 132 patients were measured. In vitro CXCL1 secretion in TLR-transfected cell lines were studied by ELISA. Results Distribution of the CXCL1 genotypes (GG/GA/AA) was 159/219/80 in patients with alcoholic cirrhosis, 52/44/19 in alcoholic controls and 158/140/44 in healthy controls. Patients with alcohol-induced cirrhosis were significantly more often carriers of the CXCL1 rs4074 A allele (65.3%) than alcoholics without liver disease (54.8%, OR=1.55; 95%CI=1.025-2.350; p=0.04) and healthy controls (53.8%, OR=1.62; 95%CI=1.212-2.151; p=0.001). Accordingly, the frequency of the CXCL1 rs4074 A allele was significantly higher in the cirrhotic patients than in the subjects without cirrhosis (41.4% vs. 33.9%, OR=1.38, 95% CI:1.14–1.66, p=0.001). Furthermore cirrhotic carriers of the CXCL1 rs4074 A allele had significantly higher CXCL1 serum levels than carriers of the GG genotype. In contrast to sera from healthy controls, sera from patients with alcoholic cirrhosis induced CXCL1 secretion in TLR2- (p=0.016) and TLR4- (p=0.008) transfected HEK293 cells. This finding indicates that sera from patients with alcoholic cirrhosis contain soluble ligands that can induce CXCL1 production via stimulation of TLRs. Conclusion The enhanced CXCL1 serum levels in carriers of the rs4074 A allele together with their increased frequency in patients with alcohol induced cirrhosis suggest the CXCL1 rs4074 A allele as a genetic risk factor for alcoholic cirrhosis. PMID:24260493

Lutz, Philipp; Langhans, Bettina; Wolter, Franziska; Eisenhardt, Marianne; Krämer, Benjamin; Kokordelis, Pavlos; Glässner, Andreas; Müller, Tobias; Rosendahl, Jonas; Fischer, Janett; Berg, Thomas; Grünhage, Frank; Leifeld, Ludger; Soyka, Michael; Nattermann, Jacob; Sauerbruch, Tilman; Stickel, Felix; Spengler, Ulrich

2013-01-01

21

The Interplay between Natural Selection and Susceptibility to Melanoma on Allele 374F of SLC45A2 Gene in a South European Population  

PubMed Central

We aimed to study the selective pressures interacting on SLC45A2 to investigate the interplay between selection and susceptibility to disease. Thus, we enrolled 500 volunteers from a geographically limited population (Basques from the North of Spain) and by resequencing the whole coding region and intron 5 of the 34 most and the 34 least pigmented individuals according to the reflectance distribution, we observed that the polymorphism Leu374Phe (L374F, rs16891982) was statistically associated with skin color variability within this sample. In particular, allele 374F was significantly more frequent among the individuals with lighter skin. Further genotyping an independent set of 558 individuals of a geographically wider population with known ancestry in the Spanish population also revealed that the frequency of L374F was significantly correlated with the incident UV radiation intensity. Selection tests suggest that allele 374F is being positively selected in South Europeans, thus indicating that depigmentation is an adaptive process. Interestingly, by genotyping 119 melanoma samples, we show that this variant is also associated with an increased susceptibility to melanoma in our populations. The ultimate driving force for this adaptation is unknown, but it is compatible with the vitamin D hypothesis. This shows that molecular evolution analysis can be used as a useful technology to predict phenotypic and biomedical consequences in humans. PMID:25093503

López, Saioa; García, Óscar; Yurrebaso, Iñaki; Flores, Carlos; Acosta-Herrera, Marialbert; Chen, Hua; Gardeazabal, Jesús; Careaga, Jesús María; Boyano, María Dolores; Sánchez, Ana; Ratón-Nieto, Juan Antonio; Sevilla, Arrate; Smith-Zubiaga, Isabel; de Galdeano, Alicia García; Martinez-Cadenas, Conrado; Izagirre, Neskuts; de la Rúa, Concepción; Alonso, Santos

2014-01-01

22

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

PubMed

Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71-80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary history of the European lactase persistence trait and its global cultural implications. PMID:24465990

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

2014-01-01

23

Improved metastasis-free survival in nonadjuvantly treated postmenopausal breast cancer patients with chemokine receptor 5 del32 frameshift mutations.  

PubMed

The CC-chemokine receptor CCR5 has been associated with cancer progression and metastasis. CCR5 blockers such as Maraviroc are tested in metastatic cancer patients. A mutant allele of CCR5, CCR5-delta32 (CCR5del32), which encodes for a protein with a trans-dominant negative effect on the wildtype protein, is frequently found in populations of northern European origin. We set out to determine if the CCR5del32 genotype is associated with progression of breast cancer. Here, we genotyped 414 breast cancer patients and investigated whether the CCR5 genotype had an association with the likelihood to metastasize within specific subgroups of this cohort. The findings were subsequently confirmed in an independent cohort of 1,017 breast cancer patients. Specifically within the postmenopausal subgroup of the initial cohort (n?=?325) individuals carrying the CCR5del32 genotype exhibited a significantly longer metastasis-free survival (MFS, p?=?0.038). In an independent cohort, CCR5del32 genotype was confirmed to be associated with prolonged MFS only in postmenopausal patients (n?=?579, hazard ratio [HR]?=?0.61, 95% confidence interval [95% CI]?=?0.38-0.99, p?=?0.044), and not in premenopausal patients (n?=?438, HR?=?1.01, 95% CI?=?0.70-1.48, p?=?0.94). Our results indicate that CCR5del32 genotype is associated with good prognosis in postmenopausal breast cancer patients. Considering this result, postmenopausal breast cancer patients who are wildtype for CCR5 genotype might benefit from CCR5 blockers, such as Maraviroc. PMID:24807072

Span, P N; Pollakis, G; Paxton, W A; Sweep, F C G J; Foekens, J A; Martens, J W M; Sieuwerts, A M; van Laarhoven, H W M

2015-01-01

24

Resolution of HLA-B*44:02:01G, -DRB1*14:01:01G and -DQB1*03:01:01G reveals a high allelic variability among 12 European populations.  

PubMed

Within the framework of the EU-funded HLA-NET action, an analysis of three G-group alleles, HLA-B*44:02:01G, DRB1*14:01:01G and DQB1*03:01:01G, was undertaken in 12 European populations. Ambiguities were resolved by polymerase chain reaction-sequence-specific amplification (PCR-SSP) or PCR-sequence-based typing (PCR-SBT) in a total of 5095 individuals. The results of the DRB1*14:01/14:54 ambiguity showed high relative ratios (24-53%) of DRB1*14:01 in Bulgarians, Croatians, Greeks, Italians and Slovenians, contrasting with low ratios (6-13%) in Austrians, Finnish, French, Hungarians, Norwegians and Swiss. Resolution of the B*44:02/44:27 ambiguity showed that B*44:27 had a high relative ratio in Slovenians (25.5%) and Bulgarians (37%) and low in French and Swiss (0.02-1%), and was not observed in Greeks and Italians. The highest relative ratio of DQB1*03:19 was found in Portuguese (11%), by contrast with low ratios (0-3%) in the other five populations. Analysis of the A, B, DRB1 phenotypes and family-derived haplotypes in 1719 and 403 individuals positive for either HLA-B*44:02G or DRB1*14:01G ambiguities, respectively, showed some preferential associations, such as A*26?DRB1*14:01, B*35?DRB1*14:01, B*38?DRB1*14:01 and B*44:27?DRB1*16. Because these ambiguities are located outside the peptide-binding site, they may not be recognized by alloreactive T-cells. However, because of strong linkage disequilibrium (LD), the DRB1*14:01 vs DRB1*14:54 and the B*44:02 vs B*44:27 mismatches are associated to DRB3-, and C-mismatches, respectively. These results are informative for algorithms searching unrelated hematopoietic stem cell donors. For B*44:27-positive patients, searches are expected to be more successful when requesting donors from Southeastern-European ancestry. Furthermore, the introduction of human leukocyte antigen (HLA)-typing strategies that allow resolving exon 4 (for class I) and exon 3 (for class II) polymorphisms can be expected to contribute significantly to population genetics studies. PMID:25209151

Vidan-Jeras, B; Buhler, S; Dubois, V; Grubic, Z; Ivanova, M; Jaatinen, T; Ligeiro, D; Lokki, M-L; Papasteriades, C; Poli, F; Spyropoulou-Vlachou, M; Tordai, A; Viken, M K; Wenda, S; Nunes, J M; Sanchez-Mazas, A; Tiercy, J-M

2014-11-01

25

Counting Alleles with Rarefaction: Private Alleles and Hierarchical Sampling Designs  

Microsoft Academic Search

The number of alleles (allelic richness) in a population is a fundamental measure of genetic variation, and a useful statistic for identifying populations for conservation. Estimating allelic richness is complicated by the effects of sample size: large samples are expected to have more alleles. Rarefaction solves this problem. This communication extends the rarefaction procedure to count private alleles and to

Steven T. Kalinowski

2004-01-01

26

HLA genes in Cubans and the detection of Amerindian alleles  

Microsoft Academic Search

Caribbean Islands including Cuba were first inhabited by Meso-American and later by Arawak-speaking Amerindians from nowadays Venezuela. Spanish invaders brought to almost extinction to the Amerindian population after 1492. Black slaves from West Africa were taken into Cuba by Europeans. The degree of admixture among populations is approached. HLA alleles were studied by DNA techniques. Comparison with other worldwide populations

Roberto Alegre; Juan Moscoso; Jorge Martinez-Laso; Manuel Martin-Villa; Jose Suarez; Almudena Moreno; Juan I. Serrano-Vela; Gilberto Vargas-Alarcon; Remedios Pacheco; Antonio Arnaiz-Villena

2007-01-01

27

Statistical inference of allelic imbalance from transcriptome data.  

PubMed

Next-generation sequencing and the availability of high-density genotyping arrays have facilitated an analysis of somatic and meiotic mutations at unprecedented level, but drawing sensible conclusions about the functional relevance of the detected variants still remains a formidable challenge. In this context, the study of allelic imbalance in intermediate RNA phenotypes may prove a useful means to elucidate the likely effects of DNA variants of unknown significance. We developed a statistical framework for the assessment of allelic imbalance in next-generation transcriptome sequencing (RNA-seq) data that requires neither an expression reference nor the underlying nuclear genotype(s), and that allows for allele miscalls. Using extensive simulation as well as publicly available whole-transcriptome data from European-descent individuals in HapMap, we explored the power of our approach in terms of both genotype inference and allelic imbalance assessment under a wide range of practically relevant scenarios. In so doing, we verified a superior performance of our methodology, particularly at low sequencing coverage, compared to the more simplistic approach of completely ignoring allele miscalls. Because the proposed framework can be used to assess somatic mutations and allelic imbalance in one and the same set of RNA-seq data, it will be particularly useful for the analysis of somatic genetic variation in cancer studies. PMID:21120951

Nothnagel, Michael; Wolf, Andreas; Herrmann, Alexander; Szafranski, Karol; Vater, Inga; Brosch, Mario; Huse, Klaus; Siebert, Reiner; Platzer, Matthias; Hampe, Jochen; Krawczak, Michael

2011-01-01

28

Microsatellite Variation in Honey Bee (Apis MeZZfera L.) Populations: Hierarchical Genetic Structure and Test of the Infinite Allele and Stepwise Mutation Models  

Microsoft Academic Search

Samples from nine populations belonging to three African (intmissa, scutellata and capensis) and four European (mellijima, liptica, carnica and cecropia) Apis mellifea subspecies were scored for seven microsatellite loci. A large amount of genetic variation (between seven and 30 alleles per locus) was detected. Average heterozygosity and average number of alleles were significantly higher in African than in European subspecies,

Lionel Garnery; Michel Solignac; Jean-Marie Cornuett

29

A Risk Allele for Nicotine Dependence in CHRNA5 Is a Protective Allele for Cocaine Dependence  

PubMed Central

Background A non-synonymous coding polymorphism, rs16969968, of the CHRNA5 gene which encodes the alpha-5 subunit of the nicotinic acetylcholine receptor (nAChR) has been found to be associated with nicotine dependence (20). The goal of the present study is to examine the association of this variant with cocaine dependence. Methods Genetic association analysis in two, independent samples of unrelated cases and controls; 1.) 504 European-American participating in the Family Study on Cocaine Dependence (FSCD); 2.) 814 European Americans participating in the Collaborative Study on the Genetics of Alcoholsim (COGA). Results In the FSCD, there was a significant association between the CHRNA5 variant and cocaine dependence (OR = 0.67 per allele, p = 0.0045, assuming an additive genetic model), but in the reverse direction compared to that previously observed for nicotine dependence. In multivariate analyses that controlled for the effects of nicotine dependence, both the protective effect for cocaine dependence and the previously documented risk effect for nicotine dependence were statistically significant. The protective effect for cocaine dependence was replicated in the COGA sample. In COGA, effect sizes for habitual smoking, a proxy phenotype for nicotine dependence, were consistent with those observed in FSCD. Conclusion The minor (A) allele of rs16969968, relative to the major G allele, appears to be both a risk factor for nicotine dependence and a protective factor for cocaine dependence. The biological plausibility of such a bidirectional association stems from the involvement of nAChRs with both excitatory and inhibitory modulation of dopamine-mediated reward pathways. PMID:18519132

Grucza, Richard A; Wang, Jen C.; Stitzel, Jerry A.; Hinrichs, Anthony L.; Saccone, Scott F.; Saccone, Nancy L.; Bucholz, Kathleen K.; Cloninger, C. Robert; Neuman, Rosalind J.; Budde, John P.; Fox, Louis; Bertelsen, Sarah; Kramer, John; Hesselbrock, Victor; Tischfield, Jay; Nurnberger, John. I.; Almasy, Laura; Porjesz, Bernice; Kuperman, Samuel; Schuckit, Marc A.; Edenberg, Howard J.; Rice, John P.; Goate, Alison M.; Bierut, Laura J.

2008-01-01

30

DLA-DRB1, DQA1, and DQB1 Alleles and Haplotypes in North American Gray Wolves  

Microsoft Academic Search

The canine major histocompatibility complex contains highly polymorphic genes, many of which are critical in regulating immune response. Since domestic dogs evolved from Gray Wolves (Canis lupus), common DLA class II alleles should exist. Sequencing was used to characterize 175 Gray Wolves for DLA class II alleles, and data from 1856 dogs, covering 85 different breeds of mostly European origin,

LORNA J. KENNEDY; J. M. Angles; A. Barnes; L. E. Carmichael; A. D. Radford; W. E. R. Ollier; G. M. Happ

2007-01-01

31

Dwindling genetic diversity in European ground squirrels?  

Microsoft Academic Search

The European ground squirrel (Spermophilus citellus) is endangered and in decline. Populations are increasingly fragmented, and only a coordinated conservation effort at the European level may guarantee its long-term survival. To obtain a general population genetic picture on a larger geographic scale, we screened 117 individuals from seven local populations in Hungary, Romania, and Austria for allelic variation at eleven

Hichem Ben Slimen; Csongor I. Gedeon; Ilse E. Hoffmann; Franz Suchentrunk

32

Chemokine coreceptor usage by diverse primary isolates of human immunodeficiency virus type 1.  

PubMed

We tested chemokine receptor subset usage by diverse, well-characterized primary viruses isolated from peripheral blood by monitoring viral replication with CCR1, CCR2b, CCR3, CCR5, and CXCR4 U87MG.CD4 transformed cell lines and STRL33/BONZO/TYMSTR and GPR15/BOB HOS.CD4 transformed cell lines. Primary viruses were isolated from 79 men with confirmed human immunodeficiency virus type 1 (HIV-1) infection from the Chicago component of the Multicenter AIDS Cohort Study at interval time points. Thirty-five additional well-characterized primary viruses representing HIV-1 group M subtypes A, B, C, D, and E and group O and three primary simian immunodeficiency virus (SIV) isolates were also used for these studies. The restricted use of the CCR5 chemokine receptor for viral entry was associated with infection by a virus having a non-syncytium-inducing phenotype and correlated with a reduced rate of disease progression and a prolonged disease-free interval. Conversely, broadening chemokine receptor usage from CCR5 to both CCR5 and CXCR4 was associated with infection by a virus having a syncytium-inducing phenotype and correlated with a faster rate of CD4 T-cell decline and progression of disease. We also observed a greater tendency for infection with a virus having a syncytium-inducing phenotype in men heterozygous for the defective CCR5 Delta32 allele (25%) than in those men homozygous for the wild-type CCR5 allele (6%) (P = 0.03). The propensity for infection with a virus having a syncytium-inducing phenotype provides a partial explanation for the rapid disease progression among some men heterozygous for the defective CCR5 Delta32 allele. Furthermore, we did not identify any primary viruses that used CCR3 as an entry cofactor, despite this CC chemokine receptor being expressed on the cell surface at a level commensurate with or higher than that observed for primary peripheral blood mononuclear cells. Whereas isolates of primary viruses of SIV also used STRL33/BONZO/TYMSTR and GPR15/BOB, no primary isolates of HIV-1 used these particular chemokine receptor-like orphan molecules as entry cofactors, suggesting a limited contribution of these other chemokine receptors to viral evolution. Thus, despite the number of chemokine receptors implicated in viral entry, CCR5 and CXCR4 are likely to be the physiologically relevant chemokine receptors used as entry cofactors in vivo by diverse strains of primary viruses isolated from blood. PMID:9765480

Zhang, L; He, T; Huang, Y; Chen, Z; Guo, Y; Wu, S; Kunstman, K J; Brown, R C; Phair, J P; Neumann, A U; Ho, D D; Wolinsky, S M

1998-11-01

33

Prediction of deleterious human alleles.  

PubMed

Single nucleotide polymorphisms (SNPs) constitute the bulk of human genetic variation, occurring with an average density of approximately 1/1000 nucleotides of a genotype. SNPs are either neutral allelic variants or are under selection of various strengths, and the impact of SNPs on fitness remains unknown. Identification of SNPs affecting human phenotype, especially leading to risks of complex disorders, is one of the key problems of medical genetics. SNPs in protein-coding regions that cause amino acid variants (non-synonymous cSNPs) are most likely to affect phenotypes. We have developed a straightforward and reliable method based on physical and comparative considerations that estimates the impact of an amino acid replacement on the three-dimensional structure and function of the protein. We estimate that approximately 20% of common human non-synonymous SNPs damage the protein. The average minor allele frequency of such SNPs in our data set was two times lower than that of benign non-synonymous SNPs. The average human genotype carries approximately 10(3) damaging non-synonymous SNPs that together cause a substantial reduction in fitness. PMID:11230178

Sunyaev, S; Ramensky, V; Koch, I; Lathe, W; Kondrashov, A S; Bork, P

2001-03-15

34

European Mink-Polecat Hybridization Events: Hazards From Natural Process?  

Microsoft Academic Search

Determining the significance of hybridization events raises essential issues both in conservation and in evolutionary biology. Here, we report a genetic investigation of sympatric polecat and endangered European mink populations. Although the two species were morphologically very similar, the European mink and the polecat were easily discriminated from allozymes and microsatellites and showed a high level of private alleles (effective

T. LODE; G. GUIRAL; D. PELTIER

2005-01-01

35

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

PubMed

Allele-specific silencing by RNA interference (ASP-RNAi) is an atypical RNAi that is capable of discriminating target alleles from non-target alleles, and may be therapeutically useful for specific inhibition of disease-causing alleles without affecting their corresponding normal alleles. However, it is difficult to design and select small interfering RNA (siRNAs) that confer ASP-RNAi. A major problem is that there are few appropriate measures in determining optimal allele-specific siRNAs. Here we show two novel formulas for calculating a new measure of allele-discrimination, named "ASP-score". The formulas and ASP-score allow for an unbiased determination of optimal siRNAs, and may contribute to characterizing such allele-specific siRNAs. PMID:25037272

Takahashi, Masaki; Hohjoh, Hirohiko

2014-11-01

36

Chemokine Receptor-5Delta32 Mutation is No Risk Factor for Ischemic-Type Biliary Lesion in Liver Transplantation.  

PubMed

It has been shown that certain chemokine receptor polymorphisms may correspond to certain complications after organ transplantation. Ischemic-type biliary lesion (ITBL) encounters for major morbidity and mortality in liver transplant recipients. So far, the exact cause for ITBL remains unclear. Certain risk factors for the development of ITBL like donor age and cold ischemic time are well described. In a previous study, a 32-nucleotide deletion of the chemokine receptor-5Delta32 (CCR-5Delta32) was strongly associated with the incidence of ITBL in adult liver transplantation. This study re-evaluates the association of CCR-5Delta32 gene polymorphism and the incidence of ITBL. 169 patients were included into this retrospective analysis. 134 patients were homozygous for wild-type CCR-5, 33 patients heterozygous, and 2 patients were homozygous for CCR-5Delta32 mutation. There were no major differences in donor or recipients demographics. No association was found between CCR-5Delta32 mutation and the development of ITBL. We conclude that CCR-5Delta32 is no risk factor for the development of ITBL in our patient cohort. PMID:20107582

Heidenhain, Christoph; Puhl, Gero; Moench, Christian; Lautem, Anja; Neuhaus, Peter

2009-01-01

37

Identification of HLA alleles with low or no cell surface expression in the Czech population.  

PubMed

The presence of the A*24020102L allele is implicated in one donor from the CBMD who serologically was typed as A2; B44, B55; Cwl, Cw7. The DRB4*01030102N allele was identified in one healthy donor and in one patient with MDS during routine HLA class II DNA typing. The DRB4*01030102N allele was identified in the patient's father, who had CML, and was associated with the HLA-A3-B7-Cw7-DRB1*0701-DQB1*0303 haplotype, which is common for European populations. In order to avoid mistyping, both techniques, serology and molecular biology must be used for HLA typing, especially for cases where just one antigen appeared to be present using serological methods. PMID:14748437

Bendukidze, N; Ivasková, E; Zahlavová, L; Slavcev, A; Kupková, L; Sajdlová, H; Day, S; Dunn, P P J

2003-01-01

38

Characterization of the treefrog null allele  

SciTech Connect

As part of the authors intensive year-long baseline ecological study, they characterized the degree of genetic polymorphism and heterozygosity in selected Feed Materials Production Center (FMPC) populations using electrophoretic techniques. These data are being used as an indicator of stress by comparing populations on and off the FMPC site. The current study was initiated to determine whether this GPI null allele is lethal, when homozygous, in spring peepers. Also, a sampling protocol was implemented to determine whether a linear effect occurs relative to the frequency of the null allele offsite and to determine the origination site of the null allele. 18 refs., 2 figs., 4 tabs.

Guttman, S.I. (Miami Univ., Oxford, OH (USA). Dept. of Zoology)

1990-12-01

39

Characterization of the treefrog null allele, 1991  

SciTech Connect

Spring peeper (Hyla crucifer) tadpoles collected from the waste storage area during the Biological and Ecological Site Characterization of the Feed Materials Production Center (FEMP) in 1986 and 1987 appeared to be unique. A null (inactive) allele was found at the glucose phosphate isomerase enzyme locus in significant frequencies (approximately 20%) each year; this allele did not appear to occur in the offsite sample collected approximately 15km from the FEMP. Null alleles at this locus have not been reported in other amphibian populations; when they have been found in other organisms they have invariably been lethal in the homozygous condition.

Guttman, S.I. (Miami Univ., Oxford, OH (United States). Dept. of Zoology)

1992-04-01

40

Family-based study of DRD2 alleles in alcohol and drug dependence.  

PubMed

Numerous case-control studies have addressed the hypothesis that variant alleles of the dopamine D2 receptor gene (DRD2) increase the liability for alcohol and/or drug dependence, and both positive and negative results have been reported. Because population frequencies of these alleles vary considerably, the conflicting results could be due to population stratification bias. Using the transmission disequilibrium test, the present study examined linkage disequilibrium of alcohol and drug (opioid and/or cocaine) dependence with three DRD2 polymorphic systems: (a) TaqI A, (b) TaqI D, and (c) the functional -141CIns/Del promoter systems. DNA samples were collected from small nuclear families (SNFs), where one or more offspring met DSM-III-R or DSM-IV criteria for alcohol and/or drug dependence. Because positive association between DRD2 alleles and alcohol and/or drug dependence has been reported only in populations of European ancestry, we limited the present study to European Americans (EAs). No evidence for linkage disequilibrium was found for any of the polymorphic systems when examined in relation to any substance dependence, alcohol dependence (with or without drug dependence), or drug dependence (with or without alcohol dependence). These results are consistent with those from a recent family-based study of alcohol dependence. Together, these studies suggest that the conflicting findings from case-control studies of the association between alleles of DRD2 and substance dependence may be attributable to population stratification in some samples. PMID:11054774

Blomqvist, O; Gelernter, J; Kranzler, H R

2000-10-01

41

Bovine Polledness – An Autosomal Dominant Trait with Allelic Heterogeneity  

PubMed Central

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

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

2012-01-01

42

Alleles of keratin 1 in families and populations.  

PubMed

Keratin 1 is found in the upper layers of the epidermis, on the surface of endothelial cells and in the membrane of the neuroblastoma NMB7. It is important for the structural integrity of the skin, has been found to regulate the activity of kinases, such as protein kinase C (PKC) and SRC, to participate in complement activation by the lectin pathway and to be involved in fibrinolysis, angiogenesis and the response to oxidative stress. Studies of the polymorphisms of the Keratin 1 (KRT1) gene have been driven mostly by interest in its role in skin diseases. However, much of the KRT1 variation occurs in normal populations and is not associated with dermal pathology. In the present experiments, we have investigated the polymorphism of KRT1 genes by nucleotide sequencing in normal families and normal populations of European, African, Hispanic and Asian background. The frequencies of the KRT1 alleles were strikingly different in the four ethnic groups and most of the mutations resulted in amino acid substitutions, with only 3 out of 19 being synonymous. Analysis of selective neutrality by the Ewens-Watterson and Tajima D statistics showed that KRT1 allele homozygosity was decreased in three of the populations suggesting that KRT1 genes may be under the influence of balancing selection. It is possible that the role of KRT1 as a receptor, rather than its structural function in the epidermis, is what drives the selective forces that are apparent in the inheritance of this gene. PMID:23707441

Han, Mei; Fan, Lin; Qin, Zhiqiang; Lavingia, Bhavna; Stastny, Peter

2013-11-01

43

Positive selection vectors for allelic exchange  

Microsoft Academic Search

We describe here the development and use of two new allelic exchange vectors, pKAS32 and pKAS46. These vectors can be used for allelic exchange in a wide variety of bacterial species because their R6K origin of replication functions only in bacteria engineered to produce the replication protein n. In addition, these vectors express the Escherichia coli rpsL gene, encoding ribosomal

Karen Skorupski; Ronald K. Taylor

1996-01-01

44

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

PubMed

HLA class II alleles were identified in 181 healthy unrelated Ethiopian children of both sexes and in 350 European controls from the South of France. The Ethiopian individuals belonged to the two major ethnic groups of the country: Oromo (N=83) and Amhara (N=98). In both panels, genetic polymorphism of HLA class II alleles was analysed for the first time by molecular typing of DRB1, DQA1 and DQB1 loci. Allelic and phenotypic frequencies were compared with those of European controls and other African populations. Construction of HLA class II three-locus haplotypes was also performed. The study revealed some differences between the two groups. Characteristic features of Central and North African populations appeared on the Ethiopian HLA genotypes. Surprisingly, DRB1*11 presented one of the lowest gene frequencies in both Ethiopian ethnic groups in contrast to Europeans and West Africans. Furthermore, this decrease was more marked than those observed using serological techniques in other geographically close East African countries. Oromo and Amhara only showed minor differences in spite of their different origins and histories. One significant difference consisted of a lower DRB1*01 gene frequency in Oromo as reported in most West African people. Some new or rare haplotypes were also observed in the Oromo group. Our results underline the distinctive features of the Ethiopian populations among the few HLA genotyping data available for East African groups and emphasise the major interest of such investigations in this region of Africa. PMID:9583804

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

1998-04-01

45

Most parsimonious haplotype allele sharing determination  

PubMed Central

Background The "common disease – common variant" hypothesis and genome-wide association studies have achieved numerous successes in the last three years, particularly in genetic mapping in human diseases. Nevertheless, the power of the association study methods are still low, in particular on quantitative traits, and the description of the full allelic spectrum is deemed still far from reach. Given increasing density of single nucleotide polymorphisms available and suggested by the block-like structure of the human genome, a popular and prosperous strategy is to use haplotypes to try to capture the correlation structure of SNPs in regions of little recombination. The key to the success of this strategy is thus the ability to unambiguously determine the haplotype allele sharing status among the members. The association studies based on haplotype sharing status would have significantly reduced degrees of freedom and be able to capture the combined effects of tightly linked causal variants. Results For pedigree genotype datasets of medium density of SNPs, we present two methods for haplotype allele sharing status determination among the pedigree members. Extensive simulation study showed that both methods performed nearly perfectly on breakpoint discovery, mutation haplotype allele discovery, and shared chromosomal region discovery. Conclusion For pedigree genotype datasets, the haplotype allele sharing status among the members can be deterministically, efficiently, and accurately determined, even for very small pedigrees. Given their excellent performance, the presented haplotype allele sharing status determination programs can be useful in many downstream applications including haplotype based association studies. PMID:19379528

Cai, Zhipeng; Sabaa, Hadi; Wang, Yining; Goebel, Randy; Wang, Zhiquan; Xu, Jiaofen; Stothard, Paul; Lin, Guohui

2009-01-01

46

Allele Workbench: Transcriptome Pipeline and Interactive Graphics for Allele-Specific Expression  

PubMed Central

Sequencing the transcriptome can answer various questions such as determining the transcripts expressed in a given species for a specific tissue or condition, evaluating differential expression, discovering variants, and evaluating allele-specific expression. Differential expression evaluates the expression differences between different strains, tissues, and conditions. Allele-specific expression evaluates expression differences between parental alleles. Both differential expression and allele-specific expression have been studied for heterosis (hybrid vigor), where the hybrid has improved performance over the parents for one or more traits. The Allele Workbench software was developed for a heterosis study that evaluated allele-specific expression for a mouse F1 hybrid using libraries from multiple tissues with biological replicates. This software has been made into a distributable package, which includes a pipeline, a Java interface to build the database, and a Java interface for query and display of the results. The required input is a reference genome, annotation file, and one or more RNA-Seq libraries with optional replicates. It evaluates allelic imbalance at the SNP and transcript level and flags transcripts with significant opposite directional allele-specific expression. The Java interface allows the user to view data from libraries, replicates, genes, transcripts, exons, and variants, including queries on allele imbalance for selected libraries. To determine the impact of allele-specific SNPs on protein folding, variants are annotated with their effect (e.g., missense), and the parental protein sequences may be exported for protein folding analysis. The Allele Workbench processing results in transcript files and read counts that can be used as input to the previously published Transcriptome Computational Workbench, which has a new algorithm for determining a trimmed set of gene ontology terms. The software with demo files is available from https://code.google.com/p/allele-workbench. Additionally, all software is ready for immediate use from an Atmosphere Virtual Machine Image available from the iPlant Collaborative (www.iplantcollaborative.org). PMID:25541944

Soderlund, Carol A.; Nelson, William M.; Goff, Stephen A.

2014-01-01

47

Allele workbench: transcriptome pipeline and interactive graphics for allele-specific expression.  

PubMed

Sequencing the transcriptome can answer various questions such as determining the transcripts expressed in a given species for a specific tissue or condition, evaluating differential expression, discovering variants, and evaluating allele-specific expression. Differential expression evaluates the expression differences between different strains, tissues, and conditions. Allele-specific expression evaluates expression differences between parental alleles. Both differential expression and allele-specific expression have been studied for heterosis (hybrid vigor), where the hybrid has improved performance over the parents for one or more traits. The Allele Workbench software was developed for a heterosis study that evaluated allele-specific expression for a mouse F1 hybrid using libraries from multiple tissues with biological replicates. This software has been made into a distributable package, which includes a pipeline, a Java interface to build the database, and a Java interface for query and display of the results. The required input is a reference genome, annotation file, and one or more RNA-Seq libraries with optional replicates. It evaluates allelic imbalance at the SNP and transcript level and flags transcripts with significant opposite directional allele-specific expression. The Java interface allows the user to view data from libraries, replicates, genes, transcripts, exons, and variants, including queries on allele imbalance for selected libraries. To determine the impact of allele-specific SNPs on protein folding, variants are annotated with their effect (e.g., missense), and the parental protein sequences may be exported for protein folding analysis. The Allele Workbench processing results in transcript files and read counts that can be used as input to the previously published Transcriptome Computational Workbench, which has a new algorithm for determining a trimmed set of gene ontology terms. The software with demo files is available from https://code.google.com/p/allele-workbench. Additionally, all software is ready for immediate use from an Atmosphere Virtual Machine Image available from the iPlant Collaborative (www.iplantcollaborative.org). PMID:25541944

Soderlund, Carol A; Nelson, William M; Goff, Stephen A

2014-01-01

48

HLA genes in the Chuvashian population from European Russia: admixture of Central European and Mediterranean populations.  

PubMed

HLA alleles have been determined for the first time in individuals from the Chuvashian population by DNA typing and sequencing. HLA-A, -B, -DR, and -DQ allele frequencies and extended haplotypes have also been determined, and the results compared to those for Central Europeans, Siberians and other Asians, Caucasians, Middle Easterners, and Mediterranean peoples. Genetic distances, neighbor-joining dendrograms, and correspondence analysis have been performed. Present-day Chuvash speak an Altaic-Turkic language and are genetically related to Caucasians (Georgians), Mediterraneans, and Middle Easterners, and not only to Central or Northern Europeans; Chuvash contain little indications of Central Asian-Altaic gene flow. Thus, present-day Chuvash who speak an Altaic-Turkic language are probably more closely related to ancient Mesopotamian-Hittites and northern European populations than to central Asia-Altaic people. PMID:14527201

Arnaiz-Villena, Antonio; Martinez-Laso, Jorge; Moscoso, Juan; Livshits, Gregory; Zamora, Jorge; Gomez-Casado, Eduardo; Silvera-Redondo, Carlos; Melvin, Kristin; Crawford, Michael H

2003-06-01

49

HLA allele detection using molecular techniques.  

PubMed

There are now many molecular biological techniques available to define HLA class I and class II alleles. Some of these are also applicable to other human polymorphic genes, in particular to those non-HLA genes encoded within the Mhc. The range of techniques available allows laboratories to choose those most suited to their purpose. The routine laboratory supporting solid organ transplants will need to type large numbers of potential recipients over a period of time, probably using PCR-SSOP while donors will be typed singly and rapidly using PCR-SSP with HLA allele compatibility determined by heteroduplex analysis. Laboratories supporting bone marrow transplantation, where time is less pressing, can choose from the whole range of techniques to determine accurately donor recipient Mhc compatibility. For disease studies, techniques defining precise HLA allele sequence polymorphisms are needed and high sample numbers have to be accommodated. When an association is established allele sequencing has to be used. In the near future, the precise role of HLA alleles in transplantation and disease susceptibility is likely to be established unambiguously. PMID:8112019

Dyer, P A; Jawaheer, D; Ollier, B; Poulton, K; Sinnott, P; Thomson, W

1993-11-01

50

European Mistletoe  

MedlinePLUS

... campaign . Top Sources American mistletoe. Natural Medicines Comprehensive Database Web site. Accessed at www.naturaldatabase.com on July 7, 2009. European mistletoe. Natural Medicines Comprehensive Database Web site. Accessed at www.naturaldatabase.com on ...

51

Demographic history and rare allele sharing among human populations.  

PubMed

High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2-4× coverage data for 179 samples from HapMap European, Asian, and African panels as well as high-coverage target sequencing of the exons of 800 genes from 697 individuals in seven populations. We use the site frequency spectra obtained from these data to infer demographic parameters for an Out-of-Africa model for populations of African, European, and Asian descent and to predict, by a jackknife-based approach, the amount of genetic diversity that will be discovered as sample sizes are increased. We predict that the number of discovered nonsynonymous coding variants will reach 100,000 in each population after ?1,000 sequenced chromosomes per population, whereas ?2,500 chromosomes will be needed for the same number of synonymous variants. Beyond this point, the number of segregating sites in the European and Asian panel populations is expected to overcome that of the African panel because of faster recent population growth. Overall, we find that the majority of human genomic variable sites are rare and exhibit little sharing among diverged populations. Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence. PMID:21730125

Gravel, Simon; Henn, Brenna M; Gutenkunst, Ryan N; Indap, Amit R; Marth, Gabor T; Clark, Andrew G; Yu, Fuli; Gibbs, Richard A; Bustamante, Carlos D

2011-07-19

52

Demographic history and rare allele sharing among human populations  

PubMed Central

High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2–4× coverage data for 179 samples from HapMap European, Asian, and African panels as well as high-coverage target sequencing of the exons of 800 genes from 697 individuals in seven populations. We use the site frequency spectra obtained from these data to infer demographic parameters for an Out-of-Africa model for populations of African, European, and Asian descent and to predict, by a jackknife-based approach, the amount of genetic diversity that will be discovered as sample sizes are increased. We predict that the number of discovered nonsynonymous coding variants will reach 100,000 in each population after ?1,000 sequenced chromosomes per population, whereas ?2,500 chromosomes will be needed for the same number of synonymous variants. Beyond this point, the number of segregating sites in the European and Asian panel populations is expected to overcome that of the African panel because of faster recent population growth. Overall, we find that the majority of human genomic variable sites are rare and exhibit little sharing among diverged populations. Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence. PMID:21730125

Gravel, Simon; Henn, Brenna M.; Gutenkunst, Ryan N.; Indap, Amit R.; Marth, Gabor T.; Clark, Andrew G.; Yu, Fuli; Gibbs, Richard A.; Bustamante, Carlos D.; Altshuler, David L.; Durbin, Richard M.; Abecasis, Gonçalo R.; Bentley, David R.; Chakravarti, Aravinda; Clark, Andrew G.; Collins, Francis S.; De La Vega, Francisco M.; Donnelly, Peter; Egholm, Michael; Flicek, Paul; Gabriel, Stacey B.; Gibbs, Richard A.; Knoppers, Bartha M.; Lander, Eric S.; Lehrach, Hans; Mardis, Elaine R.; McVean, Gil A.; Nickerson, Debbie A.; Peltonen, Leena; Schafer, Alan J.; Sherry, Stephen T.; Wang, Jun; Wilson, Richard K.; Gibbs, Richard A.; Deiros, David; Metzker, Mike; Muzny, Donna; Reid, Jeff; Wheeler, David; Wang, Jun; Li, Jingxiang; Jian, Min; Li, Guoqing; Li, Ruiqiang; Liang, Huiqing; Tian, Geng; Wang, Bo; Wang, Jian; Wang, Wei; Yang, Huanming; Zhang, Xiuqing; Zheng, Huisong; Lander, Eric S.; Altshuler, David L.; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Gabriel, Stacey B.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Bentley, David R.; Gormley, Niall; Humphray, Sean; Kingsbury, Zoya; Koko-Gonzales, Paula; Stone, Jennifer; McKernan, Kevin J.; Costa, Gina L.; Ichikawa, Jeffry K.; Lee, Clarence C.; Sudbrak, Ralf; Lehrach, Hans; Borodina, Tatiana A.; Dahl, Andreas; Davydov, Alexey N.; Marquardt, Peter; Mertes, Florian; Nietfeld, Wilfiried; Rosenstiel, Philip; Schreiber, Stefan; Soldatov, Aleksey V.; Timmermann, Bernd; Tolzmann, Marius; Egholm, Michael; Affourtit, Jason; Ashworth, Dana; Attiya, Said; Bachorski, Melissa; Buglione, Eli; Burke, Adam; Caprio, Amanda; Celone, Christopher; Clark, Shauna; Conners, David; Desany, Brian; Gu, Lisa; Guccione, Lorri; Kao, Kalvin; Kebbel, Andrew; Knowlton, Jennifer; Labrecque, Matthew; McDade, Louise; Mealmaker, Craig; Minderman, Melissa; Nawrocki, Anne; Niazi, Faheem; Pareja, Kristen; Ramenani, Ravi; Riches, David; Song, Wanmin; Turcotte, Cynthia; Wang, Shally; Mardis, Elaine R.; Wilson, Richard K.; Dooling, David; Fulton, Lucinda; Fulton, Robert; Weinstock, George; Durbin, Richard M.; Burton, John; Carter, David M.; Churcher, Carol; Coffey, Alison; Cox, Anthony; Palotie, Aarno; Quail, Michael; Skelly, Tom; Stalker, James; Swerdlow, Harold P.; Turner, Daniel; De Witte, Anniek; Giles, Shane; Gibbs, Richard A.; Wheeler, David; Bainbridge, Matthew; Challis, Danny; Sabo, Aniko; Yu, Fuli; Yu, Jin; Wang, Jun; Fang, Xiaodong; Guo, Xiaosen; Li, Ruiqiang; Li, Yingrui; Luo, Ruibang; Tai, Shuaishuai; Wu, Honglong; Zheng, Hancheng; Zheng, Xiaole; Zhou, Yan; Li, Guoqing; Wang, Jian; Yang, Huanming; Marth, Gabor T.; Garrison, Erik P.; Huang, Weichun; Indap, Amit; Kural, Deniz; Lee, Wan-Ping; Leong, Wen Fung; Quinlan, Aaron R.; Stewart, Chip; Stromberg, Michael P.; Ward, Alistair N.; Wu, Jiantao; Lee, Charles; Mills, Ryan E.; Shi, Xinghua; Daly, Mark J.; DePristo, Mark A.; Altshuler, David L.; Ball, Aaron D.; Banks, Eric; Bloom, Toby; Browning, Brian L.; Cibulskis, Kristian; Fennell, Tim J.; Garimella, Kiran V.; Grossman, Sharon R.; Handsaker, Robert E.; Hanna, Matt; Hartl, Chris; Jaffe, David B.; Kernytsky, Andrew M.; Korn, Joshua M.; Li, Heng; Maguire, Jared R.; McCarroll, Steven A.; McKenna, Aaron; Nemesh, James C.; Philippakis, Anthony A.; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis C.; Schaffner, Stephen F.; Shefler, Erica; Shlyakhter, Ilya A.; Cooper, David N.; Ball, Edward V.; Mort, Matthew; Phillips, Andrew D.; Stenson, Peter D.; Sebat, Jonathan; Makarov, Vladimir; Ye, Kenny; Yoon, Seungtai C.; Bustamante, Carlos D.; Clark, Andrew G.; Boyko, Adam; Degenhardt, Jeremiah; Gravel, Simon; Gutenkunst, Ryan N.; Kaganovich, Mark; Keinan, Alon; Lacroute, Phil; Ma, Xin; Reynolds, Andy; Clarke, Laura; Flicek, Paul; Cunningham, Fiona; Herrero, Javier; Keenen, Stephen; Kulesha, Eugene; Leinonen, Rasko; McLaren, William M.; Radhakrishnan, Rajesh; Smith, Richard E.; Zalunin, Vadim; Zheng-Bradley, Xiangqun; Korbel, Jan O.; Stütz, Adrian M.; Humphray, Sean; Bauer, Markus; Cheetham, R. Keira; Cox, Tony; Eberle, Michael; James, Terena; Kahn, Scott; Murray, Lisa; Chakravarti, Aravinda; Ye, Kai; De La Vega, Francisco M.; Fu, Yutao; Hyland, Fiona C. L.; Manning, Jonathan M.; McLaughlin, Stephen F.; Peckham, Heather E.; Sakarya, Onur; Sun, Yongming A.; Tsung, Eric F.; Batzer, Mark A.; Konkel, Miriam K.; Walker, Jerilyn A.; Sudbrak, Ralf; Albrecht, Marcus W.; Amstislavskiy, Vyacheslav S.; Herwig, Ralf; Parkhomchuk, Dimitri V.; Sherry, Stephen T.; Agarwala, Richa; Khouri, Hoda M.; Morgulis, Aleksandr O.; Paschall, Justin E.; Phan, Lon D.; Rotmistrovsky, Kirill E.; Sanders, Robert D.

2011-01-01

53

Genetic Differences between Five European Populations  

Microsoft Academic Search

Aims: We sought to examine the magnitude of the differences in SNP allele frequencies between five European populations (Scotland, Ireland, Sweden, Bulgaria and Portugal) and to identify the loci with the greatest differences. Methods: We performed a population-based genome-wide association analysis with Affymetrix 6.0 and 5.0 arrays. We used a 4 degrees of freedom ?2 test to determine the magnitude

Valentina Moskvina; Michael Smith; Dobril Ivanov; Douglas Blackwood; David StClair; Christina Hultman; Draga Toncheva; Michael Gill; Aiden Corvin; Colm O’Dushlaine; Derek W. Morris; Naomi R. Wray; Patrick Sullivan; Carlos Pato; Michele T. Pato; Pamela Sklar; Shaun Purcell; Peter Holmans; Michael C. O’Donovan; Michael J. Owen; George Kirov

2010-01-01

54

Allele and genotype frequencies of serotonin and dopamine transporter and receptor polymorphisms in a Norwegian population.  

PubMed

Polymorphisms in genes coding for dopaminergic and serotonergic receptors and transporters have been associated with the clinical effects and adverse drug reactions of antipsychotic and antidepressant drugs. The objective of this study was to investigate the frequency and combinations of common polymorphisms in the dopamine transporter (DAT1), dopamine D(2) receptor (DRD2), dopamine D(3) receptor (DRD3), serotonin transporter (5HTT), and serotonin 2A receptor (5HTR2A) genes in a Norwegian population. To determine the background frequency in the population, 250 blood samples were consecutively collected from healthy Norwegian blood donors (125 men and 125 women; mean age: 48±11 years). Samples were tested for DAT1 VNTR, DRD2 Taq1A, DRD3 Ser9Gly, 5HTTLPR, and four polymorphisms (102 T>C, His452Tyr, 516 C>T, and Thr25Asn) in the 5HTR2A, using polymerase chain reaction and real-time polymerase chain reaction. We observed the frequency of the nine-repeat allele of DAT1 VNTR polymorphism as 20% (95% confidence interval [CI]: 0.18-0.23), the A1 allele of DRD2 Taq1A polymorphism as 21% (95% CI: 0.19-0.23), the A1 allele of DRD3 Ser9Gly polymorphism as 68% (95% CI: 0.66-0.70), the short allele of 5HTTLPR as 38% (95% CI: 0.36-0.40), and the T allele of 5HTR2A 102 T>C polymorphism as 41% (95% CI: 0.39-0.41), and the frequencies of 5HTR2A His452Tyr and 5HTR2A Thr25Asn were 93% and 95%, respectively. The tested polymorphisms showed differences compared with other European populations. Further studies are necessary to better understand the effect of these alleles and their combinations on personality, mental disorders, drug response, and adverse reactions of psychotropic drugs. PMID:21453053

Güzey, Cüneyt; Lopez-Rodriguez, Rosario; Myhre, Ronny; Spigset, Olav

2011-01-01

55

Recombinational micro-evolution of functionally different metallothionein promoter alleles from Orchesella cincta  

PubMed Central

Background Metallothionein (mt) transcription is elevated in heavy metal tolerant field populations of Orchesella cincta (Collembola). This suggests that natural selection acts on transcriptional regulation of mt in springtails at sites where cadmium (Cd) levels in soil reach toxic values This study investigates the nature and the evolutionary origin of polymorphisms in the metallothionein promoter (pmt) and their functional significance for mt expression. Results We sequenced approximately 1600 bp upstream the mt coding region by genome walking. Nine pmt alleles were discovered in NW-European populations. They differ in the number of some indels, consensus transcription factor binding sites and core promoter elements. Extensive recombination events between some of the alleles can be inferred from the alignment. A deviation from neutral expectations was detected in a cadmium tolerant population, pointing towards balancing selection on some promoter stretches. Luciferase constructs were made from the most abundant alleles, and responses to Cd, paraquat (oxidative stress inducer) and moulting hormone were studied in cell lines. By using paraquat we were able to dissect the effect of oxidative stress from the Cd specific effect, and extensive differences in mt induction levels between these two stressors were observed. Conclusion The pmt alleles evolved by a number of recombination events, and exhibited differential inducibilities by Cd, paraquat and molting hormone. In a tolerant population from a metal contaminated site, promoter allele frequencies differed significantly from a reference site and nucleotide polymorphisms in some promoter stretches deviated from neutral expectations, revealing a signature of balancing selection. Our results suggest that the structural differences in the Orchesella cincta metallothionein promoter alleles contribute to the metallothionein -over-expresser phenotype in cadmium tolerant populations. PMID:17562010

Janssens, Thierry KS; Mariën, Janine; Cenijn, Peter; Legler, J; van Straalen, Nico M; Roelofs, Dick

2007-01-01

56

Molecular analysis of human leukocyte antigen class I and class II allele frequencies and haplotype distribution in Pakistani population  

PubMed Central

AIM: Distribution of HLA class I and II alleles and haplotype was studied in Pakistani population and compared with the data reported for Caucasoid, Africans, Orientals and Arab populations. MATERIALS AND METHODS: HLA class I and II polymorphisms in 1000 unrelated Pakistani individuals was studied using sequence-specific primers and polymerase chain reaction and assay. RESULTS: The most frequent class I alleles observed were A*02, B*35 and CW*07, with frequencies of 19.2, 13.7 and 20%, respectively. Fifteen distinct HLA-DRB1 alleles and eight HLA-DQB1 alleles were recognized. The most frequently observed DRB1 alleles which represented more than 60% of the subjects were DRB1 *03, *07, *11 and *15. The rare DRB1 alleles detected in this study were HLADRB1 *08 and *09, having frequencies of 0.9 and 1.7%, respectively. In addition, at DRB1-DQB1 loci there were 179 different haplotypes and 285 unique genotypes and the most common haplotype was DRB1*15-DQB1*06 which represented 17% of the total DRB1-DQB1 haplotypes. In our population, haplotype A*33-B*58-Cw*03 comprised 2.8% of the total class I haplotypes observed. This haplotype was seen only in the oriental populations and has not been reported in the African or European Caucasoid. CONCLUSION: Our study showed a close similarity of HLA class I and II alleles with that of European Caucasoid and Orientals. In Pakistani population, two rare loci and three haplotypes were identified, whereas haplotypes characteristic of Caucasians, Africans and Orientals were also found, suggesting an admixture of different races due to migration to and from this region. PMID:21206703

Moatter, T.; Aban, M.; Tabassum, S.; Shaikh, U.; Pervez, S.

2010-01-01

57

Non-random Allelic Variation Natural Selection  

E-print Network

Non-random Allelic Variation AKA Natural Selection #12;Adaptation!Adaptation! #12;#12;Venus comb or ­ a feature that is maintained because of natural selection for its function preadaptation ­ a trait history #12;Natural Selection Evolution evolution is a two step process 1) origin of genetic variation 2

Houde, Peter

58

Tetrasomic segregation for multiple alleles in alfalfa.  

PubMed

Evidence of tetrasomic inheritance in alfalfa, Medicago sativa L. and M. falcata L., for multiple codominant alleles at three isozymic loci is reported in this study. The locus Prx-1 governing anodal peroxidase and the loci Lap-1 and Lap-2 governing anodal leucine-aminopeptidase were studied by starch gel electrophoresis in seedling root tissue or seeds. The progenies from several di-, tri- or tetra-allelic plants belong to the species M. sativa and M. falcata and their hybrids were studied for the segregation of the three genes. In all cases, tetrasomic inheritance of chromosomal-type segregation was observed. In another progeny resulting from the crossing of two plants involving four different alleles at locus Lap-2, tetrasomic segregation with the possible occurrence of double reduction was observed. This study presents direct evidence of autotetraploidy and the existence of tetra-allelic loci in alfalfa. It also supports the concept that the species M. sativa and M. falcata are genetically close enough to be considered biotypes of a common species. PMID:17246077

Quiros, C F

1982-05-01

59

Original article Latitudinal clines of allelic frequencies  

E-print Network

of Ceratitis capitata (Wiedemann) A Kourti P Hatzopoulos2 1 Agricultural University of Athens, Laboratory October 1994) Summary - Collections of Ceratitis capitata from 6 different areas from 4 Mediterranean.00 to 0.63) is observed in the axis of the north-south transect. Ceratitis capitata/ allelic frequency

Paris-Sud XI, Université de

60

Original investigation Genetic diversity within Anatolian brown hares (Lepus europaeus Pallas, 1778) and differentiation among Anatolian and European populations  

Microsoft Academic Search

Genetic variability of Anatolian hares and relationships between Anatolian and European populations were assessed by a multilocus allozyme approach to infer evolutionary relationships between hares from Asia Minor and Europe. Of the 48 loci assayed, 19 (39.6%) were polymorphic with two to four alleles in the Anatolian hares. Among all Anatolian alleles, 14 were so far not found in the

H. Sert; F. Suchentrunk; A. Erdog

2005-01-01

61

Genetic diversity within Anatolian brown hares ( Lepus europaeus Pallas, 1778) and differentiation among Anatolian and European populations  

Microsoft Academic Search

Genetic variability of Anatolian hares and relationships between Anatolian and European populations were assessed by a multilocus allozyme approach to infer evolutionary relationships between hares from Asia Minor and Europe. Of the 48 loci assayed, 19 (39.6%) were polymorphic with two to four alleles in the Anatolian hares. Among all Anatolian alleles, 14 were so far not found in the

H. Sert; F. Suchentrunk; A. Erdo?an

2005-01-01

62

Linker histone subtypes and their allelic variants.  

PubMed

Members of histone H1 family bind to nucleosomal and linker DNA to assist in stabilization of higher-order chromatin structures. Moreover, histone H1 is involved in regulation of a variety of cellular processes by interactions with cytosolic and nuclear proteins. Histone H1, composed of a series of subtypes encoded by distinct genes, is usually differentially expressed in specialized cells and frequently non-randomly distributed in different chromatin regions. Moreover, a role of specific histone H1 subtype might be also modulated by post-translational modifications and/or presence of polymorphic isoforms. While the significance of covalently modified histone H1 subtypes has been partially recognized, much less is known about the importance of histone H1 polymorphic variants identified in various plant and animal species, and human cells as well. Recent progress in elucidating amino acid composition-dependent functioning and interactions of the histone H1 with a variety of molecular partners indicates a potential role of histone H1 polymorphic variation in adopting specific protein conformations essential for chromatin function. The histone H1 allelic variants might affect chromatin in order to modulate gene expression underlying some physiological traits and, therefore could modify the course of diverse histone H1-dependent biological processes. This review focuses on the histone H1 allelic variability, and biochemical and genetic aspects of linker histone allelic isoforms to emphasize their likely biological relevance. PMID:23075301

Kowalski, Andrzej; Pa?yga, Jan

2012-11-01

63

Mutant maize variety containing the glt1-1 allele  

DOEpatents

A maize plant has in its genome a non-mutable form of a mutant allele designated vitX-8132. The allele is located at a locus designated as glt which conditions kernels having an altered starch characteristic. Maize plants including such a mutant allele produce a starch that does not increase in viscosity on cooling, after heating.

Nelson, Oliver E. (Cross Plains, WI); Pan, David (Madison, WI)

1994-01-01

64

Distribution of CYP2D6 Alleles and Phenotypes in the Brazilian Population  

PubMed Central

Abstract The CYP2D6 enzyme is one of the most important members of the cytochrome P450 superfamily. This enzyme metabolizes approximately 25% of currently prescribed medications. The CYP2D6 gene presents a high allele heterogeneity that determines great inter-individual variation. The aim of this study was to evaluate the variability of CYP2D6 alleles, genotypes and predicted phenotypes in Brazilians. Eleven single nucleotide polymorphisms and CYP2D6 duplications/multiplications were genotyped by TaqMan assays in 1020 individuals from North, Northeast, South, and Southeast Brazil. Eighteen CYP2D6 alleles were identified in the Brazilian population. The CYP2D6*1 and CYP2D6*2 alleles were the most frequent and widely distributed in different geographical regions of Brazil. The highest number of CYPD6 alleles observed was six and the frequency of individuals with more than two copies ranged from 6.3% (in Southern Brazil) to 10.2% (Northern Brazil). The analysis of molecular variance showed that CYP2D6 is homogeneously distributed across different Brazilian regions and most of the differences can be attributed to inter-individual differences. The most frequent predicted metabolic status was EM (83.5%). Overall 2.5% and 3.7% of Brazilians were PMs and UMs respectively. Genomic ancestry proportions differ only in the prevalence of intermediate metabolizers. The IM predicted phenotype is associated with a higher proportion of African ancestry and a lower proportion of European ancestry in Brazilians. PM and UM classes did not vary among regions and/or ancestry proportions therefore unique CYP2D6 testing guidelines for Brazilians are possible and could potentially avoid ineffective or adverse events outcomes due to drug prescriptions. PMID:25329392

Sortica, Vinicius A.; Suarez-Kurtz, Guilherme; de Moraes, Maria Elizabete; Pena, Sergio D. J.; dos Santos, Ândrea K. Ribeiro; Romano-Silva, Marco A.; Hutz, Mara H.

2014-01-01

65

Underexpression of the apolipoprotein E2 and E4 alleles in the Greek Cypriot population of Cyprus.  

PubMed

Apolipoprotein E (APOE) plays an important role in the multifactorial etiology of both cardiovascular disease and Alzheimer's disease. Polymerase chain reaction (PCR) was used to investigate the APOE gene polymorphism in 335 unrelated Greek Cypriots living on the island of Cyprus. For the most common APOE genotypes, the Greek Cypriots followed the general Caucasian European pattern of having higher genotypic frequencies of E3/3, followed by E3/4, and then E2/3. Among the European populations compared, Greek Cypriots exhibited the lowest relative frequency of the E3/4 genotype (12.83%). Also, the relative frequencies of the E2 and E4 alleles in Greek Cypriots were among the lowest around the world (5.4% and 7.0%, respectively). This was also demonstrated by using the complete and the average clustering methods of analysis where the APOE allele relative frequencies in Greek Cypriots were compared to 46 other populations. The Greek Cypriot population in these analyses clustered with populations mainly from south Europe and Japan which have low E2 and E4 allele frequencies. The Greek Cypriot population will be studied further for elucidating the effect(s) and the role of APOE in cardiovascular disease and the APOE4 allele as a possible metabolic factor affecting the rate of expression of both Alzheimer's disease and vascular dementia. PMID:8557181

Cariolou, M A; Kokkofitou, A; Manoli, P; Christou, S; Karagrigoriou, A; Middleton, L

1995-01-01

66

KRAS mutant allele-specific imbalance in lung adenocarcinoma.  

PubMed

The significance of KRAS mutant allele-specific imbalance (MASI) in lung adenocarcinomas is unknown. KRAS MASI was defined as predominance of the mutant allele over the wild-type allele. We assessed the frequency of KRAS MASI by comparing peak heights of mutant and wild-type alleles on sequencing electropherograms and by KRAS fluorescence in situ hybridization (FISH). A review of sequencing electropherograms of 207 KRAS-mutated lung adenocarcinomas demonstrated 23 (11%) cases with the mutant allele peak higher than the wild-type allele peak and 15 (7%) cases with the mutant allele peak equal to the wild-type allele peak. Of 17 cases with the mutant allele peak higher or equal to the wild-type allele peak, 8 (47%) showed KRAS amplification by FISH. KRAS FISH analysis of 36 KRAS-mutated lung adenocarcinomas with the mutant allele peak lower than the wild-type allele peak, 21 KRAS and EGFR wild-type and 16 EGFR-mutated adenocarcinomas showed no KRAS amplification. KRAS MASI was associated with selective amplification of the KRAS mutant allele (P<0.001). Patients with KRAS MASI showed worse overall survival. The cumulative proportion surviving at 17 months for KRAS MASI group was 35% compared with 84.1% for patients with KRAS mutant allele peak lower than wild-type allele peak (P=0.012). The adverse prognostic significance of KRAS MASI was independent of clinical stage and was maintained among stage I patients. The detection of KRAS MASI in lung adenocarcinomas by sequencing electropherograms may identify patients with more aggressive disease. PMID:21743433

Chiosea, Simion I; Sherer, Carol K; Jelic, Tomislav; Dacic, Sanja

2011-12-01

67

Am. J. Hum. Genet. 74:11021110, 2004 The T Allele of a Single-Nucleotide Polymorphism 13.9 kb Upstream  

E-print Network

in populations of European descent, in which, for exam- ple, Dutch and Swedish studies recorded frequencies sugar lactose as an adult (lactase persistence) is a variable genetic trait in human populationsAm. J. Hum. Genet. 74:1102­1110, 2004 1102 The T Allele of a Single-Nucleotide Polymorphism 13.9 kb

Weale, Michael E.

68

Assignment of allelic configuration in polyploids using the MAC-PR (microsatellite DNA allele counting—peak ratios) method  

Microsoft Academic Search

Polysomic inheritance frequently results in the simultaneous occurrence of several microsatellite DNA alleles on a single locus. The MAC-PR (microsatellite DNA allele counting—peak ratios) method was recently developed for the analysis of polyploid plants and makes use of the quantitative values for microsatellite allele peak areas. To date, this approach has only been used in plants with known genetic relationships.

G. D. Esselink; H. Nybom; B. J. Vosman

2004-01-01

69

Relative predispositional effects (RPEs) of marker alleles with disease: HLA-DR alleles and Graves disease.  

PubMed Central

A method is described to reveal the relative predispositional effects (RPEs) (predisposing, protective, or neutral) of the HLA alleles or of any other marker system that is associated with a disease. When the disease is associated with two or more alleles of a locus, the RPE method identifies the associations sequentially according to their strength; thus the problem that a strong association with one allele can create misleading deviations in the frequencies of other alleles is alleviated. Using this method, we have examined the relative effects of HLA-DR alleles in susceptibility to Graves disease in the Caucasian population. The well-established positive association with DR3 was confirmed as the strongest effect. In addition, a negative association was found between DR5 and Graves disease. The reduced frequency of DR5 among patients is statistically significant and is not a result of the increase in DR3. Finally, when patients were divided according to the presence or absence of eye disease, the latter showed a significant increase in the frequency of DR4. With family data, linkage to HLA of Graves disease was established in both Caucasian and Chinese families by the sib-pair method. PMID:2491013

Payami, H; Joe, S; Farid, N R; Stenszky, V; Chan, S H; Yeo, P P; Cheah, J S; Thomson, G

1989-01-01

70

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

PubMed

Interindividual variability in xenobiotic metabolism and drug response is extensive and genetic factors play an important role in this variation. A majority of clinically used drugs are substrates for the cytochrome P450 (CYP) enzyme system and interindividual variability in expression and function of these enzymes is a major factor for explaining individual susceptibility for adverse drug reactions and drug response. Because of the existence of many polymorphic CYP genes, for many of which the number of allelic variants is continually increasing, a universal and official nomenclature system is important. Since 1999, all functionally relevant polymorphic CYP alleles are named and published on the Human Cytochrome P450 Allele (CYP-allele) Nomenclature Web site (http://www.cypalleles.ki.se). Currently, the database covers nomenclature of more than 660 alleles in a total of 30 genes that includes 29 CYPs as well as the cytochrome P450 oxidoreductase (POR) gene. On the CYP-allele Web site, each gene has its own Webpage, which lists the alleles with their nucleotide changes, their functional consequences, and links to publications identifying or characterizing the alleles. CYP2D6, CYP2C9, CYP2C19, and CYP3A4 are the most important CYPs in terms of drug metabolism, which is also reflected in their corresponding highest number of Webpage hits at the CYP-allele Web site.The main advantage of the CYP-allele database is that it offers a rapid online publication of CYP-alleles and their effects and provides an overview of peer-reviewed data to the scientific community. Here, we provide an update of the CYP-allele database and the associated nomenclature. PMID:23475683

Sim, Sarah C; Ingelman-Sundberg, Magnus

2013-01-01

71

Allelic genealogies in sporophytic self-incompatibility systems in plants.  

PubMed Central

Expectations for the time scale and structure of allelic genealogies in finite populations are formed under three models of sporophytic self-incompatibility. The models differ in the dominance interactions among the alleles that determine the self-incompatibility phenotype: In the SSIcod model, alleles act codominantly in both pollen and style, in the SSIdom model, alleles form a dominance hierarchy, and in SSIdomcod, alleles are codominant in the style and show a dominance hierarchy in the pollen. Coalescence times of alleles rarely differ more than threefold from those under gametophytic self-incompatibility, and transspecific polymorphism is therefore expected to be equally common. The previously reported directional turnover process of alleles in the SSIdomcod model results in coalescence times lower and substitution rates higher than those in the other models. The SSIdom model assumes strong asymmetries in allelic action, and the most recessive extant allele is likely to be the most recent common ancestor. Despite these asymmetries, the expected shape of the allele genealogies does not deviate markedly from the shape of a neutral gene genealogy. The application of the results to sequence surveys of alleles, including interspecific comparisons, is discussed. PMID:9799270

Schierup, M H; Vekemans, X; Christiansen, F B

1998-01-01

72

Allele-Specific KRT1 Expression Is a Complex Trait  

PubMed Central

The differential expression of alleles occurs commonly in humans and is likely an important genetic factor underlying heritable differences in phenotypic traits. Understanding the molecular basis of allelic expression differences is thus an important challenge. Although many genes have been shown to display differential allelic expression, this is the first study to examine in detail the cumulative effects of multiple cis-regulatory polymorphisms responsible for allele-specific expression differences. We have used a variety of experimental approaches to identify and characterize cis-regulatory polymorphisms responsible for the extreme allele-specific expression differences of keratin-1 (KRT1) in human white blood cells. The combined data from our analyses provide strong evidence that the KRT1 allelic expression differences result from the haplotypic combinations and interactions of five cis-regulatory single nucleotide polymorphisms (SNPs) whose alleles differ in their affinity to bind transcription factors and modulate KRT1 promoter activity. Two of these cis-regulatory SNPs bind transcriptional activators with the alleles on the high-expressing KRT1 haplotype pattern having a higher affinity than the alleles on the low-expressing haplotype pattern. In contrast, the other three cis-regulatory SNPs bind transcriptional inhibitors with the alleles on the low-expressing haplotype pattern having a higher affinity than the alleles on the high-expressing haplotype pattern. Our study provides important new insights into the degree of complexity that the cis-regulatory sequences responsible for allele-specific transcriptional regulation have. These data suggest that allelic expression differences result from the cumulative contribution of multiple DNA sequence polymorphisms, with each having a small effect, and that allele-specific expression can thus be viewed as a complex trait. PMID:16789827

Tao, Heng; Cox, David R; Frazer, Kelly A

2006-01-01

73

European Central Bank  

NSDL National Science Digital Library

Together with the national central banks of the European Union, the European Central Bank (ECB) collects statistical information and governs the European System of Central Banks (ESCB). Legal texts about the ECB, the ESCB, and the European Monetary Union (EMI) are provided in addition to press releases, speeches, euro area statistics and selected publications of the EMI (in eleven European languages).

74

Construction of Bald Eagle (Haliaeetus leucocephalus) Hal01 Locus Allelic Ladder  

Microsoft Academic Search

Allelic ladders contain all the alleles at a given locus and since the components of the allelic ladder and the sample fragments have the same length and sequence, sizing is very accurate when conducted with an allelic ladder. Allelic ladders are therefore very useful in population genetics studies. For this study, an allelic ladder for the Bald Eagle, Haliaeetus leucocephalus,

Manali Patel

2012-01-01

75

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

PubMed

The aim of this study was to estimate the HLA-A, HLA-B and HLA-DRB1 allele groups frequencies in a population of 1559 volunteer bone marrow donors from the northwestern region of São Paulo State grouped according to ethnicity. An additional objective was to compare the allele frequencies of the current study with data published for other Brazilian populations. The allele groups were characterized by the PCR-rSSO method using Luminex(®) technology. Twenty HLA-A, 32 HLA-B and 13 HLA-DRB1 allele groups were identified. The most common allele groups in European descent and mixed African and European descent samples were HLA-A*02, HLA-B*35 and HLA-DRB1*13, while HLA-A*02, HLA-B*35 and HLA-DRB1*11 were more common in African descent samples. The HLA-A*23, HLA-A*36, HLA-B*58 and HLA-B*81 allele groups were more common in sample from African descent than European descent, and the HLA-DRB1*08 was more common in mixed African and European descent than in European descent. Allele group frequencies were compared with samples from other Brazilian regions. The HLA-A*30 and HLA-A*23 were more common in this study than in the populations of Rio Grande do Sul and Paraná; and the HLA-A*01, HLA-B*18, HLA-B*57 and HLA-DRB1*11 were more common in this study than in the population of Piauí. The least frequent allele groups were HLA-A*31, HLA-B*15, HLA-B*40 and HLA-DRB1*08 for the population of Piauí, HLA-A*01 and HLA-A*11 for Parana, HLA-A*02 and -A*03 for Rio Grande do Sul and HLA-DRB1*04 for Paraná, Rio Grande do Sul and Piauí. These data provide an overview on the knowledge on HLA diversity in the population of the northwestern region of São Paulo State and show that the genes of this system are useful to distinguish different ethnic groups. PMID:25418108

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

2015-02-01

76

Cellular Adhesion Gene SELP Is Associated with Rheumatoid Arthritis and Displays Differential Allelic Expression  

PubMed Central

In rheumatoid arthritis (RA), a key event is infiltration of inflammatory immune cells into the synovial lining, possibly aggravated by dysregulation of cellular adhesion molecules. Therefore, single nucleotide polymorphisms of 14 genes involved in cellular adhesion processes (CAST, ITGA4, ITGB1, ITGB2, PECAM1, PTEN, PTPN11, PTPRC, PXN, SELE, SELP, SRC, TYK2, and VCAM1) were analyzed for association with RA. Association analysis was performed consecutively in three European RA family sample groups (Nfamilies?=?407). Additionally, we investigated differential allelic expression, a possible functional consequence of genetic variants. SELP (selectin P, CD62P) SNP-allele rs6136-T was associated with risk for RA in two RA family sample groups as well as in global analysis of all three groups (ptotal?=?0.003). This allele was also expressed preferentially (p<10?6) with a two- fold average increase in regulated samples. Differential expression is supported by data from Genevar MuTHER (p1?=?0.004; p2?=?0.0177). Evidence for influence of rs6136 on transcription factor binding was also found in silico and in public datasets reporting in vitro data. In summary, we found SELP rs6136-T to be associated with RA and with increased expression of SELP mRNA. SELP is located on the surface of endothelial cells and crucial for recruitment, adhesion, and migration of inflammatory cells into the joint. Genetically determined increased SELP expression levels might thus be a novel additional risk factor for RA. PMID:25147926

Petit-Teixeira, Elisabeth; Hugo Teixeira, Vitor; Steiner, Anke; Quente, Elfi; Wolfram, Grit; Scholz, Markus; Pierlot, Céline; Migliorini, Paola; Bombardieri, Stefano; Balsa, Alejandro; Westhovens, René; Barrera, Pilar; Radstake, Timothy R. D. J.; Alves, Helena; Bardin, Thomas; Prum, Bernard; Emmrich, Frank; Cornelis, François

2014-01-01

77

Wheat alleles introgress into selfing wild relatives: empirical estimates from approximate Bayesian computation in Aegilops triuncialis.  

PubMed

Extensive gene flow between wheat (Triticum sp.) and several wild relatives of the genus Aegilops has recently been detected despite notoriously high levels of selfing in these species. Here, we assess and model the spread of wheat alleles into natural populations of the barbed goatgrass (Aegilops triuncialis), a wild wheat relative prevailing in the Mediterranean flora. Our sampling, based on an extensive survey of 31 Ae. triuncialis populations collected along a 60 km × 20 km area in southern Spain (Grazalema Mountain chain, Andalousia, totalling 458 specimens), is completed with 33 wheat cultivars representative of the European domesticated pool. All specimens were genotyped with amplified fragment length polymorphism with the aim of estimating wheat admixture levels in Ae. triuncialis populations. This survey first confirmed extensive hybridization and backcrossing of wheat into the wild species. We then used explicit modelling of populations and approximate Bayesian computation to estimate the selfing rate of Ae. triuncialis along with the magnitude, the tempo and the geographical distance over which wheat alleles introgress into Ae. triuncialis populations. These simulations confirmed that extensive introgression of wheat alleles (2.7 × 10(-4) wheat immigrants for each Ae. triuncialis resident, at each generation) into Ae. triuncialis occurs despite a high selfing rate (Fis ? 1 and selfing rate = 97%). These results are discussed in the light of risks associated with the release of genetically modified wheat cultivars in Mediterranean agrosystems. PMID:25223217

Pajkovic, Mila; Lappe, Sylvain; Barman, Rachel; Parisod, Christian; Neuenschwander, Samuel; Goudet, Jerome; Alvarez, Nadir; Guadagnuolo, Roberto; Felber, François; Arrigo, Nils

2014-10-01

78

Demography can favour female-advantageous alleles.  

PubMed

When female fecundity is relatively independent of male abundance, while male reproduction is proportional to female abundance, females have a larger effect on population dynamics than males (i.e. female demographic dominance). This population dynamic phenomenon might not appear to influence evolution, because male and female genomes still contribute equally much to the next generation. However, here we examine two evolutionary scenarios to provide a proof of principle that spatial structure can make female demographic dominance matter. Our two simulation models combine dispersal evolution with local adaptation subjected to intralocus sexual conflict and environmentally driven sex ratio biases, respectively. Both models have equilibria where one environment (without being intrinsically poorer) has so few reproductive females that trait evolution becomes disproportionately determined by those environments where females survive better (intralocus sexual conflict model), or where daughters are overproduced (environmental sex determination model). Surprisingly, however, the two facts that selection favours alleles that benefit females, and population growth is improved when female fitness is high, together do not imply that all measures of population performance are improved. The sex-specificity of the source-sink dynamics predicts that populations can evolve to fail to persist in habitats where alleles do poorly when expressed in females. PMID:25056617

Harts, Anna M F; Schwanz, Lisa E; Kokko, Hanna

2014-09-01

79

Plasminogen Alleles Influence Susceptibility to Invasive Aspergillosis  

PubMed Central

Invasive aspergillosis (IA) is a common and life-threatening infection in immunocompromised individuals. A number of environmental and epidemiologic risk factors for developing IA have been identified. However, genetic factors that affect risk for developing IA have not been clearly identified. We report that host genetic differences influence outcome following establishment of pulmonary aspergillosis in an exogenously immune suppressed mouse model. Computational haplotype-based genetic analysis indicated that genetic variation within the biologically plausible positional candidate gene plasminogen (Plg; Gene ID 18855) correlated with murine outcome. There was a single nonsynonymous coding change (Gly110Ser) where the minor allele was found in all of the susceptible strains, but not in the resistant strains. A nonsynonymous single nucleotide polymorphism (Asp472Asn) was also identified in the human homolog (PLG; Gene ID 5340). An association study within a cohort of 236 allogeneic hematopoietic stem cell transplant (HSCT) recipients revealed that alleles at this SNP significantly affected the risk of developing IA after HSCT. Furthermore, we demonstrated that plasminogen directly binds to Aspergillus fumigatus. We propose that genetic variation within the plasminogen pathway influences the pathogenesis of this invasive fungal infection. PMID:18566672

Zaas, Aimee K.; Liao, Guochun; Chien, Jason W.; Weinberg, Clarice; Shore, David; Giles, Steven S.; Marr, Kieren A.; Usuka, Jonathan; Burch, Lauranell H.; Perera, Lalith; Perfect, John R.; Peltz, Gary; Schwartz, David A.

2008-01-01

80

Allele-specific gene targeting in Candida albicans results from heterology between alleles  

Microsoft Academic Search

The opportunistic fungal pathogen Candida albicans is asexual and diploid. Thus, introduction of recessive mutations requires targeted gene replacement of two alleles to effect expression of a recessive phenotype. This is often performed by recycling of a URA3 marker gene that is flanked by direct repeats of hisG. After targeting to a locus, recombination between the repeats excises URA3 leaving

Kyle Yesland; William A. Fonzi

2000-01-01

81

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

PubMed

The prevalence of rheumatoid arthritis and its specific autoantibodies varies in different populations. This variability depends on the genetic polymorphism of the immune response genes among which the HLA system plays a major role. In this context, we studied the HLA-DRB1 and HLA-DQB1 first-level allele frequencies in 100 Albanian patients with rheumatoid arthritis (RA), and taking into account their rheumatoid factor (RF) and anticitrullinated peptide antibodies (ACPA) serologic subgroups, we compared them with the respective frequencies in a population of 191 Albanian individuals without known pathology. No differences were found between the controls and the RA patient group as a whole, but three statistically significant differences were found: an increase in DRB1*04 among ACPA+, RF+ and ACPA+/RF+ patients, a significant decrease in DRB1*11 among ACPA+/RF+ and also a decrease in DRB1*13 among RF+ patient subgroups. Comparing allele frequencies of putatively associated RA alleles in different European populations revealed a significant negative correlation between the RA predisposing DRB1*04 and protective DRB1*11 allele frequencies. A statistically significant correlation was also found between RA prevalence rates and DRB1*04 as well as DRB1*11 frequencies. The relatively low frequencies of DRB1*04 and high DRB1*11 in the Albanian population might explain the rather low positivity rate of ACPA and RF antibodies among the Albanian RA patients. These specific association patterns suggest that this first study of RA in an Albanian population should be followed up to include second level or higher definition of HLA alleles and to compare RA patterns among European populations. PMID:24381092

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

2014-08-01

82

Polymorphism in the GBSS gene affects amylose content in US and European rice germplasm  

Microsoft Academic Search

The present study was conducted to investigate the relationship between waxy allelic forms and amylose in European and US rice germplasm. These allelic forms were defined according to the single-nucleotide polymorphisms (SNP) found in the leader intron 5? splice site (G ? T), exon 6 (A ? C) and exon 10 (C ? T). The combination of these three SNPs accounted for 89.2% of the variation

Macaire Dobo; Nicolas Ayres; Grace Walker; Williams D. Park

2010-01-01

83

Immunogenetics of two new HLA alleles: A*0108 and B*4031.  

PubMed

Two new alleles, HLA-A*0108 and B*4031, were identified in north-western European Caucasoid subjects. A*0108 differed from A*010101 by a single substitution (C to T) at position 216 in exon 3, resulting in an amino acid difference of Arg to Trp at position 163. It was present on a haplotype with B*1501/60/70/71; Cw*0303; DRB1*1301; DRB3*0202; DQA1*0103; DQB1*0603 and its product reacted as a normal HLA-A1 specificity. B*4031 differed from B*4001 by two nucleotides in exon 3 (positions 20 (G to C) and 69 (A to G)) resulting in two amino acid differences (Arg to Ser at position 97 and Asn to Asp at position 114). It was found on a haplotype with HLA-A*03; Cw*0304; DRB1*0404/32; DRB4*0101/3/5; DQA1*03; DQB1*0302 and has the HLA-B60 specificity. Both alleles have frequencies of < 0.0002 in the largely north-western European Caucasoid blood donor population resident in Wales. PMID:12753671

Street, J; Downing, J; Hammond, L; Thompson, J; Darke, C

2003-04-01

84

Allele-specific disparity in breast cancer  

PubMed Central

Background In a cancer cell the number of copies of a locus may vary due to amplification and deletion and these variations are denoted as copy number alterations (CNAs). We focus on the disparity of CNAs in tumour samples, which were compared to those in blood in order to identify the directional loss of heterozygosity. Methods We propose a numerical algorithm and apply it to data from the Illumina 109K-SNP array on 112 samples from breast cancer patients. B-allele frequency (BAF) and log R ratio (LRR) of Illumina were used to estimate Euclidian distances. For each locus, we compared genotypes in blood and tumour for subset of samples being heterozygous in blood. We identified loci showing preferential disparity from heterozygous toward either the A/B-allele homozygous (allelic disparity). The chi-squared and Cochran-Armitage trend tests were used to examine whether there is an association between high levels of disparity in single nucleotide polymorphisms (SNPs) and molecular, clinical and tumour-related parameters. To identify pathways and network functions over-represented within the resulting gene sets, we used Ingenuity Pathway Analysis (IPA). Results To identify loci with a high level of disparity, we selected SNPs 1) with a substantial degree of disparity and 2) with substantial frequency (at least 50% of the samples heterozygous for the respective locus). We report the overall difference in disparity in high-grade tumours compared to low-grade tumours (p-value < 0.001) and significant associations between disparity in multiple single loci and clinical parameters. The most significantly associated network functions within the genes represented in the loci of disparity were identified, including lipid metabolism, small-molecule biochemistry, and nervous system development and function. No evidence for over-representation of directional disparity in a list of stem cell genes was obtained, however genes appeared to be more often altered by deletion than by amplification. Conclusions Our data suggest that directional loss and amplification exist in breast cancer. These are highly associated with grade, which may indicate that they are enforced with increasing number of cell divisions. Whether there is selective pressure for some loci to be preferentially amplified or deleted remains to be confirmed. PMID:22188678

2011-01-01

85

Predicting HLA alleles from high-resolution SNP data in three Southeast Asian populations.  

PubMed

The major histocompatibility complex (MHC) containing the classical human leukocyte antigen (HLA) Class I and Class II genes is among the most polymorphic and diverse regions in the human genome. Despite the clinical importance of identifying the HLA types, very few databases jointly characterize densely genotyped single nucleotide polymorphisms (SNPs) and HLA alleles in the same samples. To date, the HapMap presents the only public resource that provides a SNP reference panel for predicting HLA alleles, constructed with four collections of individuals of north-western European, northern Han Chinese, cosmopolitan Japanese and Yoruba Nigerian ancestry. Owing to complex patterns of linkage disequilibrium in this region, it is unclear whether the HapMap reference panels can be appropriately utilized for other populations. Here, we describe a public resource for the Singapore Genome Variation Project with: (i) dense genotyping across ? 9000 SNPs in the MHC; (ii) four-digit HLA typing for eight Class I and Class II loci, in 96 southern Han Chinese, 89 Southeast Asian Malays and 83 Tamil Indians. This resource provides population estimates of the frequencies of HLA alleles at these eight loci in the three population groups, particularly for HLA-DPA1 and HLA-DPB1 that were not assayed in HapMap. Comparing between population-specific reference panels and a cosmopolitan panel created from all four HapMap populations, we demonstrate that more accurate imputation is obtained with population-specific panels than with the cosmopolitan panel, especially for the Malays and Indians but even when imputing between northern and southern Han Chinese. As with SNP imputation, common HLA alleles were imputed with greater accuracy than low-frequency variants. PMID:24698974

Pillai, Nisha Esakimuthu; Okada, Yukinori; Saw, Woei-Yuh; Ong, Rick Twee-Hee; Wang, Xu; Tantoso, Erwin; Xu, Wenting; Peterson, Trevor A; Bielawny, Thomas; Ali, Mohammad; Tay, Koon-Yong; Poh, Wan-Ting; Tan, Linda Wei-Lin; Koo, Seok-Hwee; Lim, Wei-Yen; Soong, Richie; Wenk, Markus; Raychaudhuri, Soumya; Little, Peter; Plummer, Francis A; Lee, Edmund J D; Chia, Kee-Seng; Luo, Ma; De Bakker, Paul I W; Teo, Yik-Ying

2014-08-15

86

European Dialogue: The Magazine for European Integration  

NSDL National Science Digital Library

This new bimonthly magazine published by the European Commission is targeted at "decision-makers/opinion formers having an impact on European Integration" in the ten Central European and Baltic countries that have applied to join the EU. The electronic version of the first issue contains articles on humanitarian aid, membership negotiations, pensions, and economic forecasts.

1997-01-01

87

Nomenclature for human CYP2D6 alleles.  

PubMed

To standardize CYP2D6 allele nomenclature, and to conform with international human gene nomenclature guidelines, an alternative to the current arbitrary system is described. Based on recommendations for human genome nomenclature, we propose that alleles be designated by CYP2D6 followed by an asterisk and a combination of roman letters and arabic numerals distinct for each allele with the number specifying the key mutation and, where appropriate, a letter specifying additional mutations. Criteria for classification as a separate allele and protein nomenclature are also presented. PMID:8807658

Daly, A K; Brockmöller, J; Broly, F; Eichelbaum, M; Evans, W E; Gonzalez, F J; Huang, J D; Idle, J R; Ingelman-Sundberg, M; Ishizaki, T; Jacqz-Aigrain, E; Meyer, U A; Nebert, D W; Steen, V M; Wolf, C R; Zanger, U M

1996-06-01

88

Polymorphic microsatellites identified by cross-species amplifications in the European Coot Fulica atra  

Microsoft Academic Search

We tested the cross-amplification of 26 microsatellites developed for passerines and an additional three developed for Gallinula species in eight European Coots from two populations. Sixteen microsatellite markers successfully amplified, of which nine\\u000a were polymorphic with 2–6 alleles (mean 3.7 alleles) and an expected heterozygosity (H\\u000a e) ranging from 0.375 to 0.805 (mean H\\u000a e = 0.589). On average, we found 2.22 alleles\\/locus

Adeline Loyau; Dirk S. Schmeller

2009-01-01

89

Investigation of CYP2C19 allele and genotype frequencies in Iranian population using experimental and computational approaches.  

PubMed

CytochromeP4502C19 is a genetically polymorphic gene with prominent role in drug metabolism. Regarding its critical medical importance, this study was conducted to achieve accurate CYP2C19allele frequencies in Iranian population and hereby paving the way for a tailor-made CYP2C19 DNA test. Iran is a large multi-ethnic country, however, its population structure for CYP2C19 alleles is calculated as nearly zero (Fwc (st)=0.001). The Study was conducted on 691 individuals in Tehran, the conurbation in which total population structure is significantly eroded by massive immigration and DNA was analyzed by TaqMan SNP genotyping assay. A cumulative meta-analysis was then conducted to achieve less than five percent variation range in allele frequencies with 99.9% confidence level. High degree of Hardy-Weinberg equilibrium in pooled data proved the authenticity of meta-analysis. By cumulative meta-analysis the average frequencies of CYP2C19*2 and CYP2C19*3 alleles were calculated as 0.125[99.9% CI, 0.112-0.139] and 0.006[99.9% CI, 0.004-0.009], respectively. According to the solid frequency data obtained by pooling the data and meta-analysis and comparing with other ethnicities, Iranian population's CYP2C19 allele frequencies completely differ from other Asian ethnicities and matches African and European ethnicities the most. Since this is the biggest CYP2C19 allele frequency study in the Middle East, the results of this study will also be useful in cross-population and regional CYP2C19 genetic variation studies. PMID:24315317

Saber, Morteza Mahmoudi; Boroumand, Mohammadali; Behmanesh, Mehrdad

2014-02-01

90

INVESTIGATION Evidence for a Natural Allelic Series at the Maize  

E-print Network

INVESTIGATION Evidence for a Natural Allelic Series at the Maize Domestication Locus teosinte architecture and ear morphology between domesticated maize and teosinte; however, the effect of tb1 on trait teosinte alleles of tb1 that were introgressed into an isogenic maize inbred background. Our results

Doebley, John

91

Biased allelic expression in human primary fibroblast single cells.  

PubMed

The study of gene expression in mammalian single cells via genomic technologies now provides the possibility to investigate the patterns of allelic gene expression. We used single-cell RNA sequencing to detect the allele-specific mRNA level in 203 single human primary fibroblasts over 133,633 unique heterozygous single-nucleotide variants (hetSNVs). We observed that at the snapshot of analyses, each cell contained mostly transcripts from one allele from the majority of genes; indeed, 76.4% of the hetSNVs displayed stochastic monoallelic expression in single cells. Remarkably, adjacent hetSNVs exhibited a haplotype-consistent allelic ratio; in contrast, distant sites located in two different genes were independent of the haplotype structure. Moreover, the allele-specific expression in single cells correlated with the abundance of the cellular transcript. We observed that genes expressing both alleles in the majority of the single cells at a given time point were rare and enriched with highly expressed genes. The relative abundance of each allele in a cell was controlled by some regulatory mechanisms given that we observed related single-cell allelic profiles according to genes. Overall, these results have direct implications in cellular phenotypic variability. PMID:25557783

Borel, Christelle; Ferreira, Pedro G; Santoni, Federico; Delaneau, Olivier; Fort, Alexandre; Popadin, Konstantin Y; Garieri, Marco; Falconnet, Emilie; Ribaux, Pascale; Guipponi, Michel; Padioleau, Ismael; Carninci, Piero; Dermitzakis, Emmanouil T; Antonarakis, Stylianos E

2015-01-01

92

Tests and Estimates of Allelic Association in Complex Inheritance  

Microsoft Academic Search

Family-based procedures such as the transmission disequilibrium test (TDT) were motivated by concern that sample-based methods to map disease genes by allelic association are not robust to population stratification, migration, and admixture. Other factors to consider in designing a study of allelic association are specification of gene action in a weakly parametric model, efficiency, diagnostic reliability for hypernormal individuals, interest

N. E. Morton; A. Collins

1998-01-01

93

Trans allele methylation and paramutation-like effects in mice  

PubMed Central

In mammals, imprinted genes have parent-of-origin–specific patterns of DNA methylation that cause allele-specific expression. At Rasgrf1 (encoding RAS protein-specific guanine nucleotide-releasing factor 1), a repeated DNA element is needed to establish methylation and expression of the active paternal allele1. At Igf2r (encoding insulin-like growth factor 2 receptor), a sequence called region 2 is needed for methylation of the active maternal allele2,3. Here we show that replacing the Rasgrf1 repeats on the paternal allele with region 2 allows both methylation and expression of the paternal copy of Rasgrf1, indicating that sequences that control methylation can function ectopically. Paternal transmission of the mutated allele also induced methylation and expression in trans of the normally unmethylated and silent wild-type maternal allele. Once activated, the wild-type maternal Rasgrf1 allele maintained its activated state in the next generation independently of the paternal allele. These results recapitulate in mice several features in common with paramutation described in plants4. PMID:12740578

Herman, Herry; Lu, Michael; Anggraini, Melly; Sikora, Aimee; Chang, Yanjie; Yoon, Bong June; Soloway, Paul D

2009-01-01

94

Observations Suggesting Allelism of the Achondroplasia and Hypochondroplasia Genes  

Microsoft Academic Search

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

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

1973-01-01

95

Tyrosinase and Tyrosinase Related Protein 1 Alleles Specify Domestic Cat  

E-print Network

Tyrosinase and Tyrosinase Related Protein 1 Alleles Specify Domestic Cat Coat Color Phenotypes in domestic cat coat color, we determined the complete nucleotide coding sequence of the domestic cat genes microsatellite, previously found to be fixed in a cat breed selected for the chocolate (b) allele of the B locus

Eizirik, Eduardo

96

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

PubMed Central

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

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

1980-01-01

97

MicroRNA-3148 modulates allelic expression of toll-like receptor 7 variant associated with systemic lupus erythematosus.  

PubMed

We previously reported that the G allele of rs3853839 at 3'untranslated region (UTR) of Toll-like receptor 7 (TLR7) was associated with elevated transcript expression and increased risk for systemic lupus erythematosus (SLE) in 9,274 Eastern Asians [P?=?6.5×10(-10), odds ratio (OR) (95%CI)?=?1.27 (1.17-1.36)]. Here, we conducted trans-ancestral fine-mapping in 13,339 subjects including European Americans, African Americans, and Amerindian/Hispanics and confirmed rs3853839 as the only variant within the TLR7-TLR8 region exhibiting consistent and independent association with SLE (Pmeta?=?7.5×10(-11), OR?=?1.24 [1.18-1.34]). The risk G allele was associated with significantly increased levels of TLR7 mRNA and protein in peripheral blood mononuclear cells (PBMCs) and elevated luciferase activity of reporter gene in transfected cells. TLR7 3'UTR sequence bearing the non-risk C allele of rs3853839 matches a predicted binding site of microRNA-3148 (miR-3148), suggesting that this microRNA may regulate TLR7 expression. Indeed, miR-3148 levels were inversely correlated with TLR7 transcript levels in PBMCs from SLE patients and controls (R(2)?=?0.255, P?=?0.001). Overexpression of miR-3148 in HEK-293 cells led to significant dose-dependent decrease in luciferase activity for construct driven by TLR7 3'UTR segment bearing the C allele (P?=?0.0003). Compared with the G-allele construct, the C-allele construct showed greater than two-fold reduction of luciferase activity in the presence of miR-3148. Reduced modulation by miR-3148 conferred slower degradation of the risk G-allele containing TLR7 transcripts, resulting in elevated levels of gene products. These data establish rs3853839 of TLR7 as a shared risk variant of SLE in 22,613 subjects of Asian, EA, AA, and Amerindian/Hispanic ancestries (Pmeta ?=?2.0×10(-19), OR?=?1.25 [1.20-1.32]), which confers allelic effect on transcript turnover via differential binding to the epigenetic factor miR-3148. PMID:23468661

Deng, Yun; Zhao, Jian; Sakurai, Daisuke; Kaufman, Kenneth M; Edberg, Jeffrey C; Kimberly, Robert P; Kamen, Diane L; Gilkeson, Gary S; Jacob, Chaim O; Scofield, R Hal; Langefeld, Carl D; Kelly, Jennifer A; Ramsey-Goldman, Rosalind; Petri, Michelle A; Reveille, John D; Vilá, Luis M; Alarcón, Graciela S; Vyse, Timothy J; Pons-Estel, Bernardo A; Freedman, Barry I; Gaffney, Patrick M; Sivils, Kathy Moser; James, Judith A; Gregersen, Peter K; Anaya, Juan-Manuel; Niewold, Timothy B; Merrill, Joan T; Criswell, Lindsey A; Stevens, Anne M; Boackle, Susan A; Cantor, Rita M; Chen, Weiling; Grossman, Jeniffer M; Hahn, Bevra H; Harley, John B; Alarc?n-Riquelme, Marta E; Brown, Elizabeth E; Tsao, Betty P

2013-01-01

98

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

PubMed Central

Background Polyploidy is a major component of eukaryote evolution. Estimation of allele copy numbers for molecular markers has long been considered a challenge for polyploid species, while this process is essential for most genetic research. With the increasing availability and whole-genome coverage of single nucleotide polymorphism (SNP) markers, it is essential to implement a versatile SNP genotyping method to assign allelic configuration efficiently in polyploids. Scope This work evaluates the usefulness of the KASPar method, based on competitive allele-specific PCR, for the assignment of SNP allelic configuration. Citrus was chosen as a model because of its economic importance, the ongoing worldwide polyploidy manipulation projects for cultivar and rootstock breeding, and the increasing availability of SNP markers. Conclusions Fifteen SNP markers were successfully designed that produced clear allele signals that were in agreement with previous genotyping results at the diploid level. The analysis of DNA mixes between two haploid lines (Clementine and pummelo) at 13 different ratios revealed a very high correlation (average = 0·9796; s.d. = 0·0094) between the allele ratio and two parameters [? angle = tan?1 (y/x) and y? = y/(x + y)] derived from the two normalized allele signals (x and y) provided by KASPar. Separated cluster analysis and analysis of variance (ANOVA) from mixed DNA simulating triploid and tetraploid hybrids provided 99·71 % correct allelic configuration. Moreover, triploid populations arising from 2n gametes and interploid crosses were easily genotyped and provided useful genetic information. This work demonstrates that the KASPar SNP genotyping technique is an efficient way to assign heterozygous allelic configurations within polyploid populations. This method is accurate, simple and cost-effective. Moreover, it may be useful for quantitative studies, such as relative allele-specific expression analysis and bulk segregant analysis. PMID:23422023

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

2013-01-01

99

Generation of a Conditional Null Allele of Jumonji  

PubMed Central

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

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

2007-01-01

100

Allelic sequence heterozygosity in single Giardia parasites  

PubMed Central

Background Genetic heterogeneity has become a major inconvenience in the genotyping and molecular epidemiology of the intestinal protozoan parasite Giardia intestinalis, in particular for the major human infecting genotype, assemblage B. Sequence-based genotyping of assemblage B Giardia from patient fecal samples, where one or several of the commonly used genotyping loci (beta-giardin, triosephosphate isomerase and glutamate dehydrogenase) are implemented, is often hampered due to the presence of sequence heterogeneity in the sequencing chromatograms. This can be due to allelic sequence heterozygosity (ASH) and /or co-infections with parasites of different assemblage B sub-genotypes. Thus, two important questions have arisen; i) does ASH occur at the single cell level, and/or ii) do multiple sub-genotype infections commonly occur in patients infected with assemblage B, G. intestinalis isolates? Results We used micromanipulation in order to isolate single Giardia intestinalis, assemblage B trophozoites (GS isolate) and cysts from human patients. Molecular analysis at the tpi loci of trophozoites from the GS lineage indicated that ASH is present at the single cell level. Analyses of assemblage B Giardia cysts from clinical samples at the bg and tpi loci also indicated ASH at the single cell level. Additionally, alignment of sequence data from several different cysts that originated from the same patient yielded different sequence patterns, thus suggesting the presence of multiple sub-assemblage infections in congruence with ASH within the same patient. Conclusions Our results conclusively show that ASH does occur at the single cell level in assemblage B Giardia. Furthermore, sequence heterogeneity generated during sequence-based genotyping of assemblage B isolates may possess the complexity of single cell ASH in concurrence with co-infections of different assemblage B sub-genotypes. These findings explain the high abundance of sequence heterogeneity commonly found when performing sequence based genotyping of assemblage B Giardia, and illuminates the necessity of developing new G. intestinalis genotyping tools. PMID:22554281

2012-01-01

101

Nonsynonymous SNPs: validation characteristics, derived allele frequency patterns, and suggestive evidence for natural selection.  

PubMed

We experimentally investigated more than 1,200 entries in dbSNP that would change amino-acids (nsSNPs), using various subsets of DNA samples drawn from 18 global populations (approximately 1,000 subjects in total). First, we mined the data for any SNP features that correlated with a high validation rate. Useful predictors of valid SNPs included multiple submissions to dbSNP, having a dbSNP validation statement, and being present in a low number of ESTs. Together, these features improved validation rates by almost 10-fold. Higher-abundance SNPs (e.g., T/C variants) also validated more frequently. Second, we considered derived alleles and noted a considerably (approximately 10%) increased average derived allele frequency (DAF) in Europeans vs. Africans, plus a further increase in some other populations. This was not primarily due to an SNP ascertainment bias, nor to the effects of natural selection. Instead, it can be explained as a drift-based, progressive increase in DAF that occurs over many generations and becomes exaggerated during population bottlenecks. This observation could be used as the basis for novel DAF-based tests for comparing demographic histories. Finally, we considered individual marker patterns and identified 37 SNPs with allele frequency variance or FST values consistent with the effects of population-specific natural selection. Four particularly striking clusters of these markers were apparent, and three of these coincide with genes/regions from among only several dozen such domains previously suggested by others to carry signatures of selection. PMID:16429399

Fredman, David; Sawyer, Sarah L; Strömqvist, Linda; Mottagui-Tabar, Salim; Kidd, Kenneth K; Wahlestedt, Claes; Chanock, Stephen J; Brookes, Anthony J

2006-02-01

102

Identification of the novel HLA-C allele Cw*0751.  

PubMed

We report the novel HLA-Cw allele HLA-Cw*0751. The allele was identified during routine sequence-based typing in our laboratory. The novel allele is identical to Cw*07020101 except for a single nucleotide change in codon 90.2 in position 268. HLA-Cw*0751 allele possesses an adenine at position 268 in exon 2, while HLA-Cw*07020101 has a cytosine at this position. Although this substitution does not change serologic reactivity of HLA-Cw7 molecule, it changes the amino acid at codon 90 from an aspartic acid to an alanine. Aspartic acid is polar and acidic, while alanine is non-polar and neutral. PMID:18069932

Thompson, E M; Kashi, Z M; Martin, R K; Alcorn, J L; Tidey, L

2008-02-01

103

Equine plasminogen polymorphism: allelic frequencies in 23 breeds.  

PubMed

A modified procedure for detection of the two alleles of equine plasminogen using Western blotting methods following polyacrylamide gel isoelectric focusing is described. Gene frequencies in 23 breeds and Equus przewalskii are provided. PMID:8273917

Bowling, A T; Penedo, M C; Gordon, L; Bell, K

1993-12-01

104

Fundamentals of Population Genetics Mechanisms of Allele Frequency Changes  

E-print Network

is the genetic variability in natural populations maintained: by natural selection, chance, or both? Individuals within natural populations are not genetically homogeneous Macroevolution is the cumulative consequence Genetics and Evolution Definition Evolution = Divergence Between Populations = Fixation of New Alleles

Qiu, Weigang

105

Hidden Alleles at the ?-Glycerophosphate Dehydrogenase Locus in Colias Butterflies  

PubMed Central

By varying polyacrylamide gel pore size, the ?-glycerophosphate dehydrogenase locus of Colias butterflies is shown to contain at least five alleles, rather than the two which had been reported previously. Two of the alleles have the same apparent net charge, and presumably are detected electrophoretically because of conformational differences. Additional variation occurs in the isoelectric points of the proteins. It is suggested that electrophoresis employing a single gel of intermediate pore size will fail to discriminate between many alleles, and that the concept of electrophoretic alleles as differing simply in charge may not always be appropriate. "How does one know what it is one believes When it's so difficult to know what it is one knows?" —Jumpers (Stoppard, 1972) PMID:1269917

Johnson, George B.

1976-01-01

106

Numerical and exact solutions for continuum of alleles models.  

PubMed

Two results are presented for problems involving alleles with a continuous range of effects. The first result is a simple yet highly accurate numerical method that determines the equilibrium distribution of allelic effects, moments of this distribution, and the mutational load. The numerical method is explicitly applied to the mutation-selection balance problem of stabilising selection. The second result is an exact solution for the distribution of allelic effects under weak stabilising selection for a particular distribution of mutant effects. The exact solution is shown to yield a distribution of allelic effects that, depending on the mutation rate, interpolates between the "House of Cards" approximation and the Gaussian approximation. The exact solution is also used to test the accuracy of the numerical method. PMID:12728334

Waxman, D

2003-03-01

107

Allelic exclusion of immunoglobulin genes: models and mechanisms  

PubMed Central

Summary The allelic exclusion of immunoglobulin (Ig) genes is one of the most evolutionarily conserved features of the adaptive immune system and underlies the monospecificity of B cells. While much has been learned about how Ig allelic exclusion is established during B-cell development, the relevance of monospecificity to B-cell function remains enigmatic. Here, we review the theoretical models that have been proposed to explain the establishment of Ig allelic exclusion and focus on the molecular mechanisms utilized by developing B cells to ensure the monoallelic expression of Ig? and Ig? light chain genes. We also discuss the physiological consequences of Ig allelic exclusion and speculate on the importance of monospecificity of B cells for immune recognition. PMID:20727027

Vettermann, Christian; Schlissel, Mark S.

2010-01-01

108

DRD4 dopamine receptor allelic diversity in various primate species  

SciTech Connect

The DRD4 dopamine receptor is uniquely characterized by a 48 bp repeating segment within the coding region, located in exon III. Different DRD4 alleles are produced by the presence of additional 48 bp repeats, each of which adds 16 amino acids to the length of the 3rd intracytoplasmic loop of the receptor. The DRD4 receptor is therefore an intriguing candidate gene for behaviors which are influenced by dopamine function. In several human populations, DRD4 alleles with 2-8 and 10 repeats have previously been identified, and the 4 and 7 repeat alleles are the most abundant. We have determined DRD4 genotypes in the following nonhuman primate species: chimpanzee N=2, pygmy chimpanzee N=2, gorilla N=4, siamang N=2, Gelada baboon N=1, gibbon N=1, orangutan (Bornean and Sumatran) N=62, spider monkey N=4, owl monkey N=1, Colobus monkey N=1, Patas monkey N=1, ruffed lemur N=1, rhesus macaque N=8, and vervet monkey N=28. The degree of DRD4 polymorphism and which DRD4 alleles were present both showed considerable variation across primate species. In contrast to the human, rhesus macaque monkeys were monomorphic. The 4 and 7 repeat allels, highly abundant in the human, may not be present in certain other primates. For example, the four spider monkeys we studied showed the 7, 8 and 9 repeat length alleles and the only gibbon we analyzed was homozygous for the 9 repeat allele (thus far not observed in the human). Genotyping of other primate species and sequencing of the individual DRD4 repeat alleles in different species may help us determine the ancestral DRD4 repeat length and identify connections between DRD4 genotype and phenotype.

Adamson, M.; Higley, D. [NIAAA, Rockville, MD (United States); O`Brien, S. [NCI, Frederick, MD (United States)] [and others

1994-09-01

109

Robust Identification of Local Adaptation from Allele Frequencies  

PubMed Central

Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele frequencies and neutral correlations of allele frequencies among populations due to shared population history and gene flow. Here we develop a set of methods to robustly test for unusual allele frequency patterns and correlations between environmental variables and allele frequencies while accounting for these complications based on a Bayesian model previously implemented in the software Bayenv. Using this model, we calculate a set of “standardized allele frequencies” that allows investigators to apply tests of their choice to multiple populations while accounting for sampling and covariance due to population history. We illustrate this first by showing that these standardized frequencies can be used to detect nonparametric correlations with environmental variables; these correlations are also less prone to spurious results due to outlier populations. We then demonstrate how these standardized allele frequencies can be used to construct a test to detect SNPs that deviate strongly from neutral population structure. This test is conceptually related to FST and is shown to be more powerful, as we account for population history. We also extend the model to next-generation sequencing of population pools—a cost-efficient way to estimate population allele frequencies, but one that introduces an additional level of sampling noise. The utility of these methods is demonstrated in simulations and by reanalyzing human SNP data from the Human Genome Diversity Panel populations and pooled next-generation sequencing data from Atlantic herring. An implementation of our method is available from http://gcbias.org. PMID:23821598

Günther, Torsten; Coop, Graham

2013-01-01

110

Identification of incompatibility alleles in the tetraploid species sour cherry.  

PubMed

The incompatibility genetics of sour cherry ( Prunus cerasus), an allotetraploid species thought to be derived from sweet cherry (diploid) and ground cherry (tetraploid), were investigated by test crossing and by analysis of stylar ribonucleases which are known to be the products of incompatibility alleles in sweet cherry. Stylar extracts of 36 accessions of sour cherry were separated electrophoretically and stained for ribonuclease activity. The zymograms of most accessions showed three bands, some two or four. Of the ten bands seen, six co-migrated with bands that in sweet cherry are attributed to the incompatibility alleles S(1), S(3), S(4), S(6, ) S(9) and S(13). 'Cacanski Rubin', 'Erdi Botermo B', 'Koros' and 'Ujfehertoi Furtos', which showed bands apparently corresponding to S(1) and S(4), were test pollinated with the sweet cherry 'Merton Late' ( S(1) S(4)). Monitoring pollen tube growth, and, in one case, fruit set, showed that these crosses were incompatible and that the four sour cherries indeed have the alleles S(1) and S(4). Likewise, test pollination of 'Marasca Piemonte', 'Marasca Savena' and 'Morello, Dutch' with 'Noble' ( S(6) S(13)) showed that these three sour cherries have the alleles S(6) and S(13). S(13) was very frequent in sour cherry cultivars, but is rare in sweet cherry cultivars, whereas with S(3) the situation is reversed. It was suggested that the other four bands are derived from ground cherry and one of these, provisionally attributed to S(B), occurred frequently in a small set of ground cherry accessions surveyed. Analysing some progenies from sour by sweet crosses by S allele-specific PCR and monitoring the success of some sweet by sour crosses were informative. They indicated mostly disomic inheritance, with sweet cherry S alleles belonging to one locus and, presumably, the ground cherry alleles to the other, and helped clarify the genomic arrangement of the alleles and the interactions in heteroallelic pollen. PMID:14689184

Tobutt, K R; Boskovi?, R; Cerovi?, R; Sonneveld, T; Ruzi?, D

2004-03-01

111

Apolipoprotein E ?4 Allele Frequency in Vascular Dementia  

Microsoft Academic Search

Aim: The aim of the study was to investigate whether possession of the ?4 allelic form of the apolipoprotein E (APOE) gene increases the risk of developing vascular dementia (VaD). Methods:APOE allele and genotype frequencies were determined by PCR in 89 patients with possible and probable VaD and compared with those in 97 patients with possible and probable Alzheimer’s disease

Yvonne Davidson; Linda Gibbons; Nitin Purandare; Jane Byrne; Jayne Hardicre; Joanne Wren; Antony Payton; Neil Pendleton; Michael Horan; Alistair Burns; David M. A. Mann

2006-01-01

112

However, the European Union  

E-print Network

However, the European Union presidency Monday pointed to a new willingness by Japan to compromise talks with the European Union, which has been supporting France's bid. As a result, the Yomiuri said, China and Russia backed France. However, the European Union presidency Monday pointed to a new

113

Institutional Report: European Union  

E-print Network

Institutional Report: European Union Florence Bergeaud-Blackler CRIC, University of Manchester #12, Key Action 1, Contract no. QLK1-CT-2001-00291. Institutional Report: European Union Florence Bergeaud.trustinfood.org. This report presents data and analyses from studies at the European Union level. It belongs to a series

Boyer, Edmond

114

[Characterization of null alleles in human histocompatibility complex antigens (HLA)].  

PubMed

The widespread application of DNA techniques in medicine and biology has allowed the typing of human leukocyte antigens (HLA) at the molecular level. Comparative studies between serological and molecular biology methods have shown the existence of null alleles, which code HLA antigens with low or no cell surface expression. Null alleles are not detectable by standard serological typing methods and may be overlooked/or incorrectly assigned by available DNA methods. Although null alleles are infrequent in human populations, they should not be ignored. Errors in typing of null alleles may cause complications in the evaluation of HLA matching of donor/recipient pairs that were originally considered HLA-compatible. The detection of null alleles and their frequency in various populations requires typing of a large number of individuals by both serological and DNA-based methods. Knowledge of the haplotype(s) associated with null alleles may be helpful for their identification. For this purpose, it is necessary to perform family studies. PMID:15218722

Bendukidze, N; Záhlavová, L; Kolesár, L; Pokorná, K; Slavcev, A

2004-01-01

115

Allele-specific MMP-3 transcription under in vivo conditions  

SciTech Connect

A common matrix metalloproteinases-3 (MMP-3) -1612 5A/6A promoter polymorphism is associated with risk for cardiovascular disease, rheumatoid arthritis, and other diseases. Here we used the haplotype chromatin immunoprecipitation method to study allele-specific MMP-3 expression under in vivo conditions in heterozygous THP-1 cells. Pyrosequencing was used to analyse the ratio of 5A-allele to 6A-allele after chromatin immunoprecipitation using an antibody against phosphorylated active RNA polymerase II. There was no allele-specific difference in transcriptional activity during basal conditions, i.e., in unstimulated monocytic THP-1 cells. However, after stimulation of MMP-3 expression by monocyte differentiation or incubation with IL-1{beta}, the haplotype containing the 5A-allele was associated with higher transcriptional activity compared with the 6A-containing haplotype. Electromobility shift assay demonstrated increased binding of nuclear proteins to the 5A-allele after monocyte differentiation. In conclusion, the common MMP-3 5A/6A promoter polymorphism appears to be functional only during specific environmental conditions involving inflammation.

Zhu Chaoyong [Atherosclerosis Research Unit, King Gustav V Research Institute, Department of Medicine, Karolinska Institute, Stockholm (Sweden); Odeberg, Jacob [Atherosclerosis Research Unit, King Gustav V Research Institute, Department of Medicine, Karolinska Institute, Stockholm (Sweden); Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology, Stockholm (Sweden); Hamsten, Anders [Atherosclerosis Research Unit, King Gustav V Research Institute, Department of Medicine, Karolinska Institute, Stockholm (Sweden); Eriksson, Per [Atherosclerosis Research Unit, King Gustav V Research Institute, Department of Medicine, Karolinska Institute, Stockholm (Sweden)]. E-mail: Per.Eriksson@ki.se

2006-09-29

116

Drift and mutation with a finite number of allelic states  

PubMed Central

The frequencies with which alleles are alike within (Q) and between (q) populations are formulated for monoecious populations undergoing drift and mutation with unequal mutation rates among alleles for a finite number (k) of allelic states. The effective number of alleles and an application to Nei's measure of genetic distance [Nei, M. (1972) Am. Nat. 106, 283-292] are also considered for this model. The equilibrium values of Q and q increase as k decreases. Unequal mutation rates further increase the equilibrium values and reduce the rates of approach of Q and q to these values. The transitional values of Q and q are very dependent on the initial population frequency composition when mutation rates are unequal. Reducing k, of course, reduces the effective number of alleles, which is further reduced by unequal mutation rates. Complications introduced by initial population composition, unequal mutation rates, and number of allelic states, coupled with data limitations for long-term measures of genetic distance or population differentiation, with mutation as the main driving force, are discussed. PMID:16593409

Cockerham, C. Clark

1984-01-01

117

Regression Modeling of Allele Frequencies and Testing Hardy Weinberg Equilibrium  

PubMed Central

Background/Aims Tests for whether observed genotype proportions fit Hardy Weinberg Equilibrium (HWE) are widely used in population genetics analyses, as well as to evaluate quality of genotype data. To date, all methods testing for HWE require subjects to be classified into discrete categories, yet it is becoming clear that the distribution of allele frequencies tends to be smooth over geographic regions. Methods To evaluate the HWE assumption, we develop new approaches to model allele frequencies as functions of covariates, and use these models to test whether there is residual correlation between the two alleles of subjects; lack of residual correlation supports the null hypothesis of HWE, but conditional on how the covariates influence the allele frequencies. Results By simulations, we illustrate that a simple statistical test of residual correlation of alleles adequately controls the Type-I error rate, while maintaining power that is comparable to standard tests for HWE. Conclusion Our approach can be implemented in standard software, enabling more flexible and powerful ways to evaluate the association of covariates with allele frequencies, and whether these associations “explain” departures from HWE when the covariates are ignored, opening new strategies to evaluate the quality of genotype data generated by next-generation sequencing assays. PMID:23328647

Schaid, Daniel J.; Sinnwell, Jason P.; Jenkins, Gregory D.

2013-01-01

118

Long allele designations at D2S1338 and D19S433 loci as influenced by various multiplex STR kits.  

PubMed

European forensic laboratories are replacing the STR multiplex kits with the new generation 16/17 STR kits. This study examines the influence of the new generation kits and the new Applied Biosystems 3500xL Genetic Analyzer on the designation of long D2S1338 and D19S433 off-ladder alleles. Different allele calls were obtained using the new NGM™ (Applied Biosystems) and PowerPlex(®) ESI™ (Promega) kits compared with AmpF?STR(®) SGM Plus™ kit (Applied Biosystems). Sequence analysis was used to determine accurate allele designation. The new multiplex kits and the 3500xL Genetic Analyzer improved accuracy of long allele designations. DNA databases worldwide include countless profiles obtained by previous kits. Discrepancies between the new and former technologies may cause failure to detect hits. Discordance is expected due to primer sequence differences between various kits. An additional discordance, occurring in long alleles, independent of primer sequence is reported in this study. PMID:24261684

Dell'Ariccia-Carmon, Aviva; Raziel, Aliza; Oz, Carla; Berdugo, Reouven; Zamir, Ashira

2014-05-01

119

Bi-allelic and tri-allelic 5-HTTLPR polymorphisms and triptan non-response in cluster headache  

PubMed Central

Background Triptans are only effective in terminating cluster headache (CH) attacks in 70-80% of patients. Pharmacogenetic aspects of the serotonin metabolism, specifically variation in the 5-HTTLPR may be involved. Methods Genetic association study in a well-defined cohort of 148 CH patients with information on drug response to triptans. CH was diagnosed according to the criteria of the International Headache Society. Genotypes of the 43-bp insdel (rs4795541) and A?>?G (rs25531) polymorphisms in the 5-HTTLPR promoter region were detected by restriction fragment length polymorphism analysis. We used logistic regression analysis to investigate the association between bi-allelic and tri-allelic genotypes and triptan non-response with genotype models. Results Mean age at study entry among patients was 44.6?±?10.5 years, 77.7% were men. The genotype distribution both for the bi-allelic and the tri-allelic polymorphism was in Hardy-Weinberg equilibrium. We did not find an association of the bi-allelic polymorphism with triptan non-response. While the effect estimates for the S variant of the tri-allelic polymorphisms suggested increased odds of triptan non-response in CH patients (multivariable-adjusted odds ratio [95% confidence interval]: L*L* genotype—reference; L*S* genotype—1.33 [0.53-3.32]; S*S* genotype—1.46 [0.54-3.98]), the results were not statistically significant. Conclusions Data from our study do not indicate a role of bi-allelic and tri-allelic genotypes of the 5-HTTLPR polymorphism in triptan non-response in CH. PMID:25043824

2014-01-01

120

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

PubMed Central

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

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

2012-01-01

121

Impriniting of human H19: Allele-specific CpG methylation, loss of the active allele in Wilms tumor, and potential for somatic allele switching  

SciTech Connect

Genomic imprinting and monoallelic gene expression appear to play a role in human genetic disease and tumorigenesis. The human H19 gene, at chromosome 11p15, has previously been shown to be monoallelically expressed. Since CpG methylation has been implicated in imprinting, the authors analyzed methylation of H19 DNA. In fetal and adult organs the transcriptionally silent H19 allele was extensively hypermethylated through the entire gene and its promoter, and, consistent with a functional role for DNA methylation, expression of an H19 promoter-reporter construct was inhibited by in vitro methylation. Gynogenetic ovarian teratomas were found to contain only hypomethylated H19 DNA, suggesting that the expressed H19 allele might be maternal. This was confirmed by analysis of 11p15 polymorphisms in a patient with Wilms tumor. The tumor had lost the maternal 11p15, and H19 expression in the normal kidney was exclusively from this allele. Imprinting of human H19 appears to be susceptible to tissue-specific modulation in somatic development; in one individual, cerebellar cells were found to express only the otherwise silent allele. Implications of these findings for the role of DNA methylation in imprinting and for H19 as a candidate imprinted tumor-suppressor gene are discussed. 57 refs., 7 figs.

Zhang, Y.; Shields, T.; Crenshaw, T.; Hao, Y.; Moulton, T.; Tycko, B. (Columbia Univ., New York (United States))

1993-07-01

122

How the Number of Alleles Influences Gene Expression  

NASA Astrophysics Data System (ADS)

The higher organisms, eukaryotes, are diploid and most of their genes have two homological copies (alleles). However, the number of alleles in a cell is not constant. In the S phase of the cell cycle all the genome is duplicated and then in the G2 phase and mitosis, which together last for several hours, most of the genes have four copies instead of two. Cancer development is, in many cases, associated with a change in allele number. Several genetic diseases are caused by haploinsufficiency: Lack of one of the alleles or its improper functioning. In the paper we consider the stochastic expression of a gene having a variable number of copies. We applied our previously developed method in which the reaction channels are split into slow (connected with change of gene state) and fast (connected with mRNA/protein synthesis/decay), the later being approximated by deterministic reaction rate equations. As a result we represent gene expression as a piecewise deterministic time-continuous Markov process, which is further related with a system of partial differential hyperbolic equations for probability density functions (pdfs) of protein distribution. The stationary pdfs are calculated analytically for haploidal gene or numerically for diploidal and tetraploidal ones. We distinguished nine classes of simultaneous activation of haploid, diploid and tetraploid genes. This allows for analysis of potential consequences of gene duplication or allele loss. We show that when gene activity is autoregulated by a positive feedback, the change in number of gene alleles may have dramatic consequences for its regulation and may not be compensated by the change of efficiency of mRNA synthesis per allele.

Hat, Beata; Paszek, Pawel; Kimmel, Marek; Piechor, Kazimierz; Lipniacki, Tomasz

2007-07-01

123

Further Evidence for an Association of ABCR Alleles with Age-Related Macular Degeneration  

PubMed Central

Age-related macular degeneration (AMD) accounts for >50% of the registered visual disability among North American and Western European populations and has been associated both with environmental factors, such as smoking, and with genetic factors. Previously we have reported disease-associated variants in the ABCR (also called ABCA4) gene in a subset of patients affected with this complex disorder. We have now tested our original hypothesis, that ABCR is a dominant susceptibility locus for AMD, by screening 1,218 unrelated AMD patients of North American and Western European origin and 1,258 comparison individuals from 15 centers in North America and Europe for the two most frequent AMD-associated variants found in ABCR. These two sequence changes, G1961E and D2177N, were found in one allele of ABCR in 40 patients (?3.4%), and in 13 control subjects (?0.95%). Fisher’s two-sided exact test confirmed that these two variants are associated with AMD at a statistically significant level (P<.0001). The risk of AMD is elevated approximately threefold in D2177N carriers and approximately fivefold in G1961E carriers. The identification of a gene that confers risk of AMD is an important step in unraveling this complex disorder. PMID:10880298

Allikmets, Rando

2000-01-01

124

Allelic Richness following Population Founding Events – A Stochastic Modeling Framework Incorporating Gene Flow and Genetic Drift  

PubMed Central

Allelic richness (number of alleles) is a measure of genetic diversity indicative of a population's long-term potential for adaptability and persistence. It is used less commonly than heterozygosity as a genetic diversity measure, partially because it is more mathematically difficult to take into account the stochastic process of genetic drift for allelic richness. This paper presents a stochastic model for the allelic richness of a newly founded population experiencing genetic drift and gene flow. The model follows the dynamics of alleles lost during the founder event and simulates the effect of gene flow on maintenance and recovery of allelic richness. The probability of an allele's presence in the population was identified as the relevant statistical property for a meaningful interpretation of allelic richness. A method is discussed that combines the probability of allele presence with a population's allele frequency spectrum to provide predictions for allele recovery. The model's analysis provides insights into the dynamics of allelic richness following a founder event, taking into account gene flow and the allele frequency spectrum. Furthermore, the model indicates that the “One Migrant per Generation” rule, a commonly used conservation guideline related to heterozygosity, may be inadequate for addressing preservation of diversity at the allelic level. This highlights the importance of distinguishing between heterozygosity and allelic richness as measures of genetic diversity, since focusing merely on the preservation of heterozygosity might not be enough to adequately preserve allelic richness, which is crucial for species persistence and evolution. PMID:25526062

Greenbaum, Gili; Templeton, Alan R.; Zarmi, Yair; Bar-David, Shirli

2014-01-01

125

Evaluation of Allele Frequency Estimation Using Pooled Sequencing Data Simulation  

PubMed Central

Next-generation sequencing (NGS) technology has provided researchers with opportunities to study the genome in unprecedented detail. In particular, NGS is applied to disease association studies. Unlike genotyping chips, NGS is not limited to a fixed set of SNPs. Prices for NGS are now comparable to the SNP chip, although for large studies the cost can be substantial. Pooling techniques are often used to reduce the overall cost of large-scale studies. In this study, we designed a rigorous simulation model to test the practicability of estimating allele frequency from pooled sequencing data. We took crucial factors into consideration, including pool size, overall depth, average depth per sample, pooling variation, and sampling variation. We used real data to demonstrate and measure reference allele preference in DNAseq data and implemented this bias in our simulation model. We found that pooled sequencing data can introduce high levels of relative error rate (defined as error rate divided by targeted allele frequency) and that the error rate is more severe for low minor allele frequency SNPs than for high minor allele frequency SNPs. In order to overcome the error introduced by pooling, we recommend a large pool size and high average depth per sample. PMID:23476151

Guo, Yan; Samuels, David C.; Li, Jiang; Clark, Travis; Li, Chung-I; Shyr, Yu

2013-01-01

126

Disease-associated alleles in genome-wide association studies are enriched for derived low frequency alleles relative to HapMap and neutral expectations  

Microsoft Academic Search

BACKGROUND: Genome-wide association studies give insight into the genetic basis of common diseases. An open question is whether the allele frequency distributions and ancestral vs. derived states of disease-associated alleles differ from the rest of the genome. Characteristics of disease-associated alleles can be used to increase the yield of future studies. METHODS: The set of all common disease-associated alleles found

Joseph Lachance

2010-01-01

127

Extensive HLA class I allele promiscuity among viral CTL epitopes  

PubMed Central

Summary Promiscuous binding of T helper epitopes to MHC class II molecules has been well established, but few examples of promiscuous class I restricted epitopes exist. To address the extent of promiscuity of HLA class I peptides, responses to 242 well-defined viral epitopes were tested in 100 subjects regardless of the individuals’ HLA type. Surprisingly, half of all detected responses were seen in the absence of the originally reported restricting HLA class I allele, and only 3% of epitopes were recognized exclusively in the presence of their original allele. Functional assays confirmed the frequent recognition of HLA class I-restricted T cell epitopes on several alternative alleles across HLA class I supertypes and encoded on different class I loci. These data have significant implications for the understanding of MHC class I restricted antigen presentation and vaccine development. PMID:17705138

Frahm, Nicole; Yusim, Karina; Suscovich, Todd J.; Adams, Sharon; Sidney, John; Hraber, Peter; Hewitt, Hannah S.; Linde, Caitlyn H.; Kavanagh, Daniel G.; Woodberry, Tonia; Henry, Leah M.; Faircloth, Kellie; Listgarten, Jennifer; Kadie, Carl; Jojic, Nebojsa; Sango, Kaori; Brown, Nancy V.; Pae, Eunice; Zaman, M. Tauheed; Bihl, Florian; Khatri, Ashok; John, Mina; Mallal, Simon; Marincola, Francesco M.; Walker, Bruce D.; Sette, Alessandro; Heckerman, David; Korber, Bette T.; Brander, Christian

2008-01-01

128

Implication of HLA-DMA Alleles in Corsican IDDM  

PubMed Central

The HLA-DM molecule catalyses the CLIP/antigen peptide exchange in the classical class II peptide-binding groove. As such, DM is an antigen presentation regulator and may be linked to autoimmune diseases. Using PCR derived methods, a relationship was revealed between DM gene polymorphism and IDDM, in a Corsican population. The DMA*0101 allele was observed to confer a significant predisposition to this autoimmune disease while the DMA*0102 allele protected significantly. Experiments examining polymorphism of the HLA-DRB1 gene established that these relationships are not a consequence of linkage disequilibrium with HLA-DRB1 alleles implicated in this pathology. The study of the DMA gene could therefore be an additional tool for early IDDM diagnosis in the Corsican population. PMID:10427471

Cucchi-Mouillot, P.; Lai, S.; Carcassi, C.; Sorba, P.; Stuart-Simoni, M.; Amoros, J.-P.; Genetet, B.; Haras, D.; Contu, L.

1998-01-01

129

ADH1B is associated with alcohol dependence and alcohol consumption in populations of European and African ancestry  

Microsoft Academic Search

A coding variant in alcohol dehydrogenase 1B (ADH1B) (rs1229984) that leads to the replacement of Arg48 with His48 is common in Asian populations and reduces their risk for alcoholism, but because of very low allele frequencies the effects in European or African populations have been difficult to detect. We genotyped and analyzed this variant in three large European and African-American

L J Bierut; A M Goate; N Breslau; E O Johnson; S Bertelsen; L Fox; A Agrawal; K K Bucholz; R Grucza; V Hesselbrock; J Kramer; S Kuperman; J Nurnberger; B Porjesz; N L Saccone; M Schuckit; J Tischfield; J C Wang; T Foroud; J P Rice; H J Edenberg

2012-01-01

130

Worldwide Distribution of the MYH9 Kidney Disease Susceptibility Alleles and Haplotypes: Evidence of Historical Selection in Africa  

PubMed Central

MYH9 was recently identified as renal susceptibility gene (OR 3–8, p<10?8) for major forms of kidney disease disproportionately affecting individuals of African descent. The risk haplotype (E-1) occurs at much higher frequencies in African Americans (?60%) than in European Americans (<4%), revealing a genetic basis for a major health disparity. The population distributions of MYH9 risk alleles and the E-1 risk haplotype and the demographic and selective forces acting on the MYH9 region are not well explored. We reconstructed MYH9 haplotypes from 4 tagging single nucleotide polymorphisms (SNPs) spanning introns 12–23 using available data from HapMap Phase II, and by genotyping 938 DNAs from the Human Genome Diversity Panel (HGDP). The E-1 risk haplotype followed a cline, being most frequent within sub-Saharan African populations (range 50–80%), less frequent in populations from the Middle East (9–27%) and Europe (0–9%), and rare or absent in Asia, the Americas, and Oceania. The fixation indexes (FST) for pairwise comparisons between the risk haplotypes for continental populations were calculated for MYH9 haplotypes; FST ranged from 0.27–0.40 for Africa compared to other continental populations, possibly due to selection. Uniquely in Africa, the Yoruba population showed high frequency extended haplotype length around the core risk allele (C) compared to the alternative allele (T) at the same locus (rs4821481, iHs?=?2.67), as well as high population differentiation (FST(CEU vs. YRI)?=?0.51) in HapMap Phase II data, also observable only in the Yoruba population from HGDP (FST?=?0.49), pointing to an instance of recent selection in the genomic region. The population-specific divergence in MYH9 risk allele frequencies among the world's populations may prove important in risk assessment and public health policies to mitigate the burden of kidney disease in vulnerable populations. PMID:20634883

Oleksyk, Taras K.; Nelson, George W.; An, Ping; Kopp, Jeffrey B.; Winkler, Cheryl A.

2010-01-01

131

Persistence of Common Alleles in Two Related Populations or Species  

PubMed Central

Mathematical studies are conducted on three problems that arise in molecular population genetics. (1) The time required for a particular allele to become extinct in a population under the effects of mutation, selection, and random genetic drift is studied. In the absence of selection, the mean extinction time of an allele with an initial frequency close to 1 is of the order of the reciprocal of the mutation rate when 4Nv << 1, where N is the effective population size and v is the mutation rate per generation. Advantageous mutations reduce the extinction time considerably, whereas deleterious mutations increase it tremendously even if the effect on fitness is very slight. (2) Mathematical formulae are derived for the distribution and the moments of extinction time of a particular allele from one or both of two related populations or species under the assumption of no selection. When 4Nv << 1, the mean extinction time is about half that for a single population, if the two populations are descended from a common original stock. (3) The expected number as well as the proportion of common neutral alleles shared by two related species at the tth generation after their separation are studied. It is shown that if 4Nv is small, the two species are expected to share a high proportion of common alleles even 4N generations after separation. In addition to the above mathematical studies, the implications of our results for the common alleles at protein loci in related Drosophila species and for the degeneration of unused characters in cave animals are discussed. PMID:924138

Li, Wen-Hsiung; Nei, Masatoshi

1977-01-01

132

MHC class II DR allelic diversity in bighorn sheep.  

PubMed

We hypothesized that decreased diversity and/or unique polymorphisms in MHC class II alleles of bighorn sheep (BHS, Ovis canadensis) are responsible for lower titer of antibodies against Mannheimia haemolytica leukotoxin, in comparison to domestic sheep (DS, Ovis aries). To test this hypothesis, DRA and DRB transcripts from 24 captive BHS (Ovca-DRA and Ovca-DRB) were sequenced. Based on exon 2 (?1 domain) sequences, eight different Ovca-DRB cDNA sequences were identified in BHS. Six of them were 100% identical to previously reported Ovca-DRB genomic DNA sequences. The new alleles DRB*23 and DRB*24, were closely related to two other Ovca-DRB exon 2 genomic DNA sequences. Nineteen out of 24 BHS (79%) Ovca-DRB exon 3 (?2 domain) sequences were 100% identical to exon 3 sequence of DRB1 of DS (Ovar-DRB1). Ovca-DRA full length cDNA sequences exhibited >99% identity. Based upon exon 2 sequences, this BHS herd yielded higher Ovca-DRB allelic diversity than that reported in the previous study. Positively selected amino acid positions were identified in the peptide-binding groove of BHS and DS, but BHS showed more such sites. This highlights differing population histories, and may suggest differing needs for DR peptide-binding specificities. Presence of glutamine at position 52 (52Q) in some of the desert and captive BHS is predicted to alter the efficiency of DR dimerization, which may influence antigen presentation and T(h) cell activation. Functional assays with unique alleles should reveal whether the presentation of M. haemolytica leukotoxin peptides to T(h) cells by Ovca-DRB alleles is equivalent to that of Ovar-DRB1 alleles. PMID:22750296

Subramaniam, Renuka; White, Stephen N; Herrmann-Hoesing, Lynn M; Srikumaran, Subramaniam

2012-09-10

133

A common mutation associated with the Duarte galactosemia allele.  

PubMed Central

The human cDNA and gene for galactose-1-phosphate uridyl transferase (GALT) have been cloned and sequenced. A prevalent mutation (Q188R) is known to cause classic galactosemia (G/G). G/G galactosemia has an incidence of 1/38,886 in 1,396,766 Georgia live-born infants, but a more common variant of galactosemia, Duarte, has an unknown incidence. The proposed Duarte biochemical phenotypes of GALT are as follows: D/N, D/D, and D/G, which have approximately 75%, 50%, and 25% of normal GALT activity respectively. In addition, the D allele has isoforms of its enzyme that have more acidic pI than normal. Here we systematically determine (a) the prevalence of an A-to-G transition at base pair 2744 of exon 10 in the GALT gene, transition that produces a codon change converting asparagine to aspartic acid at position 314 (N314D), and (b) the association of this mutation with the Duarte biochemical phenotype. The 2744G nucleotide change adds an AvaII (SinI) cut site, which was identified in PCR-amplified DNA. In 111 biochemically unphenotyped controls with no history of galactosemia, 13 N314D alleles were identified (prevalence 5.9%). In a prospective study, 40 D alleles were biochemically phenotyped, and 40 N314D alleles were found. By contrast, in 36 individuals known not to have the Duarte biochemical phenotype, no N314D alleles were found. We conclude that the N314D mutation is a common allele that probably causes the Duarte GALT biochemical phenotype and occurs in a predominantly Caucasian, nongalactosemic population, with a prevalence of 5.9%. Images Figure 2 Figure 3 PMID:8198125

Elsas, L. J.; Dembure, P. P.; Langley, S.; Paulk, E. M.; Hjelm, L. N.; Fridovich-Keil, J.

1994-01-01

134

A common allele on chromosome 9 associated with coronary heartdisease  

SciTech Connect

Coronary heart disease (CHD) is a major cause of death in Western countries. Here we used genome-wide association scanning to identify a 58 kb interval on chromosome 9 that was consistently associated with CHD in six independent samples. The interval contains no annotated genes and is not associated with established CHD risk factors such as plasma lipoproteins, hypertension or diabetes. Homozygotes for the risk allele comprise 20-25% of Caucasians and have a {approx}30-40% increased risk of CHD. These data indicate that the susceptibility allele acts through a novel mechanism to increase CHD risk in a large fraction of the population.

McPherson, Ruth; Pertsemlidis, Alexander; Kavaslar, Nihan; Stewart, Alexandre; Roberts, Robert; Cox, David R.; Hinds, David; Pennachio, Len; Tybjaerg-Hansen, Anne; Folsom, Aaron R.; Boerwinkle,Eric; Hobbs, Helen H.; Cohen, Jonathan C.

2007-03-01

135

Allele-specific PCR detection of sweet cherry self-incompatibility (S) alleles S1 to S16 using consensus and allele-specific primers  

Microsoft Academic Search

PCR-based identification of all 13 known self-incompatibility ( S) alleles of sweet cherry is reported. Two pairs of consensus primers were designed from our previously published cDNA sequences of S 1 to S 6 S-RNases, the stylar components of self-incompatibility, to reveal length variation of the first and the second introns. With the exception of the first intron of S

T. Sonneveld; K. R. Tobutt; T. P. Robbins

2003-01-01

136

A commonly carried allele of the obesity-related FTO gene is associated with reduced brain volume in the healthy elderly  

PubMed Central

A recently identified variant within the fat mass and obesity-associated (FTO) gene is carried by 46% of Western Europeans and is associated with an ~1.2 kg higher weight, on average, in adults and an ~1 cm greater waist circumference. With >1 billion overweight and 300 million obese persons worldwide, it is crucial to understand the implications of carrying this very common allele for the health of our aging population. FTO is highly expressed in the brain and elevated body mass index (BMI) is associated with brain atrophy, but it is unknown how the obesity-associated risk allele affects human brain structure. We therefore generated 3D maps of regional brain volume differences in 206 healthy elderly subjects scanned with MRI and genotyped as part of the Alzheimer's Disease Neuroimaging Initiative. We found a pattern of systematic brain volume deficits in carriers of the obesity-associated risk allele versus noncarriers. Relative to structure volumes in the mean template, FTO risk allele carriers versus noncarriers had an average brain volume difference of ~8% in the frontal lobes and 12% in the occipital lobes—these regions also showed significant volume deficits in subjects with higher BMI. These brain differences were not attributable to differences in cholesterol levels, hypertension, or the volume of white matter hyperintensities; which were not detectably higher in FTO risk allele carriers versus noncarriers. These brain maps reveal that a commonly carried susceptibility allele for obesity is associated with structural brain atrophy, with implications for the health of the elderly. PMID:20404173

Stein, Jason L.; Hua, Xue; Lee, Suh; Hibar, Derrek P.; Leow, Alex D.; Dinov, Ivo D.; Toga, Arthur W.; Saykin, Andrew J.; Shen, Li; Foroud, Tatiana; Pankratz, Nathan; Huentelman, Matthew J.; Craig, David W.; Gerber, Jill D.; Allen, April N.; Corneveaux, Jason J.; Stephan, Dietrich A.; DeCarli, Charles S.; DeChairo, Bryan M.; Potkin, Steven G.; Jack, Clifford R.; Weiner, Michael W.; Raji, Cyrus A.; Lopez, Oscar L.; Becker, James T.; Carmichael, Owen T.; Thompson, Paul M.; Weiner, Michael; Thal, Leon; Petersen, Ronald; Jack, Clifford R.; Jagust, William; Trojanowki, John; Toga, Arthur W.; Beckett, Laurel; Green, Robert C.; Gamst, Anthony; Potter, William Z.; Montine, Tom; Anders, Dale; Bernstein, Matthew; Felmlee, Joel; Fox, Nick; Thompson, Paul; Schuff, Norbert; Alexander, Gene; Bandy, Dan; Koeppe, Robert A.; Foster, Norm; Reiman, Eric M.; Chen, Kewei; Trojanowki, John; Shaw, Les; Lee, Virginia M.-Y.; Korecka, Magdalena; Toga, Arthur W.; Crawford, Karen; Neu, Scott; Harvey, Danielle; Gamst, Anthony; Kornak, John; Kachaturian, Zaven; Frank, Richard; Snyder, Peter J.; Molchan, Susan; Kaye, Jeffrey; Vorobik, Remi; Quinn, Joseph; Schneider, Lon; Pawluczyk, Sonia; Spann, Bryan; Fleisher, Adam S.; Vanderswag, Helen; Heidebrink, Judith L.; Lord, Joanne L.; Johnson, Kris; Doody, Rachelle S.; Villanueva-Meyer, Javier; Chowdhury, Munir; Stern, Yaakov; Honig, Lawrence S.; Bell, Karen L.; Morris, John C.; Mintun, Mark A.; Schneider, Stacy; Marson, Daniel; Griffith, Randall; Badger, Beverly; Grossman, Hillel; Tang, Cheuk; Stern, Jessica; deToledo-Morrell, Leyla; Shah, Raj C.; Bach, Julie; Duara, Ranjan; Isaacson, Richard; Strauman, Silvia; Albert, Marilyn S.; Pedroso, Julia; Toroney, Jaimie; Rusinek, Henry; de Leon, Mony J; De Santi, Susan M; Doraiswamy, P. Murali; Petrella, Jeffrey R.; Aiello, Marilyn; Clark, Christopher M.; Pham, Cassie; Nunez, Jessica; Smith, Charles D.; Given II, Curtis A.; Hardy, Peter; DeKosky, Steven T.; Oakley, MaryAnn; Simpson, Donna M.; Ismail, M. Saleem; Porsteinsson, Anton; McCallum, Colleen; Cramer, Steven C.; Mulnard, Ruth A.; McAdams-Ortiz, Catherine; Diaz-Arrastia, Ramon; Martin-Cook, Kristen; DeVous, Michael; Levey, Allan I.; Lah, James J.; Cellar, Janet S.; Burns, Jeffrey M.; Anderson, Heather S.; Laubinger, Mary M.; Bartzokis, George; Silverman, Daniel H.S.; Lu, Po H.; Fletcher, Rita; Parfitt, Francine; Johnson, Heather; Farlow, Martin; Herring, Scott; Hake, Ann M.; van Dyck, Christopher H.; MacAvoy, Martha G.; Bifano, Laurel A.; Chertkow, Howard; Bergman, Howard; Hosein, Chris; Black, Sandra; Graham, Simon; Caldwell, Curtis; Feldman, Howard; Assaly, Michele; Hsiung, Ging-Yuek R.; Kertesz, Andrew; Rogers, John; Trost, Dick; Bernick, Charles; Gitelman, Darren; Johnson, Nancy; Mesulam, Marsel; Sadowsky, Carl; Villena, Teresa; Mesner, Scott; Aisen, Paul S.; Johnson, Kathleen B.; Behan, Kelly E.; Sperling, Reisa A.; Rentz, Dorene M.; Johnson, Keith A.; Rosen, Allyson; Tinklenberg, Jared; Ashford, Wes; Sabbagh, Marwan; Connor, Donald; Obradov, Sanja; Killiany, Ron; Norbash, Alex; Obisesan, Thomas O.; Jayam-Trouth, Annapurni; Wang, Paul; Auchus, Alexander P.; Huang, Juebin; Friedland, Robert P.; DeCarli, Charles; Fletcher, Evan; Carmichael, Owen; Kittur, Smita; Mirje, Seema; Johnson, Sterling C.; Borrie, Michael; Lee, T-Y; Asthana, Sanjay; Carlsson, Cynthia M.; Potkin, Steven G.; Highum, Diane; Preda, Adrian; Nguyen, Dana; Tariot, Pierre N.; Hendin, Barry A.; Scharre, Douglas W.; Kataki, Maria; Beversdorf, David Q.; Zimmerman, Earl A.; Celmins, Dzintra; Brown, Alice D.; Gandy, Sam; Marenberg, Marjorie E.; Rovner, Barry W.; Pearlson, Godfrey; Blank, Karen; Anderson, Karen; Saykin, Andrew J.; Santulli, Robert B.; Pare, Nadia; Williamson, Jeff D.; Sink, Kaycee M.; Potter, Huntington; Ashok Raj, B.; Giordano, Amy; Ott, Brian R.; Wu, Chuang-Kuo; Cohen, Ronald; Wilks, Kerri L.

2010-01-01

137

Protective effect of the AT137RQ and ARQK176 PrP alleles against classical scrapie in Sarda breed sheep  

PubMed Central

The susceptibility of sheep to scrapie is under the control of the host’s prion protein (PrP) gene and is also influenced by the strain of the agent. PrP polymorphisms at codons 136 (A/V), 154 (R/H) and 171 (Q/R/H) are the main determinants of susceptibility/resistance of sheep to classical scrapie. They are combined in four main variants of the wild-type ARQ allele: VRQ, AHQ, ARH and ARR. Breeding programmes have been undertaken on this basis in the European Union and the USA to increase the frequency of the resistant ARR allele in sheep populations. Herein, we report the results of a multi-flock study showing the protective effect of polymorphisms other than those at codons 136, 154 and 171 in Sarda breed sheep. All ARQ/ARQ affected sheep (n = 154) and 378 negative ARQ/ARQ controls from four scrapie outbreaks were submitted to sequencing of the PrP gene. The distribution of variations other than those at the standard three codons, between scrapie cases and negative controls, was statistically different in all flocks. In particular, the AT137RQ and ARQK176 alleles showed a clear protective effect. This is the first study demonstrating a protective influence of alleles other than ARR under field conditions. If further investigations in other sheep breeds and with other scrapie sources confirm these findings, the availability of various protective alleles in breeding programmes of sheep for scrapie resistance could be useful in breeds with a low frequency of the ARR allele and would allow maintaining a wider variability of the PrP gene. PMID:19171116

Vaccari, Gabriele; Scavia, Gaia; Sala, Marcello; Cosseddu, Gianmario; Chiappini, Barbara; Conte, Michela; Esposito, Elena; Lorenzetti, Raniero; Perfetti, Gabriella; Marconi, Paola; Scholl, Francesco; Barbaro, Katia; Bella, Antonino; Nonno, Romolo; Agrimi, Umberto

2009-01-01

138

European auxiliary propulsion, 1972  

NASA Technical Reports Server (NTRS)

The chemical and electric auxiliary propulsion technology of the United Kingdom, France, and West Germany is discussed in detail, and the propulsion technology achievements of Italy, India, Japan, and Russia are reviewed. A comparison is presented of Shell 405 catalyst and a European spontaneous hydrazine catalyst called CNESRO I. Finally, conclusions are drawn regarding future trends in European auxiliary propulsion technology development.

Holcomb, L. B.

1972-01-01

139

European Biodiesel Board  

NSDL National Science Digital Library

The European Biodiesel Board (EBB), a nonprofit organization, works to promote biodiesel use in the European Union (EU). The EBB website offers downloadable articles regarding biodiesel in the EU, downloadable reports from EU member states, a list of upcoming events, an EBB email information service, and basic statistical tables representing biodiesel production by country.

140

Microsatellite Variation in Honey Bee (Apis Mellifera L.) Populations: Hierarchical Genetic Structure and Test of the Infinite Allele and Stepwise Mutation Models  

PubMed Central

Samples from nine populations belonging to three African (intermissa, scutellata and capensis) and four European (mellifera, ligustica, carnica and cecropia) Apis mellifera subspecies were scored for seven microsatellite loci. A large amount of genetic variation (between seven and 30 alleles per locus) was detected. Average heterozygosity and average number of alleles were significantly higher in African than in European subspecies, in agreement with larger effective population sizes in Africa. Microsatellite analyses confirmed that A. mellifera evolved in three distinct and deeply differentiated lineages previously detected by morphological and mitochondrial DNA studies. Dendrogram analysis of workers from a given population indicated that super-sisters cluster together when using a sufficient number of microsatellite data whereas half-sisters do not. An index of classification was derived to summarize the clustering of different taxonomic levels in large phylogenetic trees based on individual genotypes. Finally, individual population X loci data were used to test the adequacy of the two alternative mutation models, the infinite allele model (IAM) and the stepwise mutation models. The better fit overall of the IAM probably results from the majority of the microsatellites used including repeats of two or three different length motifs (compound microsatellites). PMID:7498746

Estoup, A.; Garnery, L.; Solignac, M.; Cornuet, J. M.

1995-01-01

141

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

PubMed

Alleles at the TPOX STR locus have 6-14 different numbers of a four-nucleotide (AATG) repeat motif arranged in tandem. Although tri-allelic genotypes are generally rare, the TPOX tri-allelic pattern has a higher frequency, varying widely among populations. Despite this, there are few accurate reports to disclose the nature of the TPOX third allele. In this work we present data obtained from 45 individuals belonging to the same pedigree, in which there are cases of tri-allelic TPOX genotypes. The subjects were apparently healthy with a normal biological development. We noticed six tri-allelic cases in this family, and all of them were women. Karyotype analysis showed no occurrence of partial 2p trisomy. All the tri-allelic cases had the genotype 8-10-11, probably due to three copies of the TPOX STR sequence in all cells (Type 2 tri-allelic pattern). Based on previous data we assumed the allele 10 as the TPOX third allele. The pedigree analyses show evidences that the TPOX extra-allele was the allele10, it is placed far from the main TPOX locus, and that there is a potential linkage of the TPOX extra-allele-10 with Xq. This was the first study that included a large pedigree analysis in order to understand the nature TPOX tri-allelic pattern. PMID:24144843

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

2014-02-10

142

Functional Allelic Variation at Key Photoperiod Response QTL in Maize  

Technology Transfer Automated Retrieval System (TEKTRAN)

Tropical maize represents a valuable genetic resource containing unique alleles not present in elite temperate maize. The strong delay in flowering in response to long daylength photoperiods exhibited by most tropical maize hinders its incorporation into temperate maize breeding programs. We tested ...

143

Estimating the age of alleles by use of intraallelic variability  

SciTech Connect

A method is presented for estimating the age of an allele by use of its frequency and the extent of variation among different copies. The method uses the joint distribution of the number of copies in a population sample and the coalescence times of the intraallelic gene genealogy conditioned on the number of copies. The linear birth-death process is used to approximate the dynamics of a rare allele in a finite population. A maximum-likelihood estimate of the age of the allele is obtained by Monte Carlo integration over the coalescence times. The method is applied to two alleles at the cystic fibrosis (CFTR) locus, {Delta}F508 and G542X, for which intraallelic variability at three intronic microsatellite loci has been examined. Our results indicate that G542X is somewhat older than {Delta}F508. Although absolute estimates depend on the mutation rates at the microsatellite loci, our results support the hypothesis that {Delta}F508 arose <500 generations ({approx}10,000 years) ago. 32 refs., 4 figs.

Slatkin, M.; Rannala, B. [Univ of California, Berkeley, CA (United States)

1997-02-01

144

Generation of mice with a conditional Lbh null allele.  

PubMed

Limb bud and heart (LBH) is a developmentally expressed, tissue-specific transcription cofactor in vertebrates that acts in the WNT signaling pathway, a genetic program critical for embryogenesis and adult tissue homeostasis. Aberrant gain-of-function of LBH is implicated in both human congenital disease and cancer. The normal physiological function of LBH has remained elusive owing to a lack of genetic loss-of-function models. Here, we have generated mice with a conditional null allele of Lbh by flanking exon 2 with loxP sites (Lbh(flox)). Homozygous Lbh(flox) and Lbh(loxP) mice, in which the Neo cassette was removed through FLPe-mediated recombination, were viable and fertile, indicating that these conditional Lbh alleles are fully functional. Lbh(loxP) mice were then crossed with a Rosa26-Cre line, resulting in ubiquitous deletion of exon 2 and abolishment of LBH protein expression. Mice homozygous for the Lbh null allele (Lbh(?)(2)) displayed normal embryonic development and postnatal growth with morphologies indistinguishable from wild-type littermates. However, mammary gland development, which occurs primarily after birth, was perturbed. Thus, the conditional Lbh allele will be a valuable tool to uncover the currently unknown tissue-specific roles of LBH in postnatal development and disease. PMID:23495064

Lindley, Linsey E; Briegel, Karoline J

2013-07-01

145

UNDERSTANDING GENE AND ALLELE FUNCTION WITH TWO-HYBRID METHODS  

Microsoft Academic Search

Two-hybrid schemes for detecting protein-protein interactions have deepened our understanding of biology by allowing scientists to identify individual important proteins. Recent developments will allow biologists to chart regulatory networks and to rapidly generate hypotheses for the function of genes, allelic variants, and the connections between proteins that make up these networks. Future devel- opments will allow biologists to test inferences

Roger Brent; Russell L. Finley Jr

1997-01-01

146

Multifragment alleles in DNA fingerprints of the parrot, Amazona ventralis  

USGS Publications Warehouse

Human DNA probes that identify variable numbers of tandem repeat loci are being used to generate DNA fingerprints in many animal and plant species. In most species the majority of the sc rable autoradiographic bands of the DNA fingerprint represent alleles from numerous unlinked loci. This study was initiated to use DNA fingerprints to determine the amount of band-sharing among captive Hispaniolan parrots (Amazona ventralis) with known genetic relationships. This would form the data base to examine DNA fingerprints of the closely related and endangered Puerto Rican parrot (A. vittata) and to estimate the degree of inbreeding in the relic population. We found by segregation analysis of the bands scored in the DNA fingerprints of the Hispaniolan parrots that there may be as few as two to five loci identified by the human 33.15 probe. Furthermore, at one locus we identified seven alleles, one of which is represented by as many as 19 cosegregating bands. It is unknown how common multiband alleles might be in natural populations, and their existence will cause problems in the assessment of relatedness by band-sharing analysis. We believe, therefore, that a pedigree analysis should be included in all DNA fingerprinting studies, where possible, in order to estimate the number of loci identified by a minisatellite DNA probe and to examine the nature of their alleles.

Brock, M.K.; White, B.N.

1991-01-01

147

Efficient nonmeiotic allele introgression in livestock using custom endonucleases.  

PubMed

We have expanded the livestock gene editing toolbox to include transcription activator-like (TAL) effector nuclease (TALEN)- and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-stimulated homology-directed repair (HDR) using plasmid, rAAV, and oligonucleotide templates. Toward the genetic dehorning of dairy cattle, we introgressed a bovine POLLED allele into horned bull fibroblasts. Single nucleotide alterations or small indels were introduced into 14 additional genes in pig, goat, and cattle fibroblasts using TALEN mRNA and oligonucleotide transfection with efficiencies of 10-50% in populations. Several of the chosen edits mimic naturally occurring performance-enhancing or disease- resistance alleles, including alteration of single base pairs. Up to 70% of the fibroblast colonies propagated without selection harbored the intended edits, of which more than one-half were homozygous. Edited fibroblasts were used to generate pigs with knockout alleles in the DAZL and APC genes to model infertility and colon cancer. Our methods enable unprecedented meiosis-free intraspecific and interspecific introgression of select alleles in livestock for agricultural and biomedical applications. PMID:24014591

Tan, Wenfang; Carlson, Daniel F; Lancto, Cheryl A; Garbe, John R; Webster, Dennis A; Hackett, Perry B; Fahrenkrug, Scott C

2013-10-01

148

Systematic underestimation of the age of selected alleles.  

PubMed

A common interpretation of genome-wide selection scans is that the dispersal of anatomically modern humans out of Africa and into diverse environments led to a number of genetic adaptations. If so, patterns of polymorphism from non-African individuals should show the signature of adaptations dating to 40,000-100,000 Kya, coinciding with the main exodus from Africa. However, scans of polymorphism data from a few populations have yielded conflicting results about the chronology of local, population-specific adaptations. In particular, a number of papers report very recent ages for selected alleles in humans, which postdate the development of agriculture 10 Kya, and suggest that adaptive differences among human populations are much more recent. I present an analysis of simulations suggesting a downward bias in methods commonly used to estimate the age of selected alleles. These findings indicate that an estimate of a time to the most recent common ancestor (tMRCA) obtained using standard methods (used as a proxy for the age of an allele) of less than 10 Kya is consistent with an allele that actually became selected before the onset of agriculture and potentially as early as 50 Kya. These findings suggest that the genomic scans for selection may be consistent with selective pressures tied to the Out of Africa expansion of modern human populations. PMID:22969791

Kelley, Joanna L

2012-01-01

149

Rapid screening for temperature-sensitive alleles in plants.  

PubMed

We developed a simple and fast method to identify temperature-sensitive alleles of essential plant genes. We used primary and tertiary structure information to identify residues in the core of the protein of interest. These residues were mutated and tested for temperature sensitivity, taking advantage of the exceptionally rapid 1-week complementation assay in the moss Physcomitrella patens. As test molecules, we selected the actin-binding proteins profilin and actin-depolymerizing factor, because they are essential and their loss-of-function phenotype can be fully rescued. Screening a small number of candidate mutants, we successfully identified temperature-sensitive alleles of both profilin and actin-depolymerizing factor. Plants harboring these alleles grew well at the permissive temperature of 20 degrees C to 25 degrees C but showed a complete loss of function at the restrictive temperature of 32 degrees C. Notably, the profilin mutation identified in the moss gene can be transferred to profilins from other plant species, also rendering them temperature sensitive. The ability to routinely generate temperature-sensitive alleles of essential plant proteins provides a powerful tool for the study of gene function in plants. PMID:19666707

Vidali, Luis; Augustine, Robert C; Fay, Scotty N; Franco, Paula; Pattavina, Kelli A; Bezanilla, Magdalena

2009-10-01

150

New HLA class II alleles in the Indonesian population.  

PubMed

This paper describes two new class II alleles of the major histocompatibility complex (MHC), DRB1*1431 and DRB3*0303, that have been found in the Indonesian population. In addition, the identification of DRB1*0819 is presented as a confirmatory report. PMID:10599892

Panigoro, R; Greville, W D; Kennedy, A; Tréjaut, J; Dunckley, H

1999-11-01

151

Efficient nonmeiotic allele introgression in livestock using custom endonucleases  

PubMed Central

We have expanded the livestock gene editing toolbox to include transcription activator-like (TAL) effector nuclease (TALEN)- and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-stimulated homology-directed repair (HDR) using plasmid, rAAV, and oligonucleotide templates. Toward the genetic dehorning of dairy cattle, we introgressed a bovine POLLED allele into horned bull fibroblasts. Single nucleotide alterations or small indels were introduced into 14 additional genes in pig, goat, and cattle fibroblasts using TALEN mRNA and oligonucleotide transfection with efficiencies of 10–50% in populations. Several of the chosen edits mimic naturally occurring performance-enhancing or disease- resistance alleles, including alteration of single base pairs. Up to 70% of the fibroblast colonies propagated without selection harbored the intended edits, of which more than one-half were homozygous. Edited fibroblasts were used to generate pigs with knockout alleles in the DAZL and APC genes to model infertility and colon cancer. Our methods enable unprecedented meiosis-free intraspecific and interspecific introgression of select alleles in livestock for agricultural and biomedical applications. PMID:24014591

Tan, Wenfang; Carlson, Daniel F.; Lancto, Cheryl A.; Garbe, John R.; Webster, Dennis A.; Hackett, Perry B.; Fahrenkrug, Scott C.

2013-01-01

152

A genotype probability index for multiple alleles and haplotypes.  

PubMed

We use linear algebra to calculate an index of information content in genotype probabilities which has previously been calculated using trigonometry. The new method can be generalized allowing the index to be calculated for loci with more than two alleles. Applications of this index include its use in genotyping strategies, strategies to manage genetic disorders and in estimation of genotype effects. PMID:16274422

Percy, A; Kinghorn, B P

2005-12-01

153

European Commission: Public Opinion  

NSDL National Science Digital Library

Some Scout Report readers might be wondering "How do Europeans feel about the euro?" or even "What do Europeans think about the effectiveness of different energy policies?" All of the answers to these questions (and many more) can be found on the European Commission's Public Opinion site. The site contains the results from surveys conducted with Europeans on their attitudes towards alcohol, the role of the European Union in formulating security policy, and a number of other topics. Visitors will definitely want to make their way to the Eurobarometer Interactive Search System, which allows them to choose a subject or country which is of interest to them. Visitors should also take a look at their very fine "Qualitative Studies" section, which includes reports such as "The Future of Europe" and "Integrating Gender Mainstreaming into Employment Policies". Needless to say, summaries of the reports are available in a wide range of languages, including Dutch, German, Italian, and French.

154

European Geography Test  

NSDL National Science Digital Library

European Geography Test is a collection of challenging Web-based geography exams that survey students' knowledge of European topography, European urban geography, and general map skills. Currently, this site hosts seven tests, which are available in English, Swedish, Spanish, and Dutch. Tests are divided into three different learning levels, and the focus and objectives for each test are clearly stated. The tests employ interactive maps, photographic images, pull-down menus, radio buttons, and fill-in forms to ask students a series of multiple choice, true or false, and matching questions. The questions included in European Geography Test were developed as part of an inter-university project for DGXXII of the European Commission by a consortium of instructors in the UK, Sweden, Belgium, Spain, and The Netherlands. Note: users must register at the site to take the free tests; registration requires name, email address, age, and country of residence.

155

A comparison of adjustment methods to test the robustness of an STR DNA database comprised of 24 European populations  

Microsoft Academic Search

An aim of the European Network of Forensic Science Institutes (ENFSI) is to produce a DNA database of second generation multiplex (SGM) STR profiles that is representative of the resident cosmopolitan populations. To achieve this, data were collected from 24 different populations. All of the data were combined to form one database of 5700 profiles from which allele proportions were

Peter Gill; Lindsey Foreman; John S Buckleton; Christopher M Triggs; Heather Allen

2003-01-01

156

Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y  

E-print Network

Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during by the Editorial Board February 1, 2014 (received for review September 4, 2013) Pigmentation is a polygenic trait of selection acting on functional alleles in three key genes known to be involved in human pigmentation path

157

Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y.  

PubMed

Pigmentation is a polygenic trait encompassing some of the most visible phenotypic variation observed in humans. Here we present direct estimates of selection acting on functional alleles in three key genes known to be involved in human pigmentation pathways--HERC2, SLC45A2, and TYR--using allele frequency estimates from Eneolithic, Bronze Age, and modern Eastern European samples and forward simulations. Neutrality was overwhelmingly rejected for all alleles studied, with point estimates of selection ranging from around 2-10% per generation. Our results provide direct evidence that strong selection favoring lighter skin, hair, and eye pigmentation has been operating in European populations over the last 5,000 y. PMID:24616518

Wilde, Sandra; Timpson, Adrian; Kirsanow, Karola; Kaiser, Elke; Kayser, Manfred; Unterländer, Martina; Hollfelder, Nina; Potekhina, Inna D; Schier, Wolfram; Thomas, Mark G; Burger, Joachim

2014-04-01

158

Molecular, serological and population studies of the alleles and products of HLA-B*41.  

PubMed

The HLA-B41 specificity was first identified over 25 years ago and, although both serological and biochemical studies have suggested its subdivision, it is only recently that two HLA-B*41 alleles (B*4101 and B*4102) have been identified and sequenced. We designed three oligonucleotide primers, combined in two mixtures to define these alleles by PCR using sequence-specific primers (PCR-SSP) in a random normal population of 9,464 HLA-A, B, DR, DQ typed Northern European Caucasoid donors from the Welsh Bone Marrow Donor Registry. The HLA-B41 phenotype frequency was 0.835%, and of the 79 HLA-B41 subjects 22 (27.85%) were B*4101 and 57 (72.15%) were B*4102. The phenotype frequencies of B*4101 and B*4102 were 0.232 and 0.602%, respectively, and the gene frequencies were 0.00116 and 0.00301, respectively. Formal two-locus linkage disequilibrium (LD) analysis demonstrated significant associations between B*4101 and A30 and DR11, and between B*4102 and A66 and DR13. LD analysis of three loci showed significant associations between B*4101, DR7, DQ2 and B*4101, DR11, DQ7 (DQB1*0301/0304) and between HLA-A3, B*4102, DR13; A66, B*4102, DR7; A66, B*4102, DR13; B*4102, DR13, DQ6 and B*4102, DR13, DQ7. Examination of the HLA phenotypes (including HLA-C) of the B*41 subjects, together with the LD analysis findings, suggested four different HLA haplotypes bearing B*4101 and five B*4102 haplotypes. The most frequent B*4101 haplotype was: HLA- A30 or other A allele, Cw*1701, B*4101, DRB1*1102, DQB1*0301 and the most freqent B*4102 haplotype was: A*6601 or A3 or other A allele, Cw*1701, B*4102, DRB1*1303, DQB1*0301. In addition, the well-known association of A66 with B41 was between A*6601 and B*4102, and although both B*41 alleles were commonly in association with Cw*1701, B*4101 was found with Cw*07. One-dimensional isoelectric focusing (1D-IEF) analysis of HLA-B proteins from 2 B*4101 and 2 B*4102 subjects clearly showed that the B41.1 and B41.2 1D-IEF variants, identified in the 10th International Histocompatibility Workshop, corresponded to B*4101 and B*4102 products, respectively. Serological titration studies, with 59 lymphocytotoxic pregnancy antisera, containing an HLA-B41 component and stimulated by up to five different HLA-B specificities, were unable to differentiate the two groups of B*41 subjects. This suggests that partition of the HLA-B41 specificity will not normally be achieved by classical serological methods. It is suggested that the previous alleged serological subdivision of HLA-B41 was founded on the unwitting use of antisera detecting the HLA-Cw*17 products. PMID:10394052

Darke, C; Winkler, S; Guttridge, M G; Street, J; Thomas, M; Thompson, J; McNamara, S

1999-01-01

159

Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole genome amplified DNA  

PubMed Central

Besides their use in mRNA expression profiling, oligonucleotide microarrays have also been applied to single-nucleotide polymorphism (SNP) and loss of heterozygosity (LOH) or allelic imbalance studies. In this report, we evaluate the reliability of using whole genome amplified DNA for analysis with an oligonucleotide microarray containing 11 560 SNPs to detect allelic imbalance and chromosomal copy number abnormalities. Whole genome SNP analyses were performed with DNA extracted from osteosarcoma tissues and patient-matched blood. SNP calls were then generated by Affymetrix® GeneChip® DNA Analysis Software. In two osteosarcoma cases, using unamplified DNA, we identified 793 and 1070 SNP loci with allelic imbalance, respectively. In a parallel experiment with amplified DNA, 78% and 83% of these SNP loci with allelic imbalance was detected. The average false-positive rate is 13.8%. Furthermore, using the Affymetrix® GeneChip® Chromosome Copy Number Tool to analyze the SNP array data, we were able to detect identical chromosomal regions with gain or loss in both amplified and unamplified DNA at cytoband resolution. PMID:15148342

Wong, Kwong-Kwok; Tsang, Yvonne T. M.; Shen, Jianhe; Cheng, Rita S.; Chang, Yi-Mieng; Man, Tsz-Kwong; Lau, Ching C.

2004-01-01

160

Slovenian population data for five new European Standard Set Short tandem repeat loci and SE33 locus  

PubMed Central

Aim To establish the allele distribution and statistical parameters of forensic interest for the D10S1248, D22S1045, D2S441, D1S1656, D12S391, and SE33 loci in Slovenian population and to compare allele frequencies with those from other populations. Methods We analyzed blood and buccal swab samples from 333 unrelated, healthy Slovenian individuals. All samples were genotyped using the AmpFlSTR NGM Kit to obtain the allele frequency data for the loci D10S1248, D22S1045, D2S441, D1S1656, and D12S391. Samples from 113 individuals were also analyzed using the PowerPlex ESX 17 system to obtain the allele frequency data for the SE33 locus. Allele frequencies and statistical parameters of forensic interest were determined and frequency profiles compared between Slovenian and other European Caucasian populations using the Arlequin software, version 3.5.1.3. Results The investigated short tandem repeat (STR) loci in Slovenian population had a great discriminating potential with a combined discrimination power of 0.99999998. The highest discrimination power and polymorphism information content were observed for the SE33 locus, followed by loci D1S1656, D12S391, D10S1248, D2S441, and D22S1045. When Slovenian allele frequency distribution was compared with other European populations, deviations were found only for Spanish and Italian population for D2S441 and D12S391. Conclusion Slovenian population does not differ significantly from other European populations in terms of allele frequency distributions for the six analyzed STR loci. Based on forensic efficiency values, SE33 may be considered the most informative locus, which makes it especially useful in forensic investigations. PMID:24577822

Zupani? Pajni?, Irena; Podovšovnik Axelsson, Eva; Balažic, Jože

2014-01-01

161

The European Fusion Programme  

SciTech Connect

The long-term objective of the European fusion programme is the harnessing of the power of fusion to help meet mankind's future energy needs.This paper describes the current research programme, the unique organisational character of the fusion programme, and European and world-wide co-operation. The future evolution of the programme as part of the European Research Area and the developments currently taking place in preparation for the possible construction of ITER, the next major step towards the realisation of fusion power, are discussed.

Antidormi, R.; Bartlett, D.; Bruhns, H. [European Commission (Belgium)

2004-03-15

162

The European Values Study  

NSDL National Science Digital Library

Curious minds want to know: "What exactly do Europeans believe?" It's an important and interesting question, and the directors and researchers in charge of the European Values Study (EVS) have been looking into this subject since the early 1980s. Based in the Netherlands the EVS concerns itself with asking Europeans about religion and morality, politics, work and leisure, and relationships. On their homepage, visitors can learn about their work and view previous and current surveys. While visitors do not have access to the raw data on the site, they can look at the questionnaires and read publications based on this research.

163

European Union Center of Excellence European Studies Center  

E-print Network

NEWSLETTER European Union Center of Excellence European Studies Center Continued on page 6 Turkey're dealing with energy, NATO, the European Union, the Middle East, Iran, Cyprus, Greece; there's hardly, University of Pittsburgh At a recent speech in Brussels, U.S. Assistant Secretary of State for European

Sibille, Etienne

164

European Union Center of Excellence European Studies Center  

E-print Network

NEWSLETTER European Union Center of Excellence European Studies Center URAL Continued on page 6 the Arab perspective on the European Neighborhood Policy. 4 Fellowships, Grants, and Opportunities. 5 to immigration and substantive inter-group tensions exist in many European countries. Therefore, understanding

Sibille, Etienne

165

European Union Center of Excellence European Studies Center  

E-print Network

NEWSLETTER European Union Center of Excellence European Studies Center Life in Libraries: A Project conferences we co-organized with the European Union Center of Excellence (EUCE) at the University of Pittsburgh, one on farming issues in 2008 and another on minority languages in the European Union region

Sibille, Etienne

166

European Union Center of Excellence European Studies Center  

E-print Network

NEWSLETTER European Union Center of Excellence European Studies Center Continued on page 6 countries and backgrounds, such as the European Union. The recent enlargement of the EU, which admitted 10 The Impact of Enlargement on the European Commission: Coming in at the Bottom and at the Top by Carolyn Ban

Sibille, Etienne

167

Contemporary evolution, allelic recycling, and adaptive radiation of the threespine stickleback  

E-print Network

, invasive species, parallelism, recessive allele, threespine stickleback. INTRODUCTION Charles Darwin (1859 not attempt to study natural selection and evolution in contemporary natural populations. Darwin's successorsContemporary evolution, allelic recycling, and adaptive radiation of the threespine stickleback

Aguirre, Windsor E.

168

European Judicial Network  

NSDL National Science Digital Library

As a part of the European Commission, the European Judicial Network is primarily concerned with providing information about community law, European law, and various aspects of civil and commercial law. The homepage is well-organized, and visitors can start by clicking on the topic page sections, which cover everything from bringing a case to court to alternative dispute resolutions. On the right-side of the homepage, visitors can click on the flags of member states to learn more about each nation's legal system. The site will certainly be of interest to those with a legal background, but the main stated objective of the site is "to make life easier for people facing litigation of whatever kind where there is a transnational element." Not surprisingly, all of this information is available in the twenty official languages of the European Union.

2007-01-01

169

European Molecular Biology Laboratory  

E-print Network

On 10 May an Agreement was signed at CERN setting up a new European Laboratory. It will be concerned with research in molecularbiology and will be located at Heidelberg in the Federal Republic of Germany.

1973-01-01

170

Entrepreneurship in European Regions  

Microsoft Academic Search

Policy makers’ interest in stimulating entrepreneurship suggests a general consensus about their beneficiary economic effects\\u000a that exist. For example, the goal of the EU 2000 Lisbon Agenda to become the world’s most innovative area by 2010 relies on\\u000a the entrepreneurial power of regions. The European Commission , in its Green paper on Entrepreneurship in Europe (European\\u000a Commission 2003 , p.

Niels Bosma; Veronique Schutjens; Erik Stam

171

Bacteriophage lambda repressor allelic modulation of the Rex exclusion phenotype.  

PubMed

The sensitivity of delta red-gam delta ren mutants of bacteriophage lambda to Rex exclusion by lambda rexA+ rexB+ lysogens is modulated by the prophage cI repressor allele. We show the following: (i) lambda spi156 delta nin5 forms plaques on a cI+-rexA+-rexB+ lysogen with 10(5)-fold higher efficiency than on cI[Ts]-rexA+-rexB+ derivatives. (ii) The cI[Ts]857 allele augmentation of Rex exclusion is recessive to cI+. (iii) The cI857-mediated increase in Rex exclusion activity involves the participation of a genetic element mapping outside of cI-rexA-rexB. PMID:12795410

Slavcev, Roderick A; Bull, Harold J; Hayes, Sidney

2003-03-01

172

Attenuated APC alleles produce functional protein from internal translation initiation  

PubMed Central

Some truncating mutations of the APC tumor suppressor gene are associated with an attenuated phenotype of familial adenomatous polyposis coli (AAPC). This work demonstrates that APC alleles with 5? mutations produce APC protein that down-regulates ?-catenin, inhibits ?-catenin/T cell factor-mediated transactivation, and induces cell-cycle arrest. Transfection studies demonstrate that cap-independent translation is initiated internally at an AUG at codon 184 of APC. Furthermore, APC coding sequence between AAPC mutations and AUG 184 permits internal ribosome entry in a bicistronic vector. These data suggest that AAPC alleles in vivo may produce functional APC by internal initiation and establish a functional correlation between 5? APC mutations and their associated clinical phenotype. PMID:12034871

Heppner Goss, Kathleen; Trzepacz, Chris; Tuohy, Thérèse M. F.; Groden, Joanna

2002-01-01

173

S-allele diversity in Sorbus aucuparia and Crataegus monogyna (Rosaceae: Maloideae)  

Microsoft Academic Search

RT-PCR was used to obtain the first estimates from natural populations of allelic diversity at the RNase-based gametophytic self-incompatibility locus in the Rosaceae. A total of 20 alleles were retrieved from 20 Sorbus aucuparia individuals, whereas 17 alleles were found in 13 Crataegus monogyna samples. Estimates of population-level allele numbers fall within the range observed in the Solanaceae, the only

O Raspé; J R Kohn

2002-01-01

174

Archive of European Integration  

NSDL National Science Digital Library

The creation of a so-called âÂÂcommon marketâ and throughout the European countries has taken decades, and this valuable scholarly resource created by a team of academics will be of great interest to anyone with a penchant for this subject. The idea for this archive of European Integration was devised by Phil Wilkin (who now serves as its editor), and over the years, his efforts have been aided by a team of other dedicated individuals. Simply put, the Archive of European Integration (AEI) is âÂÂan electronic repository and archive for research materials on the topic of European integration and unification.â As such, it is primarily concerned with collecting official European Community/European Union documents and certain independently-produced research materials. First-time visitors to the site can search the archive by six different methods, view a list of the latest additions, and also register at no charge for an account that will let them submit items to the archive. All told, the archive currently contains over 4800 documents ranging from working papers on topics such as the common agricultural policy as well as cultural policy.

175

Immunogenetic study of a new HLA allele, B*2723.  

PubMed

A novel HLA-B*27 allele (B*2723) detected by irregular serological and PCR-SSP typing results was identified by nucleotide sequencing of exons 2 and 3. B*2723 differs from B*27052 by nine nucleotides which encode seven amino acid changes at positions 63 (Glu to Asn), 67 (Cys to Phe), 69 (Ala to Thr), 70 (Lys to Asn), 71 (Ala to Thr), 74 (Asp to Tyr) and 77 (Asp to Ser) in the alpha1 helix. All these substitutions are possessed by B*35 alleles suggesting that B*2723 was created by a gene conversion-like event involving B*27052 and a B*35 allele. Using the HLA-A*26 and DRB1*12 alleles of the B*2723-bearing haplotype as 'markers', two further examples of B*2723 were found in 29,851 blood donors. Therefore, B*2723 has a 'minimum' gene frequency of 0.000034 (phenotype frequency 0.0067%) in blood donors resident in Wales. In all three families, B*2723 was present on a haplotype with: A*26; Cw*0202; DRB1*1201/6/7; DRB3*02; DQA1*05; DQB1*0301. The B*2723 product failed to react with HLA-B27 antisera and reacted weakly or not at all with Bw4 antisera. Lack of the ECAKA motif at amino acid positions 63, 67, 69-71 probably accounts for lack of the B27 specificity while the amino acid combination 74Y, 77S, 80T, 81L may cause aberrant Bw4 reactivity. PMID:12492816

Darke, C; Street, J; Hammond, L; Downing, J; Thompson, J

2002-11-01

176

Prediction of bone density from vitamin D receptor alleles  

Microsoft Academic Search

BONE density achieved in early adulthood is the major determinant of risk of osteoporotic fracture. Up to 60% of women1,2 suffer osteoporotic fractures as a result of low bone density2, which is under strong genetic control3-6 acting through effects on bone turnover7,8. Here we show that common allelic variants in the gene encoding the vitamin D receptor9 can be used

Nigel A. Morrison; Jian Cheng Qi; Akifumi Tokita; Paul J. Kelly; Linda Crofts; Tuan V. Nguyen; Philip N. Sambrook; John A. Eisman

1994-01-01

177

ALLELE-SPECIFIC EXPRESSION OF APC IN ADENOMATOUS POLYPOSIS FAMILIES  

PubMed Central

Backgound & Aims Germline mutations of the APC gene are the pathogenic cause of most cases of familial adenomatous polyposis (FAP) and a lesser proportion of attenuated FAP (AFAP). Systematic analysis of APC at the RNA level may provide insight into the pathogenicity of identified mutations and uncover the molecular basis of FAP/AFAP in families without identifiable mutations. Here, we analyzed the prevalence of imbalances in the allelic expression of APC in polyposis families with germline mutations in the gene and without detectable mutations in APC or and MUTYH. Methods Allele-specific expression (ASE) was determined by single nucleotide primer extension using an exon 11 polymorphism as an allele-specific marker. In total, 52 APC-mutation-positive (36 families) and 24 APC/MUTYH-mutation-negative (23 families) informative patients were analyzed. Seventy-six controls were also included. Results Of the APC-mutation-positive families, most of those in which the mutation was located before the last exon of the gene (12 of 14) showed ASE imbalance, which is consistent with a mechanism of nonsense-mediated decay (NMD). Of the APC/MUTYH mutation-negative families, two (9%) showed ASE imbalance as a hallmark of the putative pathogenic cause of the disease. Normal allele expression was restored after treatment of short-term cultured lymphocytes with puromycin, supporting the NMD hypothesis. Conclusions ASE analysis may be an indicator of pathogenicity for some cases of FAP and AFAP in which APC mutations are not found. ASE might also be useful for prioritizing the order in which different areas of APC should be tested. Our results underline the importance of RNA-level studies in molecular diagnosis of FAP. PMID:20434453

Castellsagué, Ester; González, Sara; Guinó, Elisabet; Stevens, Kristen N.; Borràs, Ester; Raymond, Victoria M.; Lázaro, Conxi; Blanco, Ignacio; Gruber, Stephen B.; Capellá, Gabriel

2010-01-01

178

Allelic Sequence Divergence in the Apomictic Boechera holboellii Complex  

Microsoft Academic Search

\\u000a It has been suggested that the absence of meiosis in asexual lineages should lead to higher interallelic divergence at any\\u000a given locus within an individual (i.e., allelic sequence divergence – ASD) compared to sexual populations (i.e., Meselson effect; Mark Welch\\u000a and Meselson 2000). In the present study, ASD was investigated in 2 diploid sexual, 3 diploid apomictic and 3 triploid

Jose M. Corral; Marcin Piwczynski; Tim F. Sharbel

179

TETRASOMIC SEGREGATION FOR MULTIPLE ALLELES IN ALFALFA1  

Microsoft Academic Search

Evidence of tetrasomic inheritance in alfalfa, Medicago sativa L. and M. falcata L., for multiple codominant alleles at three isozymic loci is reported in this study. The locus Prx-I governing anodal peroxidase and the loci Lap-I and Lap2 governing anodal leucine-aminopeptidase were studied by starch gel electrophoresis in seedling root tissue or seeds. The progenies from several di-, tri- or

CARLOS F. QUIROSZ

180

Novel carbonic anhydrase ( Car2 ) allele in Spanish mice  

Microsoft Academic Search

A unique electrophoretic form of carbonic anhydrase is characteristic of some laboratory-maintained mice of the wild mouse species Mus spretus. This isozyme has been characterized by cellulose acetate electrophoresis and by isolectric focusing. It is proposed that this isozyme be called CAR-2C and that its encoding allele be designated Car-2c. Fertile hybrids of Mus spretus and C57BL\\/6J (Car-2a) show both

J. Barry Whitney

1984-01-01

181

Genotyping by apyrase-mediated allele-specific extension  

Microsoft Academic Search

This report describes a single-step extension approach suitable for high-throughput single- nucleotide polymorphism typing applications. The method relies on extension of paired allele-specific primers and we demonstrate that the reaction kinetics were slower for mismatched configurations compared with matched configurations. In our approach we employ apyrase, a nucleotide degrading enzyme, to allow accurate discrimination between matched and mismatched primer-template configurations.

Afshin Ahmadian; Baback Gharizadeh; Deirdre O'Meara; Jacob Odeberg; Joakim Lundeberg

2001-01-01

182

The Timing of Pigmentation Lightening in Europeans  

PubMed Central

The inverse correlation between skin pigmentation and latitude observed in human populations is thought to have been shaped by selective pressures favoring lighter skin to facilitate vitamin D synthesis in regions far from the equator. Several candidate genes for skin pigmentation have been shown to exhibit patterns of polymorphism that overlap the geospatial variation in skin color. However, little work has focused on estimating the time frame over which skin pigmentation has changed and on the intensity of selection acting on different pigmentation genes. To provide a temporal framework for the evolution of lighter pigmentation, we used forward Monte Carlo simulations coupled with a rejection sampling algorithm to estimate the time of onset of selective sweeps and selection coefficients at four genes associated with this trait in Europeans: KITLG, TYRP1, SLC24A5, and SLC45A2. Using compound haplotype systems consisting of rapidly evolving microsatellites linked to one single-nucleotide polymorphism in each gene, we estimate that the onset of the sweep shared by Europeans and East Asians at KITLG occurred approximately 30,000 years ago, after the out-of-Africa migration, whereas the selective sweeps for the European-specific alleles at TYRP1, SLC24A5, and SLC45A2 started much later, within the last 11,000–19,000 years, well after the first migrations of modern humans into Europe. We suggest that these patterns were influenced by recent increases in size of human populations, which favored the accumulation of advantageous variants at different loci. PMID:22923467

Beleza, Sandra; Santos, António M.; McEvoy, Brian; Alves, Isabel; Martinho, Cláudia; Cameron, Emily; Shriver, Mark D.; Parra, Esteban J.; Rocha, Jorge

2013-01-01

183

Mapping a disease locus by allelic?association  

PubMed Central

Allelic association provides a means to map disease genes that, in a dense map of polymorphic markers, has considerably higher resolution than linkage methods. We describe here a composite likelihood estimate of location for a disease gene against a high-resolution marker map by using allele frequencies at linked loci. Data may be family-based, as in the transmission disequilibrium test, or from a case-control study. ?2 tests, logarithm of odds, standard errors, and information weights are provided. The method is illustrated by analysis of published cystic fibrosis haplotypes, in which ?F508 is more accurately localized than by other association studies. This differs from current approaches by adopting a more general Malecot model for isolation by distance, where distance here is between marker and disease locus, allowance for errors in the map and model, and freedom from assumptions about demography, systematic pressures, and the ratio of physical to genetic distance. When these assumptions are introduced the number of generations since the original mutation may be estimated, but this is not required to determine location and its standard error, so that evidence from allelic association may be efficiently combined with linkage evidence to identify a region for positional cloning of a disease gene. PMID:9465087

Collins, A.; Morton, N. E.

1998-01-01

184

NUMBER OF SEX ALLELES IN A SAMPLE OF HONEYBEE COLONIES Jean-Marie CORNUET Franck ARIES  

E-print Network

NUMBER OF SEX ALLELES IN A SAMPLE OF HONEYBEE COLONIES Jean-Marie CORNUET Franck ARIES Station of bree- ding work, this paper gives the theoretical distribution of the number of sex alleles in a sample the factors interfering with this trait, there is the possible identity of sex alleles of the workers' parents

Paris-Sud XI, Université de

185

Molecular characterization and clinical presentation of HK?? and anti-HK?? alleles in southern Chinese subjects.  

PubMed

The HK?? allele is a rearrangement occurring in the ?-globin gene cluster containing both the -?(3.7) and ???(anti4.2) unequal crossover junctions. The anti-HK?? allele is the reciprocal product containing both the -?(4.2) and ???(anti3.7) unequal crossover junctions, which had been predicted but had not been detected previously. The phenotypic feature and population frequency of these two unusual alleles were not described. We report the identification of nine individuals carrying the HK?? allele and two individuals carrying the anti-HK?? allele in southern China and describe their phenotype and haplotype data. The molecular structures of HK?? allele and anti-HK?? allele were confirmed by two-round nested polymerase chain reaction assay. The mechanism of origin of both alleles is related to probably simultaneous double crossover. Heterozygotes of HK?? or anti-HK?? allele show a normal hematological phenotype. Finally, we report the carrier rates of these both alleles in the Guangxi Zhuang Autonomous Region of southern China, namely, ?0.07% for the HK?? allele and ?0.02% for the anti-HK?? allele. PMID:22989259

Shang, X; Li, Q; Cai, R; Huang, J; Wei, X; Xu, X

2013-05-01

186

Distinctions among Allelic Variants Associated with Chromosome 3 Inversions in DROSOPHILA PSEUDOOBSCURA and DROSOPHILA PERSIMILIS  

PubMed Central

Efforts were made to discriminate new genetic variants among electrophoretic alleles that are associated with chromosome 3 inversions of Drosophila pseudoobscura and D. persimilis. Apparent genetic similarities for electrophoretic alleles between these two species and among the common inversions they carry were reexamined by altering gel concentration and buffer pH. At the amylase locus, the 1.09 electrophoretic allele could be further separated into two allelic classes that differentiated the WT and KL arrangements. Similarly, the 0.84 electrophoretic allele was divided into two allelic classes, one characteristic of the Santa Cruz phylad arrangements, TL and SC, and the other found in strains of the Standard phylad arrangements and CH. Uncommon amylase alleles proved to be different alleles in the two species. No new allelic variants, however, could be found among strains with the amylase 1.00 allele, the commonest allele in the Standard phylad of both species. No major new allelic variation was detected for acid phosphatase-3 and larval protein-10 that revealed any further differentiation among species or inversions. Variation at all three loci in strains of the Bogota population remained genetically similar to variation in strains of mainland D. pseudoobscura. PMID:6167488

Norman, R. A.; Prakash, Satya

1980-01-01

187

CCR5 as a Natural and Modulated Target for Inhibition of HIV  

PubMed Central

Human immunodeficiency virus type 1 (HIV-1) infection of target cells requires CD4 and a co-receptor, predominantly the chemokine receptor CCR5. CCR5-delta32 homozygosity results in a truncated protein providing natural protection against HIV infection—this without detrimental effects to the host—and transplantation of CCR5-delta32 stem cells in a patient with HIV (“Berlin patient”) achieved viral eradication. As a more feasible approach gene-modification strategies are being developed to engineer cellular resistance to HIV using autologous cells. We have developed a dual therapeutic anti-HIV lentiviral vector (LVsh5/C46) that down-regulates CCR5 and inhibits HIV-1 fusion via cell surface expression of the gp41-derived peptide, C46. This construct, effective against multiple strains of both R5- and X4-tropic HIV-1, is being tested in Phase I/II trials by engineering HIV-resistant hematopoietic cells. PMID:24381033

Burke, Bryan P.; Boyd, Maureen P.; Impey, Helen; Breton, Louis R.; Bartlett, Jeffrey S.; Symonds, Geoff P.; Hütter, Gero

2013-01-01

188

Autoantibodies, autoimmune risk alleles and clinical associations in rheumatoid arthritis cases and non-RA controls in the electronic medical records  

PubMed Central

Objectives The significance of non-RA autoantibodies in patients with rheumatoid arthritis (RA) is unclear. We studied associations between autoimmune risk alleles and autoantibodies in RA cases and non-RA controls, and autoantibodies and clinical diagnoses from the electronic medical records (EMR). Methods We studied 1,290 RA cases and 1,236 non-RA controls of European genetic ancestry from the EMR from two large academic centers. We measured antibodies to citrullinated peptides (ACPA), anti-nuclear antibodies (ANA), antibodies to tissue transglutaminase (anti-tTG), antibodies to thyroid peroxidase (anti-TPO). We genotyped subjects for autoimmune risk alleles, and studied the association between number of autoimmune risk alleles and number of types of autoantibodies present. We conducted a phenome-wide association study (PheWAS) to study potential associations between autoantibodies and clinical diagnoses among RA cases and controls. Results Mean age was 60.7 in RA and 64.6 years in controls, and both were 79% female. The prevalence of ACPA and ANA was higher in RA cases compared to controls (p<0.0001, both); we observed no difference in anti-TPO and anti-tTG. Carriage of higher numbers of autoimmune risk alleles was associated with increasing types of autoantibodies in RA cases (p=4.4x10?6) and controls (p=0.002). From the PheWAS, ANA was significantly associated with Sjogren’s/siccain RA cases. Conclusion The increased frequency of autoantibodies in RA cases and controls was associated with the number of autoimmune risk alleles carried by an individual. PheWAS analyses within the EMR linked to blood samples provide a novel method to test for the clinical significance of biomarkers in disease. PMID:23233247

Liao, Katherine P.; Kurreeman, Fina; Li, Gang; Duclos, Grant; Murphy, Shawn; Raul Guzman, P; Cai, Tianxi; Gupta, Namrata; Gainer, Vivian; Schur, Peter; Cui, Jing; Denny, Joshua C.; Szolovits, Peter; Churchill, Susanne; Kohane, Isaac; Karlson, Elizabeth W.; Plenge, Robert M.

2012-01-01

189

Immunogenetics of a new HLA-B null allele, HLA-B*4423N.  

PubMed

The second example of an HLA-B*44 null allele (B*4423N) was identified by discrepancies between serological and polymerase chain reaction-sequence-specific primer (PCR-SSP) typing in two north-western European Caucasoid unrelated stem cell donor volunteers. HLA-B*4423N was identical to B*440201 except for a single nucleotide substitution at position 493 in exon 3, resulting in a premature stop codon at bases 493-495 (TAG rather than CAG at codon 141). As expected, comprehensive serological testing using 54 antisera, directed towards B44 or Bw4, failed to identify the HLA-B44 (Bw4) specificity. The B*4423N-bearing haplotype was identified as A*0201, Cw*0501, DRB1*0408, DRB4*01, DQA1*03, DQB1*0304 and the frequency of B*4423N estimated as 0.00006 (carriage frequency 0.0121%) in 16 533 subjects resident in Wales. PMID:14675390

Hammond, L; Street, J; Downing, J; Thompson, J; Darke, C

2003-12-01

190

Allelic Frequencies of 20 Visible Phenotype Variants in the Korean Population  

PubMed Central

The prediction of externally visible characteristics from DNA has been studied for forensic genetics over the last few years. Externally visible characteristics include hair, skin, and eye color, height, and facial morphology, which have high heritability. Recent studies using genome-wide association analysis have identified genes and variations that correlate with human visible phenotypes and developed phenotype prediction programs. However, most prediction models were constructed and validated based on genotype and phenotype information on Europeans. Therefore, we need to validate prediction models in diverse ethnic populations. In this study, we selected potentially useful variations for forensic science that are associated with hair and eye color, iris pattern, and facial morphology, based on previous studies, and analyzed their frequencies in 1,920 Koreans. Among 20 single nucleotide polymorphisms (SNPs), 10 SNPs were polymorphic, 6 SNPs were very rare (minor allele frequency < 0.005), and 4 SNPs were monomorphic in the Korean population. Even though the usability of these SNPs should be verified by an association study in Koreans, this study provides 10 potential SNP markers for forensic science for externally visible characteristics in the Korean population. PMID:23843775

Lim, Ji Eun

2013-01-01

191

Distribution of Mytilus taxa in European coastal areas as inferred from molecular markers  

NASA Astrophysics Data System (ADS)

The genetic constitution of mussels ( Mytilus spp.) was studied by means of three nuclear (Me 15/16, EF-bis, ITS) and one mtDNA (ND2-COIII) marker on a large European scale. In addition to a sharp cline between Atlantic and Mediterranean M. galloprovincialis, we observed a clear genetic distinction between the Black Sea and Mediterranean populations and a higher incidence of M. trossulus than reported so far in northern European populations. The frequency of M. galloprovincialis nuclear alleles was high along the Iberian Peninsula and decreased abruptly along the French coasts with a high frequency of M. edulis alleles in the Bay of Biscay, The Netherlands, Germany, Iceland, Barents and White Seas, and with little evidence of introgression between the two taxa. M. trossulus alleles were observed in the Baltic Sea and Danish Straits as expected. In addition, occurrence of M. trossulus alleles in cold waters of Iceland, Barents Sea and White Sea is reported for the first time.

Kijewski, T.; ?mietanka, B.; Zbawicka, M.; Gosling, E.; Hummel, H.; Wenne, R.

2011-02-01

192

Novel Method for Analysis of Allele Specific Expression in Triploid Oryzias latipes Reveals Consistent Pattern of Allele Exclusion  

PubMed Central

Assessing allele-specific gene expression (ASE) on a large scale continues to be a technically challenging problem. Certain biological phenomena, such as X chromosome inactivation and parental imprinting, affect ASE most drastically by completely shutting down the expression of a whole set of alleles. Other more subtle effects on ASE are likely to be much more complex and dependent on the genetic environment and are perhaps more important to understand since they may be responsible for a significant amount of biological diversity. Tools to assess ASE in a diploid biological system are becoming more reliable. Non-diploid systems are, however, not uncommon. In humans full or partial polyploid states are regularly found in both healthy (meiotic cells, polynucleated cell types) and diseased tissues (trisomies, non-disjunction events, cancerous tissues). In this work we have studied ASE in the medaka fish model system. We have developed a method for determining ASE in polyploid organisms from RNAseq data and we have implemented this method in a software tool set. As a biological model system we have used nuclear transplantation to experimentally produce artificial triploid medaka composed of three different haplomes. We measured ASE in RNA isolated from the livers of two adult, triploid medaka fish that showed a high degree of similarity. The majority of genes examined (82%) shared expression more or less evenly among the three alleles in both triploids. The rest of the genes (18%) displayed a wide range of ASE levels. Interestingly the majority of genes (78%) displayed generally consistent ASE levels in both triploid individuals. A large contingent of these genes had the same allele entirely suppressed in both triploids. When viewed in a chromosomal context, it is revealed that these genes are from large sections of 4 chromosomes and may be indicative of some broad scale suppression of gene expression. PMID:24945156

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

2014-01-01

193

European Union Scandal  

NSDL National Science Digital Library

This week's In the News examines the recent high-level corruption scandal in the European Union. Last Tuesday, the European Commission -- the executive body that initiates and implements EU legislation -- resigned en masse, plunging the supranational organization into unprecedented political chaos. All 20 commissioners, led by commission President Jacques Santer of Luxembourg, abdicated their positions the day after the release of a scathing report by the Committee of Independent Experts. The independent panel of experts, who were appointed by the European Parliament, had investigated allegations of bureaucratic malfeasance perpetrated by the European Commission. The committee's report collectively accused the commission of financial "fraud, mismanagement, and nepotism." In the wake of the incriminating report and subsequent resignations, EU foreign ministers are scrambling to find successors for the commissioners to placate the bewildered European citizenry and return to business as usual. This political upheaval happened at a crucial transitional time in the EU's 42-year history, undermining its credibility at a time when it plans to expand into eastern Europe. The current tumult occurred just three months after launching a new unified currency, seven weeks before the new Treaty of Amsterdam commences, and three months before the next European Parliamentary elections, which will determine the future composition of the EU's 626-member assembly. During the next two days, distracted leaders from all fifteen EU member states will meet in Berlin to discuss the reconstruction of the European Commission and formulate a seven-year budget for the entire EU, an organization with about 18,000 officials who administer nearly $100 billion annually. The eight resources discussed provide news, commentary, and analysis.

Osmond, Andrew.

194

A family with two female compound heterozygous for the FMR1 premutation alleles  

PubMed Central

Premutation alleles (55-200 CGG repeats) of the fragile X mental retardation (FMR1) gene have been linked to various types of clinical involvement ranging from mood and anxiety disorders to immunological disorders and executive function deficits. Carrier females typically have a premutation allele and a normal allele (<55 CGG repeats). Although rare, 7 cases of females that carry two expanded alleles (compound heterozygous premutation) have been reported. Here we report on four members of a family including two compound heterozygous premutation sisters with similar CGG allele sizes, affected with different levels of clinical severity. PMID:23786467

Basuta, Kirin; Lozano, Reymundo; Schneider, Andrea; Yrigollen, Carolyn M.; Hessl, David; Hagerman, Randi J.; Tassone, Flora

2014-01-01

195

Genetic variation in the major histocompatibility complex of the European brown hare (Lepus europaeus) across distinct phylogeographic areas.  

PubMed

The major histocompatibility complex is one of the best studied systems in vertebrates providing evidence for the long-term action of selection. Here, we examined the intra- and inter-population genetic diversity of the MHC class II DRB locus in European brown hare (Lepus europaeus) and correlated the results with genetic variability already estimated from the MHC DQA locus and from maternally (mitochondrial DNA (mtDNA)) and biparentally (allozymes, microsatellites) inherited loci. L. europaeus showed remarkable genetic polymorphism in both DQA and DRB1 loci. The Anatolian populations exhibited the highest genetic polymorphism for both loci. Balancing selection has established increased variability in the European populations despite the founder effects after the last glaciation. Different evolutionary rates were traced for DRB1 and DQA loci, as evidenced by the higher number of common DRB1 than DQA alleles and the greater differences between DRB1 alleles with common origin in comparison with DQA alleles. The high number of rare alleles with low frequencies detected implies that frequency-dependent selection drives MHC evolution in the brown hare through the advantage of rare alleles. Both loci were under the influence of positive selection within the peptide-binding region. The functional polymorphism, recorded as amino acid substitutions within the binding pockets, fell also within distinct geographic patterns, yet it was much narrower than the genetic polymorphism. We hypothesize that certain structural and functional characteristics of the binding pockets set limitations to the actual shape of genetic polymorphism in MHC. PMID:24743946

Koutsogiannouli, Evagelia A; Moutou, Katerina A; Stamatis, Costas; Walter, Lutz; Mamuris, Zissis

2014-06-01

196

Report of the European DNA profiling group (EDNAP): an investigation of the complex STR loci D21S11 and HUMFIBRA (FGA)  

Microsoft Academic Search

This paper describes a collaborative exercise which was intended to demonstrate whether uniformity of DNA profiling results could be achieved between European laboratories using two complex short tandem repeat (STR) loci. The loci D21S11 and HUMFIBRA (FGA) were chosen because they are commonly used by different European laboratories. D21S11 has approximately 14 common alleles (f>0.001), whereas HUMFIBRA has 19 common

Peter Gill; E d'Aloja; J Andersen; B Dupuy; M Jangblad; V Johnsson; A. D Kloosterman; A Kratzer; M. V Lareu; M Meldegaard; C Phillips; H Pfitzinger; S Rand; M Sabatier; R Scheithauer; H Schmitter; P Schneider; M. C Vide

1997-01-01

197

European Monetary Institute (EMI)  

NSDL National Science Digital Library

The European Monetary Institute was established in 1994 to oversee the implementation of a single currency for Europe. The EMI site contains information on its staff, organization, structure, and financial resources, and outlines the process of entering the third and final phase of the European Monetary Union. After months of doubt and political difficulties in France, Germany, and most recently, Italy, it now appears that the unified European currency, the Euro, will indeed begin on January 1, 1999 to replace the national currencies of as many as 10 or 11 countries. The path to a unified currency is by no means smooth, however. Many European Union member states are finding it politically difficult to reduce their budget deficit to 3 percent of gross domestic product and other states, such as Britain and Denmark, are choosing to remain out for now regardless. On the other hand, European economic growth will apparently exceed earlier expectations, allowing leaders to use increased tax revenues instead of cutting social services to qualify.

198

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

PubMed

DRB genes have been studied for the first time in green monkeys (Cercopithecus aethiops). Eleven new DRB alleles (exon 2, exon 3) have been obtained and sequenced from cDNA. A limited number of lineages have been identified: DRB1*03 (4 alleles), DRB1*07 (3 alleles), DRB5 (1 allele), DRB*w6 (1 allele), and DRB*w7 (2 alleles). The existence of Ceae-DRB1 duplications is supported by the finding of 3 DRB1 alleles in 3 different individuals. Ceae-DRB1*0701 may be non-functional because it bears serine at position 82, which hinders molecule surface expression in mice; the allele is only found in Ceae-DRB duplicated haplotypes. Base changes in cDNA Ceae-DRB alleles are consistent with the generation of polymorphism by point mutations or short segment exchanges between alleles. The eleven green monkey DRB alleles meet the requirements for functionality as antigen-presenting molecules (perhaps, excluding DRB1*0701), since: 1) they have been isolated from cDNA and do not present deletions, insertions or stop codons: 2) structural motifs necessary for a correct folding of the molecule, for the formation of DR/DR dimers and for CD4 interactions are conserved, and 3) the number of non-synonymous substitutions is higher than the number of synonymous substitutions in the peptide binding region (PBR), while the contrary holds true for the non-PBR region. PMID:9672153

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

1998-05-01

199

European Forest Institute: Research  

NSDL National Science Digital Library

This European Forest Institute (EFI) is "An independent non-governmental organization conducting European forest research." This website provides information about EFI's mission, research goals, strategies and programs. Site users can view information about on-going and completed projects in any of the four EFI research programs which include: Forest Ecology and Management, Forest Products Markets and Socio-Economics, Policy Analysis, and Forest Resources and Information. EFI also provides a search engine for locating specific research projects as well as information about how to propose an EFI project.

200

European security and France  

SciTech Connect

A French authority on security argues for new European initiatives in the face of the ''danger represented by Soviet military power deployed in support of an imperialistic ideology.'' His proposals, including the strengthening of conventional forces without abandoning the option of the first use of nuclear weapons, are meant to give substance to President Mitterrand's declaration in 1983: ''The European nations now need to realize that their defense is also their responsibility....'' A part of the increasingly important debate in France over defense policy in Europe.

deRose, A.

1985-01-01

201

The apolipoprotein E ?2 allele and decline in episodic memory  

PubMed Central

Objectives: The apolipoprotein E (apoE) ?4 allele is related to decline in multiple cognitive domains, especially episodic memory, but the effect of the ?2 allele on change in different forms of cognitive function has been difficult to establish. Methods: Participants are from the Religious Orders Study. At baseline, they were at least 65 years old and free of clinical evidence of dementia. For up to eight years, they underwent annual clinical evaluations that included detailed cognitive function assessment from which previously established summary measures of episodic memory, semantic memory, working memory, perceptual speed, and visuospatial ability were derived. Growth curve models were used to assess change in each measure and its relation to apoE genotype, controlling for age, sex, education, and baseline level of cognition. Follow up data were available in 669 persons (98% of those eligible). We treated those with the ?3/3 genotype as the reference group (n=425), which was contrasted with ?2 (?2/2, ?2/3; n=86), and ?4 (?3/4, ?4/4; n=158) subgroups. Results: Rate of episodic memory change in the three subgroups significantly differed, with an average annual increase of 0.016 units in the ?2 subgroup and annual decreases of 0.022 units in those with ?3/3 and of 0.073 units in the ?4 subgroup. The ?2 subgroup did not differ from those with ?3/3 in rate of decline in other cognitive systems. The ?4 subgroup declined more rapidly than those with ?3/3 in semantic memory and perceptual speed but not in working memory or visuospatial ability. Conclusion: Possession of one or more apoE ?2 alleles is associated with reduced decline in episodic memory in older persons. PMID:12438469

Wilson, R; Bienias, J; Berry-Kravis, E; Evans, D; Bennett, D

2002-01-01

202

Genetic transferrin types and iron-binding: a comparative study of a European and an African population sample  

Microsoft Academic Search

Two population samples, one from Europe and one from Africa, were analyzed for the distribution of genetic transferrin (TF) types, serum concentrations of TF, serum iron concentrations and free iron-binding capacities. In Europeans the distribution of the TF alleles was C1=0.816, C2=0.143, C3=0.037 and B2=0.004. In black Africans the allele frequencies were: C1, 0.823; C2, 0.104; and D1=0.073; TF*C3 was

H. Cleve; E. Schwendner; A. Rodewald; A. Bidlingmaier

1988-01-01

203

What can I do with a degree in European and European Union Studies?  

E-print Network

What can I do with a degree in European and European Union Studies? ARTS Planning your career analysis and of isolation from short-term trends. European and European Union Studies. #12;ARTS `European to www.canterbury.ac.nz/liaison/best_prep.shtml What is European and European Union Studies? The European

Hickman, Mark

204

European Union Center of Excellence European Studies Center  

E-print Network

Image courtesy of the European Commission Audiovisual Service. In this Issue: Spotlight on ArtNEWSLETTER European Union Center of Excellence European Studies Center LIVEZEANU Continued on page Students! 3 Izabel Galliera studies con- temporary art in Hungary. 4 Fellowships, Grants, and Opportunities

Sibille, Etienne

205

Null allele, allelic dropouts or rare sex detection in clonal organisms: simulations and application to real data sets of pathogenic microbes  

PubMed Central

Background Pathogens and their vectors are organisms whose ecology is often only accessible through population genetics tools based on spatio-temporal variability of molecular markers. However, molecular tools may present technical difficulties due to the masking of some alleles (allelic dropouts and/or null alleles), which tends to bias the estimation of heterozygosity and thus the inferences concerning the breeding system of the organism under study. This is especially critical in clonal organisms in which deviation from panmixia, as measured by Wright’s FIS, can, in principle, be used to infer both the extent of clonality and structure in a given population. In particular, null alleles and allelic dropouts are locus specific and likely produce high variance of Wright’s FIS across loci, as rare sex is expected to do. In this paper we propose a tool enabling to discriminate between consequences of these technical problems and those of rare sex. Methods We have performed various simulations of clonal and partially clonal populations. We introduce allelic dropouts and null alleles in clonal data sets and compare the results with those that exhibit increasing rates of sexual recombination. We use the narrow relationship that links Wright’s FIS to genetic diversity in purely clonal populations as assessment criterion, since this relationship disappears faster with sexual recombination than with amplification problems of certain alleles. Results We show that the relevance of our criterion for detecting poorly amplified alleles depends partly on the population structure, the level of homoplasy and/or mutation rate. However, the interpretation of data becomes difficult when the number of poorly amplified alleles is above 50%. The application of this method to reinterpret published data sets of pathogenic clonal microbes (yeast and trypanosomes) confirms its usefulness and allows refining previous estimates concerning important pathogenic agents. Conclusion Our criterion of superimposing between the FIS expected under clonality and the observed FIS, is effective when amplification difficulties occur in low to moderate frequencies (20-30%). PMID:25027508

2014-01-01

206

Polymorphisms in Chemokine Receptor 5 and Toll-Like Receptor 3 Genes Are Risk Factors for Clinical Tick-Borne Encephalitis in the Lithuanian Population  

PubMed Central

Background Tick-borne encephalitis virus (TBEV) infections can be asymptomatic or cause moderate to severe injuries of the nervous system. We previously reported that a nonfunctional chemokine receptor 5 (CCR5) and a functional Toll-like receptor 3 (TLR3) predispose adults to clinical tick-borne encephalitis (TBE). This study expands our previous findings and further examines polymorphisms in CCR5 and TLR3 genes in different age and disease severity groups. Methods 117 children and 129 adults, stratified into mild, moderate and severe forms of TBE, and 103 adults with severe TBE were analyzed. 135 healthy individuals and 79 patients with aseptic meningoencephalitis served as controls. CCR5 delta 32 and rs3775291 TLR3 genotypes were established by pyrosequencing, and their frequencies were analyzed using recessive genetic, genotype and allelic models. Findings The prevalence of CCR5?32 homozygotes was higher in children (2.5%), in adults with severe TBE (1.9%), and in the combined cohort of TBE patients (2.3%) than in controls (0%) (p<0.05). The nonfunctional homozygous TLR3 genotype was less prevalent among the combined TBE cohort (11.5%) than among controls (19.9%) (p?=?0.025), but did not differ between children TBE and controls. The genotype and allele prevalence of CCR5 and TLR3 did not differ in children nor adult TBE cohorts stratified by disease severity. However, in the severe adult TBE cohort, homozygous functional TLR3 genotype and wt allele were less prevalent compared to the adult cohort with the whole disease severity spectrum (44.4% vs 59.8% p?=?0.022 and 65.2% vs 76.4% p?=?0.009; respectively). Conclusions Independently of age, nonfunctional CCR5?32 mutation is a significant risk factor for development of clinical TBE, but not for disease severity. The polymorphism of TLR3 gene predisposes to clinical TBE in adults only and may be associated with disease severity. Further studies are needed to clarify the role of these polymorphisms in susceptibility to TBEV infection. PMID:25226020

Nordgren, Johan; Carlsson, Beatrice; Hagbom, Marie; Svensson, Lennart; Lindquist, Lars

2014-01-01

207

Russian and East European Studies  

E-print Network

complementary for Russian, political science, economics, history, geography, journalism, global studiesRussian and East European Studies Certificate About Us The Russian and East European Studies (REES) Certificate program develops students' knowledge of the language, history, culture, and con- temporary

Saldin, Dilano

208

Eastern European Cinema.  

ERIC Educational Resources Information Center

Presents a structure for a course that highlights the best cinemas of Eastern European countries, in order to acquaint students with cinematic traditions of the region. Discusses course activities, coursework and evaluation, and resources. Advocates structuring the course around the film of experience of Eastern Europe, and presents and discusses…

Iordanova, Dina

1999-01-01

209

European Green Crab  

USGS Multimedia Gallery

The European green crab (Carcinus maenas), has invaded fisheries in Northern California and in British Columbia, where it may compete with the much more valuable Dungeness crab. The CD it holds in its claws is a database for the USGS Pacific Coast Estuarine Information System, just one source used t...

210

Teaching European Identities  

ERIC Educational Resources Information Center

The political, cultural and social make-up of Europe is changing fast. A new European identity is under construction, but old contradictions and diversity challenge its contents, forms and boundaries. Migration, the changing role of the nation-state and Europe's regions, the reshaping of politico-administrative and perceptional boundaries, the…

Raento, Pauliina

2008-01-01

211

The European Union  

Microsoft Academic Search

The European Union has established itself as a leading text that provides readers from all disciplines with a sound understanding of the economics and policies of the EU. Its wealth of information, detail and analysis has ensured that previous editions have been read by a generation of students, researchers and policy makers. It covers all major EU policy areas as

Ali M. El-Agraa

1990-01-01

212

European Music Year 1985.  

ERIC Educational Resources Information Center

Articles concerning music are included in this newsletter dedicated to cultural venture to be jointly carried out by the Council of Europe and the European communities. Many events will mark Music Year 1985, including concerts, dance performances, operas, publications, recordings, festivals, exhibitions, competitions, and conferences on musical…

Alexanderson, Thomas; And Others

1984-01-01

213

European Southern Observatory  

E-print Network

- Garching - 2nd to 4th Nov 2005 #12;2 European Southern Observatory Cloudiness; Humidity, Precipitable Water, Seismicity; Survival loads (earthquakes, wind, precipitations); Present and future potential light pollution that skies are clear (%) at night for the years 1999 and 2000 over Canaries, NW Africa and Southern Spain (A

Liske, Jochen

214

European Commission Agriculture and  

E-print Network

European Commission Agriculture and Rural Development Good practice guidance on the sustainable Commission (EC) DG Agriculture and Rural Development 130, Rue de la Loi B ­ 1049 Brussels, Belgium Phone: +32 (0) 2-2969909 Fax: +32 (0) 2-29211 33 E-mail: info@ec.europa.eu Web: https://www.ec.europa.eu/agriculture

215

European inflation dynamics  

Microsoft Academic Search

We provide evidence on the fit of the New Phillips Curve (NPC) for the Euro area over the period 1970–1998, and use it as a tool to compare the characteristics of European inflation dynamics with those observed in the U.S. We also analyze the factors underlying inflation inertia by examining the cyclical behavior of marginal costs, as well as that

Jordi Gal??; Mark Gertler; J. David López-Salido

2001-01-01

216

The European Vibration Directive  

Microsoft Academic Search

The European Union adopted a Directive in 2002 on minimum requirements for the health and safety of workers exposed to vibration. This is known as the Physical Agents (Vibration) Directive. It builds on existing general employers' duties to manage risks to health and safety, and introduces exposure action and limit values for both hand-arm vibration and whole-body vibration, setting minimum

Chris M. NELSON; Paul F. BRERETON

2005-01-01

217

Susceptibility alleles for testicular germ cell tumour: a review.  

PubMed

Family history is among the strongest and most consistent of the risk factors for testicular germ cell tumour (TGCT). Brothers of affected cases have an 8- to10-fold relative risk and fathers/sons have a risk between four and sixfold. The familial relative risk of TGCT is higher than for most other cancer types, which rarely exceeds four. The high relative risk suggests that inherited susceptibility to TGCT may account for a substantial fraction of TGCT cases. The search for TGCT susceptibility genes has proven difficult and a recent genome-wide linkage study for TGCT susceptibility loci demonstrated no statistically significant regions of linkage with all LOD scores less than two. Moreover, a previous report of linkage to a region on Xq27 was not replicated. The results from genetic linkage analysis demonstrate that TGCT susceptibility is likely to be due to several genes, each with a modest effect on disease risk. The Y chromosome, which cannot be analysed by genetic linkage, carries a number of testis- and germ cell-specific genes. We recently demonstrated that a deletion on the Y chromosome known as 'gr/gr' is a rare, low-penetrance allele that is associated with susceptibility to TGCT. Based on the evidence from the linkage search the 'gr/gr' deletion represents one of possibly many TGCT susceptibility alleles, and new and emerging technologies will be employed in future work to identify these genes. PMID:17705805

Rapley, E

2007-08-01

218

Allele-specific demethylation at an imprinted mammalian promoter  

PubMed Central

A screen for imprinted genes on mouse Chromosome 7 recently identified Inpp5f_v2, a paternally expressed retrogene lying within an intron of Inpp5f. Here, we identify a novel paternally expressed variant of the Inpp5f gene (Inpp5f_v3) that shows a number of unusual features. Inpp5f_v3 initiates from a CpG-rich repeat region adjoining two B1 elements, despite previous reports that SINEs are generally excluded from imprinted promoters. Accordingly, we find that the Inpp5f_v3 promoter acquires methylation around the time of implantation, when many repeat families undergo de novo epigenetic silencing. Methylation is then lost specifically on the paternally derived allele during the latter stages of embryonic development, resulting in imprinted transcriptional activation on the demethylated allele. Methylation analyses in embryos lacking maternal methylation imprints suggest that the primary imprinting mark resides within an intronic CpG island ?1 kb downstream of the Inpp5f_v3 transcriptional start site. These data support the hypothesis that SINEs can influence gene expression by attracting de novo methylation during development, a property likely to explain their exclusion from other imprinted promoters. PMID:17942418

Wood, Andrew J.; Bourc’his, Déborah; Bestor, Timothy H.; Oakey, Rebecca J.

2007-01-01

219

Allelic Imbalance in Drosophila Hybrid Heads: Exons, Isoforms, and Evolution  

PubMed Central

Unraveling how regulatory divergence contributes to species differences and adaptation requires identifying functional variants from among millions of genetic differences. Analysis of allelic imbalance (AI) reveals functional genetic differences in cis regulation and has demonstrated differences in cis regulation within and between species. Regulatory mechanisms are often highly conserved, yet differences between species in gene expression are extensive. What evolutionary forces explain widespread divergence in cis regulation? AI was assessed in Drosophila melanogaster–Drosophila simulans hybrid female heads using RNA-seq technology. Mapping bias was virtually eliminated by using genotype-specific references. Allele representation in DNA sequencing was used as a prior in a novel Bayesian model for the estimation of AI in RNA. Cis regulatory divergence was common in the organs and tissues of the head with 41% of genes analyzed showing significant AI. Using existing population genomic data, the relationship between AI and patterns of sequence evolution was examined. Evidence of positive selection was found in 30% of cis regulatory divergent genes. Genes involved in defense, RNAi/RISC complex genes, and those that are sex regulated are enriched among adaptively evolving cis regulatory divergent genes. For genes in these groups, adaptive evolution may play a role in regulatory divergence between species. However, there is no evidence that adaptive evolution drives most of the cis regulatory divergence that is observed. The majority of genes showed patterns consistent with stabilizing selection and neutral evolutionary processes. PMID:22319150

Graze, R. M.; Novelo, L. L.; Amin, V.; Fear, J. M.; Casella, G.; Nuzhdin, S. V.; McIntyre, L. M.

2012-01-01

220

A matching-allele model explains host resistance to parasites.  

PubMed

The maintenance of genetic variation and sex despite its costs has long puzzled biologists. A popular idea, the Red Queen Theory, is that under rapid antagonistic coevolution between hosts and their parasites, the formation of new rare host genotypes through sex can be advantageous as it creates host genotypes to which the prevailing parasite is not adapted. For host-parasite coevolution to lead to an ongoing advantage for rare genotypes, parasites should infect specific host genotypes and hosts should resist specific parasite genotypes. The most prominent genetics capturing such specificity are matching-allele models (MAMs), which have the key feature that resistance for two parasite genotypes can reverse by switching one allele at one host locus. Despite the lack of empirical support, MAMs have played a central role in the theoretical development of antagonistic coevolution, local adaptation, speciation, and sexual selection. Using genetic crosses, we show that resistance of the crustacean Daphnia magna against the parasitic bacterium Pasteuria ramosa follows a MAM. Simulation results show that the observed genetics can explain the maintenance of genetic variation and contribute to the maintenance of sex in the facultatively sexual host as predicted by the Red Queen Theory. PMID:23707426

Luijckx, Pepijn; Fienberg, Harris; Duneau, David; Ebert, Dieter

2013-06-17

221

EUROPEAN STUDIES MINOR REQUIREMENTS CHECKLIST  

E-print Network

credit with approval of the Faculty Coordinator for European Studies. ART 101 Survey of Western ArtEUROPEAN STUDIES MINOR REQUIREMENTS CHECKLIST Name: ID#: Expected Graduation Date: Course Number and Title Waiver/ Substitution Semester Units REQUIRED COURSE (4 units) BAIS 370 European Lives & Culture

Galles, David

222

5, 59575985, 2005 European ozone  

E-print Network

ACPD 5, 5957­5985, 2005 European ozone trends J. E. Jonson et al. Title Page Abstract Introduction explain the trends in European ozone levels? J. E. Jonson 1 , D. Simpson 1 , H. Fagerli 1 , and S. Solberg License. 5957 #12;ACPD 5, 5957­5985, 2005 European ozone trends J. E. Jonson et al. Title Page Abstract

Paris-Sud XI, Université de

223

A description of a new DR allele, DRB1*1113.  

PubMed

We have discovered a previously unpublished HLA-DRB1 allele, observed in a patient (SB), his mother, and one sibling. The undefined allele gave sporadic positive reactions with sera in the DR52-associated group. SSOPH analysis utilizing both generic and group specific primers and probes also gave ambiguous results. SB typed clearly as a DRB1*0301 (paternal allele) but the DNA from SB also bound probes specific for DRB1*14 and DRB1*11. Sequencing revealed that the undefined allele was similar to a DRB1*14 allele with a segment of sequence found in DRB1*11 alleles. The patient was MLC reactive with donors who express DRB1*0301, *1401 and *0301, *11 and was nonreactive solely to DRB1*0301 (Dw3) homozygous typing cells. PMID:7792759

Rosenberg, S M; Wollenzien, T F; Johnson, M M; Eberly, L; Hurley, C K; Reinsmoen, N L; Steiner, N; Goeken, N E

1995-02-01

224

Allelic diversity at the DLA-88 locus in Golden Retriever and Boxer breeds is limited  

PubMed Central

In the dog, previous analyses of major histocompatibility complex (MHC) class I genes suggest a single polymorphic locus, Dog Leukocyte Antigen (DLA)-88. While 51 alleles have been reported, estimates of prevalence have not been made. We hypothesized that, within a breed, DLA-88 diversity would be restricted, and one or more dominant alleles could be identified. Accordingly, we determined allele usage in 47 Golden Retrievers and 39 Boxers. In each population, 10 alleles were found; 4 were shared. Seven novel alleles were identified. DLA-88*05101 and *50801 predominated in Golden Retrievers, while most Boxers carried *03401. In these breeds DLA-88 polymorphisms are limited and largely non-overlapping. The finding of highly prevalent alleles fulfills an important prerequisite for studying canine CD8+ T-cell responses. PMID:22571293

Ross, Peter; Buntzman, Adam S.; Vincent, Benjamin G.; Grover, Elise N.; Gojanovich, Gregory S.; Collins, Edward J.; Frelinger, Jeffrey A.; Hess, Paul R.

2012-01-01

225

Epigenetic Regulation of Monoallelic Rearrangement (Allelic Exclusion) of Antigen Receptor Genes  

PubMed Central

While most genes in the mammalian genome are transcribed from both parental chromosomes in cells where they are expressed, approximately 10% of genes are expressed monoallelically, so that any given cell will express either the paternal or maternal allele, but not both. The antigen receptor genes in B and T cells are well-studied examples of a gene family, which is expressed in a monoallelic manner, in a process coined “allelic exclusion.” During lymphocyte development, only one allele of each antigen receptor undergoes V(D)J rearrangement at a time, and once productive rearrangement is sensed, rearrangement of the second allele is prevented. In this mini review, we discuss the epigenetic processes, including asynchronous replication, nuclear localization, chromatin condensation, histone modifications, and DNA methylation, which appear to regulate the primary rearrangement of a single allele, while blocking the rearrangement of the second allele. PMID:25538709

Levin-Klein, Rena; Bergman, Yehudit

2014-01-01

226

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

PubMed

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. PMID:22117406

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

2011-09-01

227

ERPA: European Research Papers Archive  

NSDL National Science Digital Library

ERPA, the European Research Papers Archive, provides a common interface for searching a database of online working papers relevant to European integration. Contributors to the archive include the Robert Schuman Centre of the Academy of European Law at the European University Institute, the Max Planck Institute for the Study of Societies, the Jean Monnet Working Papers Series at Harvard Law School, and the European Communities Studies Association-Austria. Users can select either a short form to search recent additions to the archive or a long form to either or to also access the many advanced search options, including full-text searches.

228

Estimating Y-STR allelic drop-out rates and adjusting for interlocus balances.  

PubMed

Y chromosome short tandem repeats (Y-STRs) are valuable genetic markers in certain areas of forensic case-work. However, when the Y-STR DNA profile is weak, the observed Y-STR profile may not be complete--i.e. locus drop-out may have occurred. Another explanation could be that the stain DNA did not have a Y-STR allele that was detectable with the method used (the allele is a 'null allele'). If the Y-STR profile of a stain is strong, one would be reluctant to consider drop-out as a reasonable explanation of lack of a Y-STR allele and would maybe consider 'null allele' as an explanation. On the other hand, if the signal strengths are weak, one would most likely accept drop-out as a possible explanation. We created a logistic regression model to estimate the probability of allele drop-out with the Life Technologies/Applied Biosystems AmpFlSTR(®) Yfiler(®) kit such that the trade-off between drop-outs and null alleles could be quantified using a statistical model. The model to estimate the probability of drop-out uses information about locus imbalances, signal strength, the number of PCR cycles, and the fragment size of Yfiler. We made two temporarily separated experiments and found no evidence of temporal variation in the probability of drop-out. Using our model, we found that for 30 PCR cycles with a 150 bp allele, the probability of drop-out was 1:5000 corresponding to the average estimate of the probability of Y-STR null alleles at a signal strength of 1249 RFU. This means that the probability of a null allele is higher than that of an allele drop-out at e.g. 4000 RFU and the probability of drop-out is higher than that of a null allele at e.g. 75 RFU. PMID:23453365

Andersen, Mikkel Meyer; Mogensen, Helle Smidt; Eriksen, Poul Svante; Olofsson, Jill Katharina; Asplund, Maria; Morling, Niels

2013-05-01

229

Identification of resistant carboxylesterase alleles in Culex pipiens complex via PCR-RFLP  

PubMed Central

Background Carboxylesterase overproduction is a frequently observed resistance mechanism of insects to organophosphate insecticides. As a major transmitter of human diseases, mosquitoes in the Culex pipiens complex have evolved 13 carboxylesterase alleles (Ester) that confer organophosphate resistance. Six alleles, EsterB1, Ester2, Ester8, Ester9, EsterB10, and Ester11, have been observed in field populations in China, sometimes co-existing in one population. To differentiate the carboxylesterase alleles found in these field populations, PCR-RFLP was designed for use in resistance monitoring. Results Based on the DNA sequences of resistant and nonresistant carboxylesterase alleles, Ester B alleles were first amplified with PCR-specific primers and then digested with the restriction enzyme DraI. In this step, Ester2 and Ester11 were differentiated from the other Ester alleles. When the other Ester B alleles were digested with the restriction enzyme XbaI, EsterB1 and the susceptible C. p. pallens Ester were screened out. Ester8 and Ester9 were differentiated from EsterB10 and the susceptible C. p. quinquefasciatus esterase allele, respectively, by amplifying and digesting the Ester A alleles with the restriction enzyme ApaLI. The effectiveness of the custom-designed PCR-RFLP was verified in two field mosquito populations. Conclusions A PCR-RFLP based approach was developed to differentiate carboxylesterase alleles in Culex pipiens complex mosquitoes. These processes may be useful in monitoring the evolutionary dynamics of known carboxylesterase alleles as well as in the identification of new alleles in field populations. PMID:23006470

2012-01-01

230

Numbers of sporophytic self-incompatibility alleles in populations of wild radish  

Microsoft Academic Search

To estimate the numbers of sporophytic S-alleles in two adjacent populations of wild radish, we performed 701 reciprocal crosses among 50 individuals. Each cross was replicated five times in each direction. Sixteen plants were fully intercompatible, indicating the presence of at least 32 S-alleles in the two populations. A minimum of 22 S-alleles occur in a single population. The frequency

J. D. Karron; D. L. Marshall; D. M. Oliveras

1990-01-01

231

Association of apolipoprotein E allele {epsilon}4 with late-onset sporadic Alzheimer`s disease  

SciTech Connect

Apolipoprotein E, type {epsilon}4 allele (ApoE {epsilon}4), is associated with late-onset sporadic Alzheimer`s disease (AD) in French patients. The association is highly significant (0.45 AD versus 0.12 controls for {epsilon}4 allele frequencies). These data support the involvement of ApoE {epsilon}4 allele as a very important risk factor for the clinical expression of AD. 22 refs., 1 fig., 3 tabs.

Lucotte, G.; David, F.; Berriche, S. [Regional Center of Neurogenetics, Reims (France)] [and others

1994-09-15

232

Allelic Variation in KIR2DL3 Generates a KIR2DL2-like Receptor with Increased Binding to Its HLA-C Ligand12  

PubMed Central

Although extensive homology exists between their extracellular domains, natural killer cell inhibitory receptors KIR2DL2*001 and KIR2DL3*001 have previously been shown to differ substantially in their HLA-C binding avidity. To explore the largely uncharacterized impact of allelic diversity, the most common KIR2DL2/3 allelic products in European American and African American populations were evaluated for surface expression and binding affinity to their HLA-C group 1 and 2 ligands. Although no significant differences in the degree of cell membrane localization were detected in a transfected human NKL cell line by flow cytometry, surface plasmon resonance and KIR binding to a panel of HLA allotypes demonstrated that KIR2DL3*005 differed significantly from other KIR2DL3 allelic products in its ability to bind HLA-C. The increased affinity and avidity of KIR2DL3*005 for its ligand was also demonstrated to have a larger impact on the inhibition of IFN-? production by the human KHYG-1 NK cell line compared to KIR2DL3*001, a low affinity allelic product. Site-directed mutagenesis established that the combination of arginine at residue 11 and glutamic acid at residue 35 in KIR2DL3*005 were critical to the observed phenotype. Although these residues are distal to the KIR/HLA-C interface, molecular modeling suggests that alteration in the interdomain hinge angle of KIR2DL3*005 towards that found in KIR2DL2*001, another strong receptor of the KIR2DL2/3 family, may be the cause of this increased affinity. The regain of inhibitory capacity by KIR2DL3*005 suggests that the rapidly evolving KIR locus may be responding to relatively recent selective pressures placed upon certain human populations. PMID:23686481

Frazier, William R.; Steiner, Noriko; Hou, Lihua; Dakshanamurthy, Sivanesan; Hurley, Carolyn Katovich

2013-01-01

233

Haplotype Variation of Glu-D1 Locus and the Origin of Glu-D1d Allele Conferring Superior End-Use Qualities in Common Wheat  

PubMed Central

In higher plants, seed storage proteins (SSPs) are frequently expressed from complex gene families, and allelic variation of SSP genes often affects the quality traits of crops. In common wheat, the Glu-D1 locus, encoding 1Dx and 1Dy SSPs, has multiple alleles. The Glu-D1d allele frequently confers superior end-use qualities to commercial wheat varieties. Here, we studied the haplotype structure of Glu-D1 genomic region and the origin of Glu-D1d. Using seven diagnostic DNA markers, 12 Glu-D1 haplotypes were detected among common wheat, European spelt wheat (T. spelta, a primitive hexaploid relative of common wheat), and Aegilops tauschii (the D genome donor of hexaploid wheat). By comparatively analyzing Glu-D1 haplotypes and their associated 1Dx and 1Dy genes, we deduce that the haplotype carrying Glu-D1d was likely differentiated in the ancestral hexaploid wheat around 10,000 years ago, and was subsequently transmitted to domesticated common wheat and T. spelta. A group of relatively ancient Glu-D1 haplotypes was discovered in Ae. tauschii, which may serve for the evolution of other haplotypes. Moreover, a number of new Glu-D1d variants were found in T. spelta. The main steps in Glu-D1d differentiation are proposed. The implications of our work for enhancing the utility of Glu-D1d in wheat quality improvement and studying the SSP alleles in other crop species are discussed. PMID:24098671

Li, Yiwen; Zhang, Kunpu; Lou, Haijuan; An, Xueli; Dong, Lingli; Gu, Yong Qiang; Anderson, Olin D.; Liu, Xin; Qin, Huanju; Wang, Daowen

2013-01-01

234

European Environment Agency (EEA)  

NSDL National Science Digital Library

The European Environment Agency (EEA) Website contains a huge selection of online environmental information, data, and reports pertaining to all fifteen EU states, as well as Iceland, Lichtenstein, and Norway. Information is organized by themes, and the site employs a powerful multilingual search feature. Themes include environmental issues, sectors and activities, information related to specific media, regions, and actions for environmental improvement. The site also contains EEA publications and reports, as well as a data service providing access to data sets covering at least all EU member states. Finally, the European Environment Information and Observation Network (EIONET) provides a network which "facilitates co-operation and flow of data and information between EIONET partners and with the EEA." The EEA Website is a large, research-oriented repository of information.

235

Chestnut, European (Castanea sativa).  

PubMed

Development of a system for direct transfer of antifungal candidate genes into European chestnut (Castanea sativa) would provide an alternative approach to conventional breeding for production of chestnut trees that are tolerant to ink disease caused by Phytophthora spp. Overexpression of genes encoding PR proteins (such as thaumatin-like proteins), which display antifungal activity, may represent an important advance in control of the disease. We have used a chestnut thaumatin-like protein gene (CsTL1) isolated from European chestnut cotyledons and have achieved overexpression of the gene in chestnut somatic embryogenic lines used as target material. We have also acclimatized the transgenic plants and grown them on in the greenhouse. Here, we describe the various steps of the process, from the induction of somatic embryogenesis to the production of transgenic plants. PMID:25416257

Corredoira, Elena; Valladares, Silvia; Vieitez, Ana M; Ballester, Antonio

2015-01-01

236

Allele-specific enzymatic amplification of. beta. -globin genomic DNA for diagnosis of sickle cell anemia  

SciTech Connect

A rapid nonradioactive approach to the diagnosis of sickle cell anemia is described based on an allele-specific polymerase chain reaction (ASPCR). This method allows direct detection of the normal or the sickle cell {beta}-globin allele in genomic DNA without additional steps of probe hybridization, ligation, or restriction enzyme cleavage. Two allele-specific oligonucleotide primers, one specific for the sickle cell allele and one specific for the normal allele, together with another primer complementary to both alleles were used in the polymerase chain reaction with genomic DNA templates. The allele-specific primers differed from each other in their terminal 3{prime} nucleotide. Under the proper annealing temperature and polymerase chain reaction conditions, these primers only directed amplification on their complementary allele. In a single blind study of DNA samples from 12 individuals, this method correctly and unambiguously allowed for the determination of the genotypes with no false negatives or positives. If ASPCR is able to discriminate all allelic variation (both transition and transversion mutations), this method has the potential to be a powerful approach for genetic disease diagnosis, carrier screening, HLA typing, human gene mapping, forensics, and paternity testing.

Wu, D.Y.; Ugozzoli, L.; Pal, B.K.; Wallace, B. (Beckman Research Institute of the City of Hope, Duarte, CA (USA))

1989-04-01

237

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

ERIC Educational Resources Information Center

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

Nussbaum, Francis, Jr.

1988-01-01

238

Using Quality Measures to Facilitate Allele Calling in High-Throughput Genotyping  

PubMed Central

Currently, the main limitation in high-throughput microsatellite genotyping is the required manual editing of allele calls. Even though programs for automated allele calling have been available for several years, they have limited capability because accurate data could only be assured by manual inspection of the electropherograms for confirmation. Here we describe the development of a parametric approach to allele call quality control that eliminates much of the time required for manual editing of the data. This approach was implemented in an editing tool, Decode-GT, that works downstream of the allele calling program, TrueAllele (TA). Decode-GT reads the output data from TA, displays the underlying electropherograms for the genotypes, and sorts the allele calls into three categories: good, bad, and ambiguous. It discards the bad calls, accepts the good calls, and suggests that the user inspect the ambiguous calls, thereby reducing dependence on manual editing. For the categorization we use the following parameters: (1) the quality value for each allele call from TrueAllele; (2) the peak height of the alleles; and (3) the size of the peak shift needed to move peaks into the nearest bin. Here we report how we optimized the parameters such that the size of the ambiguous category was minimized, and both the number of miscalled genotypes in the good category and the useable genotypes in the bad category were negligible. This approach reduces the manual editing time and results in <1% miscalls. PMID:10523529

Pálsson, Birgir; Pálsson, Frosti; Perlin, Mark; Gudbjartsson, Hákon; Stefánsson, Kári; Gulcher , Jeffrey

1999-01-01

239

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

PubMed Central

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

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

1992-01-01

240

Pharmacogenomic diversity in Singaporean populations and Europeans.  

PubMed

Differences in the frequency of pharmacogenomic variants may influence inter-population variability in drug efficacy and risk of adverse drug reactions (ADRs). We investigated the diversity of ? 4500 genetic variants in key drug-biotransformation and -response genes among three South East Asian populations compared with individuals of European ancestry. We compared rates of reported ADRs in these Asian populations to determine if the allelic differentiation corresponded to an excess of the associated ADR. We identified an excess of ADRs related to clopidogrel in Singaporean Chinese, consistent with a higher frequency of a known risk variant in CYP2C19 in that population. We also observed an excess of ADRs related to platinum compounds in Singaporean CHS, despite a very low frequency of known ADR risk variants, suggesting the presence of additional genetic and non-genetic risk factors. Our results point to substantial diversity at specific pharmacogenomic loci that may contribute to inter-population variability in drug response phenotypes. PMID:24861855

Brunham, L R; Chan, S L; Li, R; Aminkeng, F; Liu, X; Saw, W Y; Ong, R T H; Pillai, E N; Carleton, B C; Toh, D; Tan, S H; Koo, S H; Lee, E J D; Chia, K S; Ross, C J D; Hayden, M R; Sung, C; Teo, Y Y

2014-12-01

241

Identification of Allelic Heterogeneity at Type-2 Diabetes Loci and Impact on Prediction  

PubMed Central

Although over 60 single nucleotide polymorphisms (SNPs) have been identified by meta-analysis of genome-wide association studies for type-2 diabetes (T2D) among individuals of European descent, much of the genetic variation remains unexplained. There are likely many more SNPs that contribute to variation in T2D risk, some of which may lie in the regions surrounding established SNPs - a phenomenon often referred to as allelic heterogeneity. Here, we use the summary statistics from the DIAGRAM consortium meta-analysis of T2D genome-wide association studies along with linkage disequilibrium patterns inferred from a large reference sample to identify novel SNPs associated with T2D surrounding each of the previously established risk loci. We then examine the extent to which the use of these additional SNPs improves prediction of T2D risk in an independent validation dataset. Our results suggest that multiple SNPs at each of 3 loci contribute to T2D susceptibility (TCF7L2, CDKN2A/B, and KCNQ1; p<5×10?8). Using a less stringent threshold (p<5×10?4), we identify 34 additional loci with multiple associated SNPs. The addition of these SNPs slightly improves T2D prediction compared to the use of only the respective lead SNPs, when assessed using an independent validation cohort. Our findings suggest that some currently established T2D risk loci likely harbor multiple polymorphisms which contribute independently and collectively to T2D risk. This opens a promising avenue for improving prediction of T2D, and for a better understanding of the genetic architecture of T2D. PMID:25393876

Klimentidis, Yann C.; Zhou, Jin; Wineinger, Nathan E.

2014-01-01

242

The European Spallation Source  

SciTech Connect

The European Spallation Source (ESS) is a 5 MW, 2.5 GeV long pulse proton linac, to be built and commissioned in Lund, Sweden. The Accelerator Design Update (ADU) project phase is under way, to be completed at the end of 2012 by the delivery of a Technical Design Report. Improvements to the 2003 ESS design will be summarised, and the latest design activities will be presented.

Peggs, S; Eshraqi, M; Hahn, H; Jansson, A; Lindroos, M; Ponton, A; Rathsman, K; Trahern, G; Bousso, S; Calaga, R; Devanz, G; Duperrier, R D; Eguia, J; Gammino, S; Moller, S P; Oyon, C; Ruber, R.J.M.Y.

2011-03-01

243

European constellation development  

Microsoft Academic Search

\\u000a Previously, we considered the native constellation systems that developed in China, Mesopotamia, Egypt, and India. Here, we\\u000a will trace the development of European constellations, which form the basis of the star maps we will consider in subsequent\\u000a chapters. Like many other things astronomical, we will begin with the ancient Greeks, whose classical 48 constellations greatly\\u000a influenced star map development and

Nick Kanas

244

Telemedicine and European law.  

PubMed

A Directive of the European Union was first published in 2000, which dealt with telemedicine as part of its provisions. This E-Commerce Directive, as it became known, was subjected to further study which revealed some problems relative to the practice of telemedicine. Among the subjects discussed in this paper are those of privacy, data protection, free movement of services, the impact of electronic communication and ethical issues. PMID:15074761

Callens, Stefaan

2003-01-01

245

ALADYN – a spatially explicit, allelic model for simulating adaptive dynamics  

PubMed Central

ALADYN is a freely available cross-platform C++ modeling framework for stochastic simulation of joint allelic and demographic dynamics of spatially-structured populations. Juvenile survival is linked to the degree of match between an individual’s phenotype and the local phenotypic optimum. There is considerable flexibility provided for the demography of the considered species and the genetic architecture of the traits under selection. ALADYN facilitates the investigation of adaptive processes to spatially and/or temporally changing conditions and the resulting niche and range dynamics. To our knowledge ALADYN is so far the only model that allows a continuous resolution of individuals’ locations in a spatially explicit landscape together with the associated patterns of selection.

Schiffers, Katja H; Travis, Justin MJ

2014-01-01

246

New York State TrueAllele® Casework Validation Study*  

PubMed Central

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

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

2013-01-01

247

Non-Equilibrium Allele Frequency Spectra Via Spectral Methods  

PubMed Central

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

Hey, Jody; Chen, Kevin

2011-01-01

248

Fine-mapping natural alleles: quantitative complementation to the rescue  

PubMed Central

Mapping the genes responsible for natural variation and divergence is a challenging task. Many studies have mapped genes to genomic regions, or generated lists of candidates, but few studies have implicated specific genes with a high standard of evidence. I propose that combining recent advances in genomic engineering with a modified version of the quantitative complementation test will help turn candidate genes into causal genes. By creating loss-of-function mutations in natural strains, and using these mutations to quantitatively fail-to-complement natural alleles, fine mapping should be greatly facilitated. As an example, I propose that the CRISPR/Cas9 system could be combined with the FLP/FRT system to fine-map genes in the numerous systems where inversions have frustrated these efforts. PMID:24628660

Turner, Thomas L.

2014-01-01

249

A Melanocortin 1 Receptor Allele Suggests Varying Pigmentation Among Neanderthals  

Microsoft Academic Search

The melanocortin 1 receptor (MC1R) regulates pigmentation in humans and other vertebrates. Variants of MC1R with reduced function are associated with pale skin color and red hair in humans of primarily European origin. We amplified and sequenced a fragment of the MC1R gene (mc1r) from two Neanderthal remains. Both specimens have a mutation that was not found in ~3700 modern

Carles Lalueza-Fox; Holger Römpler; David Caramelli; Claudia Stäubert; Giulio Catalano; David Hughes; Nadin Rohland; Elena Pilli; Laura Longo; Silvana Condemi; Marco de la Rasilla; Javier Fortea; Antonio Rosas; Mark Stoneking; Torsten Schöneberg; Jaume Bertranpetit; Michael Hofreiter

2007-01-01

250

European Monetary Union  

NSDL National Science Digital Library

The EMU site was created by a group of students at the King's Hospital Secondary School in Palmerston, Dublin, Ireland. Their site discusses the potential positive and negative effects of the EMU, popular opinion on the Euro, and the possible side effects for Ireland, which will join, when its neighbor Britain does not join. After months of doubt and political difficulties in France, Germany, and most recently, Italy, it now appears that the unified European currency, the Euro, will indeed begin on January 1, 1999 to replace the national currencies of as many as 10 or 11 countries. The path to a unified currency is by no means smooth, however. Many European Union member states are finding it politically difficult to reduce their budget deficit to 3 percent of gross domestic product and other states, such as Britain and Denmark, are choosing to remain out for now regardless. On the other hand, European economic growth will apparently exceed earlier expectations, allowing leaders to use increased tax revenues instead of cutting social services to qualify.

251

The Microcephalin Ancestral Allele in a Neanderthal Individual  

PubMed Central

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

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

2010-01-01

252

Proportionally more deleterious genetic variation in European than in African populations.  

PubMed

Quantifying the number of deleterious mutations per diploid human genome is of crucial concern to both evolutionary and medical geneticists. Here we combine genome-wide polymorphism data from PCR-based exon resequencing, comparative genomic data across mammalian species, and protein structure predictions to estimate the number of functionally consequential single-nucleotide polymorphisms (SNPs) carried by each of 15 African American (AA) and 20 European American (EA) individuals. We find that AAs show significantly higher levels of nucleotide heterozygosity than do EAs for all categories of functional SNPs considered, including synonymous, non-synonymous, predicted 'benign', predicted 'possibly damaging' and predicted 'probably damaging' SNPs. This result is wholly consistent with previous work showing higher overall levels of nucleotide variation in African populations than in Europeans. EA individuals, in contrast, have significantly more genotypes homozygous for the derived allele at synonymous and non-synonymous SNPs and for the damaging allele at 'probably damaging' SNPs than AAs do. For SNPs segregating only in one population or the other, the proportion of non-synonymous SNPs is significantly higher in the EA sample (55.4%) than in the AA sample (47.0%; P < 2.3 x 10(-37)). We observe a similar proportional excess of SNPs that are inferred to be 'probably damaging' (15.9% in EA; 12.1% in AA; P < 3.3 x 10(-11)). Using extensive simulations, we show that this excess proportion of segregating damaging alleles in Europeans is probably a consequence of a bottleneck that Europeans experienced at about the time of the migration out of Africa. PMID:18288194

Lohmueller, Kirk E; Indap, Amit R; Schmidt, Steffen; Boyko, Adam R; Hernandez, Ryan D; Hubisz, Melissa J; Sninsky, John J; White, Thomas J; Sunyaev, Shamil R; Nielsen, Rasmus; Clark, Andrew G; Bustamante, Carlos D

2008-02-21

253

AGG interruptions and maternal age affect FMR1 CGG repeat allele stability during transmission  

PubMed Central

Background The presence of AGG interruptions in the CGG repeat locus of the fragile X mental retardation 1 (FMR1) gene decreases the instability of the allele during transmission from parent to child, and decreases the risk of expansion of a premutation allele to a full mutation allele (the predominant cause of fragile X syndrome) during maternal transmission. Methods To strengthen recent findings on the utility of AGG interruptions in predicting instability or expansion to a full mutation of FMR1 CGG repeat alleles, we assessed the outcomes of 108 intermediate (also named gray zone) and 710 premutation alleles that were transmitted from parent to child, and collected from four international clinical sites. We have used the results to revise our initial model that predicted the risk of a maternal premutation allele expanding to a full mutation during transmission and to test the effect of AGG interruptions on the magnitude of expanded allele instability of intermediate or premutation alleles that did not expand to a full mutation. Results Consistent with previous studies, the number of AGG triplets that interrupts the CGG repeat locus was found to influence the risk of allele instability, including expansion to a full mutation. The total length of the CGG repeat allele remains the best predictor of instability or expansion to a full mutation, but the number of AGG interruptions and, to a much lesser degree, maternal age are also factors when considering the risk of transmission of the premutation allele to a full mutation. Conclusions Our findings demonstrate that a model with total CGG length, number of AGG interruptions, and maternal age is recommended for calculating the risk of expansion to a full mutation during maternal transmission. Taken together, the results of this study provide relevant information for the genetic counseling of female premutation carriers, and improve the current predictive models which calculate risk of expansion to a full mutation using only total CGG repeat length. PMID:25110527

2014-01-01

254

Apolipoprotein E alleles in Alzheimer`s and Parkinson`s patients  

SciTech Connect

A number of investigators have found an association between the apolipoprotein E4 allele and Alzheimer`s disease. The E4 allele appears at a higher frequency in late onset familial Alzheimer`s patients. In our studies we obtained blood samples from early and late onset familial and sporadic Alzheimer`s patients and spouses, as well as from Parkinson`s patients. The patients were diagnosed as probable Alzheimer`s patients after a neurological examination, extensive blood work, and a CAT scan. The diagnosis was made according to the NINCDS-ADRDA criteria. The apolipoprotein E4 polymorphism was detected after PCR amplification of genomic DNA, restriction enzyme digestion with Hhal, and polyacrylamide gel electrophoresis. Ethidium bromide-stained bands at 91 bp were designated as allele 3, at 83 bp as allele 2, and at 72 bp as allele 4. Of the 84 probable Alzheimer`s patients (all of whom were Caucasian), 47 were heterozygous and 13 were homozygous for the E4 allele. There were 26 early onset patients; 13 were heterozygous and 7 homozygous for the E4 allele. The frequencies for the E4 allele for late onset familial patients was 0.45 and for sporadic patients was 0.37. We analyzed 77 spouses with an average age of 71.9 {plus_minus} 7.4 years as controls, and 15 were heterozygous for the E4 allele for an E4 frequency of 0.097. Of the 53 Parkinson`s patients, 11 had the E4 allele for a frequency of 0.113. Thus our findings support the association of the ApoE4 allele with Alzheimer`s disease.

Poduslo, S.E. [Texas Tech Univ., Lubbock, TX (United States); Schwankhaus, J.D. [Department of Veterans Affairs, Lubbock, TX (United States)

1994-09-01

255

Global diversity and genetic contributions of chicken populations from African, Asian and European regions.  

PubMed

Genetic diversity and population structure of 113 chicken populations from Africa, Asia and Europe were studied using 29 microsatellite markers. Among these, three populations of wild chickens and nine commercial purebreds were used as reference populations for comparison. Compared to commercial lines and chickens sampled from the European region, high mean numbers of alleles and a high degree of heterozygosity were found in Asian and African chickens as well as in Red Junglefowl. Population differentiation (FST ) was higher among European breeds and commercial lines than among African, Asian and Red Junglefowl populations. Neighbour-Net genetic clustering and structure analysis revealed two main groups of Asian and north-west European breeds, whereas African populations overlap with other breeds from Eastern Europe and the Mediterranean region. Broilers and brown egg layers were situated between the Asian and north-west European clusters. structure analysis confirmed a lower degree of population stratification in African and Asian chickens than in European breeds. High genetic differentiation and low genetic contributions to global diversity have been observed for single European breeds. Populations with low genetic variability have also shown a low genetic contribution to a core set of diversity in attaining maximum genetic variation present from the total populations. This may indicate that conservation measures in Europe should pay special attention to preserving as many single chicken breeds as possible to maintain maximum genetic diversity given that higher genetic variations come from differentiation between breeds. PMID:25315897

Lyimo, C M; Weigend, A; Msoffe, P L; Eding, H; Simianer, H; Weigend, S

2014-12-01

256

Molecular-genetic characterization of CMS-S restorer-of-fertility alleles identified in Mexican maize and teosinte.  

PubMed

Restorer-of-fertility (Rf) alleles for S-type cytoplasmic male sterility (CMS-S) are prevalent in Mexican races of maize and teosinte. Forty-five Rf alleles from 26 races of maize and 6 Rf alleles from different accessions of teosinte were found to be homozygous viable, consistent with the hypothesis that they are naturally occurring Rf alleles. Mapping and allelism studies were performed to assess the number of genes represented by these 51 alleles. Forty-two of the Rf alleles mapped to the long arm of chromosome 2 (2L), and 5 of these were further mapped to the whp1-rf3 region. The Rf3 restoring allele, found in some U.S. maize inbred lines, cosegregates with internal processing of CMS-S mitochondrial transcripts. Three of the 5 mapped Rf alleles were associated with a similar RNA processing event. Allelism or tight linkage was confirmed between Rf3 and 2 teosinte alleles (Rf K-69-6 and Rf 9477) and between Rf3 and the Cónico Norteño allele Rf C-N (GTO 22). The rf3 region of 2L potentially encodes a complex of linked rf genes. The prevalence of restoring alleles in this chromosomal region, among normal-cytoplasm accessions of Mexican maize and teosinte, supports the conclusion that these alleles have functions in normal mitochondrial gene expression that by chance allow them to restore male fertility in S cytoplasm. PMID:15020480

Gabay-Laughnan, Susan; Chase, Christine D; Ortega, Victor M; Zhao, Liming

2004-02-01

257

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

PubMed

The human leukocyte antigen (HLA) loci are among the most polymorphic genes in the human genome. The diversity of these genes is thought to be generated by different mechanisms including point mutation, gene conversion and crossing-over. During routine HLA typing, we discovered seven novel HLA alleles which were probably generated by different evolutionary mechanisms. HLA-B*41:21, HLA-DQB1*02:10 and HLA-DQA1*01:12 likely emerged from the common alleles of their groups by point mutations, all of which caused non-synonymous amino acid substitutions. In contrast, a deletion of one nucleotide leading to a frame shift with subsequent generation of a stop codon is responsible for the appearance of a null allele, HLA-A*01:123N. Whereas HLA-B*35:231 and HLA-B*53:31 were probably products of intralocus gene conversion between HLA-B alleles, HLA-C*07:294 presumably evolved by interlocus gene conversion between an HLA-C and an HLA-B allele. Our analysis of these novel alleles illustrates the different mechanisms which may have contributed to the evolution of HLA polymorphism. PMID:25500251

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

2015-01-01

258

Postglacial-period and Recent Invasions Shape the Population Genetics of Botryllid Ascidians along European Atlantic Coasts  

Microsoft Academic Search

The colonial urochordate Botryllus schlosseri is a sedentary species of Mediterranean origin that became cosmopolitan, probably because of postglacial-period dispersal\\u000a and human-mediated invasions of colonies attached to ship hulls. Here we studied microsatellite allele diversity of Atlantic\\u000a coast populations from an area ranging from European regions south of the last glacial front to regions that had been permanently\\u000a ice-covered. Gene

Rachel Ben-Shlomo; Guy Paz; Baruch Rinkevich

2006-01-01

259

The Fixation Probability of a Beneficial Allele in a Population Dividing by Binary Fission  

Microsoft Academic Search

We derive formulae for the fixation probability, P, of a rare benefical allele segregating in a population of fixed size which reproduces by binary fission, in terms of the selection coefficient for the beneficial allele, s. We find that an earlier result P ? 4s does not depend on the assumption of binary fission, but depends on an assumption about

Toby Johnson; Philip J. Gerrish

2002-01-01

260

Single-Locus Tests of Microsatellite Evolution: Multi-Step Mutations and Constraints on Allele Size  

E-print Network

obtained from nine different baleen whale popula- tions. High agreement was found between results obSingle-Locus Tests of Microsatellite Evolution: Multi-Step Mutations and Constraints on Allele Size- tions; constraints on allele size; stepwise mutation model. INTRODUCTION Microsatellite loci

Nielsen, Rasmus

261

Pigmentation phenotypes of variant extension locus alleles result from point mutations that alter MSH receptor function  

Microsoft Academic Search

Coat colors in the chestnut horse, the yellow Labrador retriever, the red fox, and one type of yellow mouse are due to recessive alleles at the extension locus. Similarly, dominant alleles at this locus are often responsible for dark coat colors in mammals, such as the melanic form of the leopard, Panthera pardus. We show here that the murine extension

L S Robbins; J H Nadeau; K R Johnson; M A Kelly; Rehfuss L Roselli; E Baack; K G Mountjoy; R D Cone

1993-01-01

262

Comparing computational methods for identification of allele-specific expression based on next generation sequencing data.  

PubMed

Allele-specific expression (ASE) studies have wide-ranging implications for genome biology and medicine. Whole transcriptome RNA sequencing (RNA-Seq) has emerged as a genome-wide tool for identifying ASE, but suffers from mapping bias favoring reference alleles. Two categories of methods are adopted nowadays, to reduce the effect of mapping bias on ASE identification-normalizing RNA allelic ratio with the parallel genomic allelic ratio (pDNAar) and modifying reference genome to make reads carrying both alleles with the same chance to be mapped (mREF). We compared the sensitivity and specificity of both methods with simulated data, and demonstrated that the pDNAar, though ideally practical, was lower in sensitivity, because of its lower mapping rate of reads carrying nonreference (alternative) alleles, although mREF achieved higher sensitivity and specificity for its efficiency in mapping reads carrying both alleles. Application of these two methods in real sequencing data showed that mREF were able to identify more ASE loci because of its higher mapping efficiency, and able to correcting some seemly incorrect ASE loci identified by pDNAar due to the inefficiency in mapping reads carrying alternative alleles of pDNAar. Our study provides useful information for RNA sequencing data processing in the identification of ASE. PMID:25183311

Liu, Zhi; Yang, Jing; Xu, Huayong; Li, Chao; Wang, Zhen; Li, Yuanyuan; Dong, Xiao; Li, Yixue

2014-11-01

263

INVOLVEMENT OF THE FGFR4 Arg388 ALLELE IN HEAD AND NECK SQUAMOUS CELL CARCINOMA  

E-print Network

INVOLVEMENT OF THE FGFR4 Arg388 ALLELE IN HEAD AND NECK SQUAMOUS CELL CARCINOMA Sylvia STREIT 1- gated the expression pattern of FGFR4 and the clinical significance of the recently identified Gly/Arg, as intermediate in 59 and as low in 28 cases. The FGFR4 Arg388 allele was found in 59 tumors, 46 of them having

Ullrich, Axel

264

Allelic polymorphism synergizes with variable gene content to individualize human KIR genotype.  

PubMed

Killer Ig-like receptor (KIR) genes are a multigene family on human chromosome 19. KIR genes occur in various combinations on different haplotypes. Additionally, KIR genes are polymorphic. To examine how allelic polymorphism diversifies KIR haplotypes with similar or identical combinations of KIR genes, we devised methods for discriminating alleles of KIR2DL1, -2DL3, -3DL1, and -3DL2. These methods were applied to 143 individuals from 34 families to define 98 independent KIR haplotypes at the allele level. Three novel 3DL2 alleles and a chimeric 3DL1/3DL2 sequence were also identified. Among the A group haplotypes were 22 different combinations of 2DL1, 2DL3, 3DL1, and 3DL2 alleles. Among the B group haplotypes that were unambiguously determined were 15 distinct haplotypes involving 9 different combinations of KIR genes. A and B haplotypes both exhibit strong linkage disequilibrium (LD) between 2DL1 and 2DL3 alleles, and between 3DL1 and 3DL2 alleles. In contrast, there was little LD between the 2DL1/2DL3 and 3DL1/3DL2 pairs that define the two halves of the KIR gene complex. The synergistic combination of allelic polymorphism and variable gene content individualize KIR genotype to an extent where unrelated individuals almost always have different KIR types. This level of diversity likely reflects strong pressure from pathogens on the human NK cell response. PMID:11859120

Shilling, Heather G; Guethlein, Lisbeth A; Cheng, Nathalie W; Gardiner, Clair M; Rodriguez, Roberto; Tyan, Dolly; Parham, Peter

2002-03-01

265

A new model for the origins of allelic dimorphism in Plasmodium falciparum.  

PubMed

In his landmark 1987 study of the merozoite surface protein-1 locus in Plasmodium falciparum, Kazuyuki Tanabe and coauthors introduced the phenomenon of allelic dimorphism, in which antigenic diversity is arranged into two maximally diverged haplotypes. Further work has extended this finding to other loci in P. falciparum. Each of the loci at which allelic dimorphism is observed encodes major surface antigens of blood-stage malaria parasites, and is consequently a major vaccine target, thus understanding the origins and implications of allelic dimorphism is of crucial importance. Here we examine the essential features of allelic dimorphism in dimorphic malarial surface antigens. From sequence analysis, we conclude that the ancestral population may have been recombining/multimorphic rather than dimorphic. We hypothesize a pathway to allelic dimorphism in which an ancestral allele-rich recombining population could have undergone a severe population bottleneck, putatively caused by the lateral transfer of P. falciparum from apes to humans. This bottleneck produced a reduction in allelic diversity, favoring the survival of the most divergent alleles, which in turn led to recombination suppression by strong natural selection against recombinants. PMID:25251164

Roy, Scott W; Ferreira, Marcelo U

2014-09-22

266

Adaptive Mutation with Fitness and Allele Distribution Correlation for Genetic Algorithms  

E-print Network

Adaptive Mutation with Fitness and Allele Distribution Correlation for Genetic Algorithms 34469 Istanbul, Turkey etaner@cs.itu.edu.tr ABSTRACT In this paper, a new gene based adaptive mutation and on gene based allele distribution statistics are correlated to explicitly adapt the mutation probability

Yang, Shengxiang

267

Frequencies of erythrocyte blood groups alleles and haplotyphes in women with benign tumors of the uterus.  

PubMed

The erythrocyte blood groups antigens are associated with risk of certain malignancies though the correlation between blood groups and diseases is still unclear. The investigation is aimed at determining the correlation between benign tumors of the uterus and erythrocyte blood groups alleles and haplotyphes in patients of Adjara Oncology Centre. Blood of 60 women with benign tumors of the uterus and of 60 healthy women of reproductive age were investigated for ABO and Rh system alleles and haplotypes. Immunoserological methods have been used to identify the antigens. The obtained results were statistically processed. The ABO system gene alleles' frequency was computed by the formula proposed by F. Bernstein and used in investigation of three-allele genetic systems. The frequency of Rh-system genes, Rh-haplotypes is computed by the formula proposed by A. E. Mourant. According to ABO systems in women with benign tumors of the uterus high frequencies of p (0,12) and q (0,21) alleles are found. When studying individual alleles of the Rh system in women with benign tumors, high frequency of D was noticed (0.8). In women with benign tumor of the uterus RhD allele frequency is statistically different to healthy women. ABO systems gene alleles' significantly differ in healthy and diseased women. In women with benign tumor of the uterus only three Rh-system haplotypes have been found: CDe, cDe, cde haplotypes. PMID:22870829

Nakashidze, I; Diasamidze, A; Nagervadze, M

2012-05-01

268

Estimating minimum allele frequencies for DNA profile frequency estimates for PCR-based loci  

Microsoft Academic Search

In order that there can be confidence that DNA profile frequency estimates will not place undue bias against a defendant, 2 methods are described for estimating minimum allele frequency bounds for PCR-based loci. One approach estimates minimum allele frequencies for VNTR and STR loci using sample size and the observed heterozygosity at a locus, while the second approach, appropriate for

B. Budowle; K. L. Monson; R. Chakraborty

1996-01-01

269

PCR/RFLP-based allelic variants of streptokinase and their plasminogen activation potencies.  

PubMed

PCR-restriction fragment length polymorphism (PCR/RFLP)-based analysis of ?-domain variable region of streptokinase genes (sk) has previously identified 14 sk alleles (sk1-sk14) in group A (GAS), C (GCS) and G (GGS) streptococci isolates from a few geographically distinct regions. However, the relation of sk allelic variants to their plasminogen activation potencies remained as a matter of debate. Herein, employing the same PCR/RFLP assay, we analysed sk allelic variants of GAS and GCS/GGS isolates from Iranian patients. In total, 21 sk allelic variants including 14 new alleles (sk14-sk28) were identified. Results implied the horizontal gene transfer of sk fragments between GAS and GCS/GGS strains and did not prove the specificity of particular sk alleles to GCS/GGS or GAS groups. Measurement of streptokinase (SK) activity in streptococcal culture supernatants by colorimetric assay (S2251 substrate) ranged from 9 to 182 IU mL(-1). Although some strains with the highest SK activity were detected in definite variants, no significant correlation between sk alleles and plasminogen activation was detected (P value > 0.05). Analysis of DNA sequences and restriction site mapping of selective sk variants with similar SK activity pointed to the inadequacy of the currently available PCR/RFLP method for differentiation of critical/silent nucleotides to precisely categorize sk alleles for their functional properties. PMID:22812485

Keramati, Malihe; Roohvand, Farzin; Eslaminejad, Zahra; Mirzaie, Amir; Nikbin, Vajihe Sadat; Aslani, Mohammad Mehdi

2012-10-01

270

Stem Cell Reports Single-Cell Analysis of Proxy Reporter Allele-Marked Epithelial Cells  

E-print Network

Stem Cell Reports Resource Single-Cell Analysis of Proxy Reporter Allele-Marked Epithelial Cells Establishes Intestinal Stem Cell Hierarchy Ning Li,1 Maryam Yousefi,1,5 Angela Nakauka-Ddamba,1 Rajan Jain,2 development of targeted murine reporter alleles as proxies for intestinal stem cell activity has led

Jensen, Shane T.

271

Retention of agronomically important variation in germplasm core collections: implications for allele mining  

Technology Transfer Automated Retrieval System (TEKTRAN)

The primary targets of allele mining efforts are loci of agronomic importance. Agronomic loci typically exhibit patterns of allelic diversity consistent with a history of natural or artificial selection. Natural or artificial selection causes the distribution of genetic diversity at such loci to d...

272

RESEARCH ARTICLE Open Access Sequence analysis of two alleles reveals that  

E-print Network

recombination played a role in the evolution of the radish fertility restorer (Rfo) José R Hernandez Mora1 sequenced a non-restoring allele (L7rfo) of the Rfo radish locus whose restoring allele (D81Rfo fragment, likely originating from another part of the radish genome, inserted into the L7rfo sequence

Boyer, Edmond

273

Genome-wide Detection of Allelic Imbalance Using Human SNPs and High-density DNA Arrays  

Microsoft Academic Search

Most human cancers are characterized by genomic instability, the accumulation of multiple genetic alterations and allelic imbalance throughout the genome. Loss of heterozygosity (LOH) is a common form of allelic imbalance and the detection of LOH has been used to identify genomic regions that harbor tumor suppressor genes and to characterize tumor stages and progression. Here we describe the use

Rui Mei; Patricia C. Galipeau; Cynthia Prass; Anthony Berno; Ghassan Ghandour; Nila Patil; Roger K. Wolff; Mark S. Chee; Brian J. Reid; David J. Lockhart

2000-01-01

274

A loss-of-alleles model for the evolution of distyly  

Microsoft Academic Search

Distyly is characterized by a diallelic incompatibility system. Crowe (1964) hypothesized that this has arisen by a loss of alleles from multiallelic systems. I have examined a mechanism for such a loss in a simulated population with sporophytic incompatibility and four alleles at the incompatibility locus. If a second locus is tightly linked to the incompatibility locus and a favoured

Gayle Muenchow

1982-01-01

275

Apolipoprotein E ε4 Allele Frequency and Age at Onset of Alzheimer’s Disease  

Microsoft Academic Search

The age distribution of the ε4 allelic form of the apolipoprotein E gene (APOE) was investigated in 630 patients with Alzheimer’s disease (AD) with onset age ranging from 35 to 90 years. Overall, mean age at onset in APOE ε4 allele bearers was significantly later than that in nonbearers. However, when stratified into early onset AD (EOAD) and late onset

Yvonne Davidson; Linda Gibbons; Antonia Pritchard; Jayne Hardicre; Joanne Wren; Cheryl Stopford; Camille Julien; Jennifer Thompson; Antony Payton; Stuart M. Pickering-Brown; Neil Pendleton; Michael A. Horan; Alistair Burns; Nitin Purandare; Corinne L. Lendon; David Neary; Julie S. Snowden; David M. A. Mann

2007-01-01

276

Researching the European Union  

NSDL National Science Digital Library

This site is the European Union's official and comprehensive guide for scholars and researchers studying its institutions. Users will find information on document access, treaties and institutions, legislation, and EU publishing operations. The site also provides overviews of official and related institutions and the legislative process in the Union. Researchers will be especially interested in the sections on Legislative Documents and Print Research Tools, Using Annual Reports and Informational Documents, and Bibliographic and Other Guides. The synoptic tables of basic documents, quick visual guides to the documents described on the site and their availability, are additional valuable tools.

1997-01-01

277

European Environmental Law Homepage  

NSDL National Science Digital Library

The European Environmental Law Homepage provides access to the full text of treaties, legislation, case law, scholarly legal articles, and EU and NGO documents relevant to environmental law in Europe. In addition, the site has compiled a directory of important governmental Websites for most nations in Europe and maintains a list of pointers to other legal sites with environmental information. The site is edited by Wybe Th. Douma of the T.M.C. Asser Institute, and Jurgen G.J. Lefevere of both the Foundation for International Environmental Law and Development, and the METRO Institute, Maastricht University.

278

Independent recruitment of Igh alleles in V(D)J recombination.  

PubMed

How the vast majority of B cells express only one of the two alleles at their immunoglobulin loci remains a biological puzzle. Here, in mice reconstituted with a single haematopoietic stem cell, we demonstrate that each of the two immunoglobulin heavy chain (Igh) alleles has a similar probability to be the first to undergo VH to DJH rearrangement. We also observe this similar probability in clones from multipotent and common lymphoid precursors. The extreme biases in the expression of the alleles that we find in more differentiated subsets are mostly due to constraints imposed by early rearrangements. Our data demonstrate that each of the two Igh alleles in a B cell behaves independently of the other, up to the moment when a successful rearrangement in one allele triggers a feedback mechanism that prevents further recombination. PMID:25517887

Alves-Pereira, Clara F; de Freitas, Raquel; Lopes, Telma; Gardner, Rui; Marta, Filipa; Vieira, Paulo; Barreto, Vasco M

2014-01-01

279

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

SciTech Connect

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

Chang, F.M.; Kidd, J.R. [Yale Univ. School of Medicine, New Haven, CT (United States); Livak, K.J. [DuPont-Merch Pharmaceutical Company, Wilmington, DE (United States)] [and others

1994-09-01

280

Does 5HTTLPR long allele prevent hospitalization? Test of Hardy-Weinberg equilibrium.  

PubMed

Many studies suggest an association of the serotonin transporter gene polymorphism (5HTTLPR) long allele with better antidepressant treatment response than the short allele. However, there is controversy over these findings. We hypothesized that if the long allele is associated with a better outcome, we would find fewer inpatients with the long allele compared with the short allele. Chart review identified 925 depressed inpatients and 201 outpatients genotyped for 5HTTLPR. The sample was primarily White (>90%). We tested potential departures from Hardy-Weinberg equilibrium for each sample. We analyzed three independent sets of inpatient samples separately and combined, a White subgroup of 791 patients of the total 925 inpatients, and 201 outpatients. There was no departure from Hardy-Weinberg equilibrium with any of these samples. We also compared 5HTTLPR genotype prevalence between 925 inpatients and 201 outpatients, which showed no statistically significant difference. PMID:24300662

Shinozaki, Gen; Kung, Simon; Mrazek, David A

2014-02-01

281

European Anti Poverty Network (EAPN)  

NSDL National Science Digital Library

European Anti Poverty Network was created in 1989 "to put the fight against poverty and social exclusion on the political agenda of the European Union." The Network consists of 25 European organizations that work to alleviate poverty and 15 national networks that fight poverty specifically inside the EU. EAPN offers a nice collection of position papers and reports analyzing the ongoings of the European Union, its member countries and their policies, as well as news releases and news flashes. The site gives general information about the EAPN including its mission, members, and activities, as well as providing a tightly organized set of links.

282

EIOP: European Integration Online Papers  

NSDL National Science Digital Library

The European Community Studies Association Austria provides this new working paper archive to house peer-reviewed, interdisciplinary working papers in the field of European integration research, including legal studies, political science, economics, and history. At present eleven papers are available, including "Democracy and Governance in the European Union," "The Economic Consequences of a Large EMU--Results of Macroeconomic Model Simulations," and "The Making of a Polity: The Struggle Over European Integration." Though English is the preferred language for papers, papers in German may also be included; abstracts are presented in both languages. A mailing list is available for those wishing to be informed when new papers are posted.

283

European Industrial Relations Observatory Online  

NSDL National Science Digital Library

The European Industrial Relations Observatory Online (EIROnline) was developed by the European Foundation for the Improvement of Living and Working Conditions, an autonomous body created by the European Community. The aim of the site is to "initiate, collect, store, disseminate and provide access to information and analysis on developments in industrial relations" in the 15 European Union member states and Norway. Visitors will find the latest industrial relations news and feature articles arranged by country. There is also a bimonthly publication called the EIRObserver summarizing the news and items over the past two months.

284

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

PubMed

HLA-A molecules are highly polymorphic. Their accurate typing at a high-resolution level is crucial for successful organ, bone marrow and cord blood transplantation. Furthermore, several HLA alleles have been involved in susceptibility to autoimmune diseases, allergies, cancers and inflammations. In order to determine common HLA-A alleles in Syria and their frequencies, sequence-based typing (SBT) was used to genotype HLA-A alleles at high resolution (four digit level) among one hundred and thirty randomly selected Syrian individuals. Exons 2, 3 and 4 of the HLA-A gene were amplified by PCR and sequenced. The sbt-engine software was used for allele assignment. Ambiguities were solved using group-specific sequencing primers (GSSPs). We could identify 32 different HLA-A alleles which were divided into 3 groups: high frequency (approximately 10%, A*01:01; A*24:02; A*03:01; A*02:01), moderate frequency (approximately 3%, such as A*02:05, A*31:01 and A*33:01), and low frequency (approximately 1%, such as A*02:11, A*29:01, A*02:02 and A*36:01). Homozygosity rate was higher than expected (11.5% vs. 7.15%). For high frequency alleles, our results show similarity to neighbouring countries. However, 15 alleles (such as A*02:04, A*02:06, A*02:11 and A*02:17) found in our cohort in low frequencies were never reported in some or all neighbouring countries. This is the first report on HLA-A allele frequencies in Syria. In spite of the relatively low number of tested subjects, our results revealed a high degree of diversity, with 32 different alleles, reflecting the high ethnic heterogeneity of the Syrian population. The identification of alleles rarely or never reported in neighbouring countries indicates a higher genetic diversity in Syria. PMID:25053398

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

2014-10-01

285

Distinct allelic patterns of nanog expression impart embryonic stem cell population heterogeneity.  

PubMed

Nanog is a principal pluripotency regulator exhibiting a disperse distribution within stem cell populations in vivo and in vitro. Increasing evidence points to a functional role of Nanog heterogeneity on stem cell fate decisions. Allelic control of Nanog gene expression was reported recently in mouse embryonic stem cells. To better understand how this mode of regulation influences the observed heterogeneity of NANOG in stem cell populations, we assembled a multiscale stochastic population balance equation framework. In addition to allelic control, gene expression noise and random partitioning at cell division were considered. As a result of allelic Nanog expression, the distribution of Nanog exhibited three distinct states but when combined with transcriptional noise the profile became bimodal. Regardless of their allelic expression pattern, initially uniform populations of stem cells gave rise to the same Nanog heterogeneity within ten cell cycles. Depletion of NANOG content in cells switching off both gene alleles was slower than the accumulation of intracellular NANOG after cells turned on at least one of their Nanog gene copies pointing to Nanog state-dependent dynamics. Allelic transcription of Nanog also raises issues regarding the use of stem cell lines with reporter genes knocked in a single allelic locus. Indeed, significant divergence was observed in the reporter and native protein profiles depending on the difference in their half-lives and insertion of the reporter gene in one or both alleles. In stem cell populations with restricted Nanog expression, allelic regulation facilitates the maintenance of fractions of self-renewing cells with sufficient Nanog content to prevent aberrant loss of pluripotency. Our findings underline the role of allelic control of Nanog expression as a prime determinant of stem cell population heterogeneity and warrant further investigation in the contexts of stem cell specification and cell reprogramming. PMID:23874182

Wu, Jincheng; Tzanakakis, Emmanuel S

2013-01-01

286

Distinct Allelic Patterns of Nanog Expression Impart Embryonic Stem Cell Population Heterogeneity  

PubMed Central

Nanog is a principal pluripotency regulator exhibiting a disperse distribution within stem cell populations in vivo and in vitro. Increasing evidence points to a functional role of Nanog heterogeneity on stem cell fate decisions. Allelic control of Nanog gene expression was reported recently in mouse embryonic stem cells. To better understand how this mode of regulation influences the observed heterogeneity of NANOG in stem cell populations, we assembled a multiscale stochastic population balance equation framework. In addition to allelic control, gene expression noise and random partitioning at cell division were considered. As a result of allelic Nanog expression, the distribution of Nanog exhibited three distinct states but when combined with transcriptional noise the profile became bimodal. Regardless of their allelic expression pattern, initially uniform populations of stem cells gave rise to the same Nanog heterogeneity within ten cell cycles. Depletion of NANOG content in cells switching off both gene alleles was slower than the accumulation of intracellular NANOG after cells turned on at least one of their Nanog gene copies pointing to Nanog state-dependent dynamics. Allelic transcription of Nanog also raises issues regarding the use of stem cell lines with reporter genes knocked in a single allelic locus. Indeed, significant divergence was observed in the reporter and native protein profiles depending on the difference in their half-lives and insertion of the reporter gene in one or both alleles. In stem cell populations with restricted Nanog expression, allelic regulation facilitates the maintenance of fractions of self-renewing cells with sufficient Nanog content to prevent aberrant loss of pluripotency. Our findings underline the role of allelic control of Nanog expression as a prime determinant of stem cell population heterogeneity and warrant further investigation in the contexts of stem cell specification and cell reprogramming. PMID:23874182

Wu, Jincheng; Tzanakakis, Emmanuel S.

2013-01-01

287

An American Construction of European Education Space  

ERIC Educational Resources Information Center

The construction of the European education space has typically been attributed to European education policy makers, institutions, and networks. Rarely do scholars consider the role of outside, non-European actors in shaping the terrain of European education thought and practice. This article considers the construction of the European education…

Silova, Iveta; Brehm, William C.

2010-01-01

288

MHC associations with clinical and autoantibody manifestations in European SLE.  

PubMed

Systemic lupus erythematosus (SLE) is a clinically heterogeneous disease affecting multiple organ systems and characterized by autoantibody formation to nuclear components. Although genetic variation within the major histocompatibility complex (MHC) is associated with SLE, its role in the development of clinical manifestations and autoantibody production is not well defined. We conducted a meta-analysis of four independent European SLE case collections for associations between SLE sub-phenotypes and MHC single-nucleotide polymorphism genotypes, human leukocyte antigen (HLA) alleles and variant HLA amino acids. Of the 11 American College of Rheumatology criteria and 7 autoantibody sub-phenotypes examined, anti-Ro/SSA and anti-La/SSB antibody subsets exhibited the highest number and most statistically significant associations. HLA-DRB1*03:01 was significantly associated with both sub-phenotypes. We found evidence of associations independent of MHC class II variants in the anti-Ro subset alone. Conditional analyses showed that anti-Ro and anti-La subsets are independently associated with HLA-DRB1*0301, and that the HLA-DRB1*03:01 association with SLE is largely but not completely driven by the association of this allele with these sub-phenotypes. Our results provide strong evidence for a multilevel risk model for HLA-DRB1*03:01 in SLE, where the association with anti-Ro and anti-La antibody-positive SLE is much stronger than SLE without these autoantibodies. PMID:24598797

Morris, D L; Fernando, M M A; Taylor, K E; Chung, S A; Nititham, J; Alarcón-Riquelme, M E; Barcellos, L F; Behrens, T W; Cotsapas, C; Gaffney, P M; Graham, R R; Pons-Estel, B A; Gregersen, P K; Harley, J B; Hauser, S L; Hom, G; Langefeld, C D; Noble, J A; Rioux, J D; Seldin, M F; Vyse, T J; Criswell, L A

2014-04-01

289

FINDbase: a worldwide database for genetic variation allele frequencies updated  

PubMed Central

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

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

2011-01-01

290

Maintenance of an aminopeptidase allele frequency cline by natural selection.  

PubMed

The product of the Lap locus in the marine bivalve Mytilus edulis is a neutral, membrane-associated aminopeptidase that is primarily localized on intestinal microvilli and in digestive cell lysosomes. Natural populations are genetically differentiated at the Lap locus between areas of differing salinity. A steep (0.55-0.15) allele frequency cline connects differentiated populations between the Atlantic Ocean and Long Island Sound. We demonstrate an annual gene flow/mortality cycle in cline populations whereby gene frequencies after mortality are correlated with salinity and enzyme activity. The cline is spatially and temporally unstable in immigrants, but stable in residents after mortality. Mortality is nonrandom with regard to the Lap locus; genotype-dependent properties of the aminopeptidase enzyme apparently led to a differential rate of the utilizaiton of nutrient reserves because selected genotypes exhibited an increased rate of tissue weight loss. Aminopeptidase genotypes are differentially adapted to different temperatures and salinities, which provides a mechanism for the relationship among biochemical, physiological, and population phenotypes. PMID:6933563

Koehn, R K; Newell, R I; Immermann, F

1980-09-01

291

Impact of common KIBRA allele on human cognitive functions.  

PubMed

The rs17070145 polymorphism (C ? T substitution, intron 9) of the KIBRA gene has recently been associated with episodic memory and cognitive flexibility. These findings were inconsistent across reports though, and largely lacked gene-gene or gene-environment interactions. The aim of the present study was to determine the impact of the rs17070145 polymorphism on clinically relevant cognitive domains and its interaction with the modifiers 'lifestyle' and 'cardiovascular risk factors'. Five-hundred forty-five elderly volunteers (mean age 64 years, ±7 years, 56% women) accomplished a comprehensive cognitive testing. Principal component analysis was used to reveal the internal structure of the data, rendering four composite scores: verbal memory, word fluency, executive function/psychomotor speed, and working memory. Lifestyle was assessed with a detailed questionnaire, age-associated risk factors by clinical interview and examination. There was no main effect of the rs17070145 genotype on any cognitive composite scores. However, we found worse performance in executive functions for T-allele carriers in the presence of arterial hypertension (?=-0.365, p=0.0077 and 0.031 after Bonferroni correction). This association was further modified by gender, showing the strongest association in hypertensive females (?=-0.500, p=0.0072 and 0.029 after Bonferroni correction). The effect of KIBRA on cognitive function seems to be complex and modified by gender and arterial hypertension. PMID:21346737

Wersching, H; Guske, K; Hasenkamp, S; Hagedorn, C; Schiwek, S; Jansen, S; Witte, V; Wellmann, J; Lohmann, H; Duning, K; Kremerskothen, J; Knecht, S; Brand, E; Floel, A

2011-05-01

292

Novel carbonic anhydrase (Car-2) allele in Spanish mice.  

PubMed

A unique electrophoretic form of carbonic anhydrase is characteristic of some laboratory-maintained mice of the wild mouse species Mus spretus. This isozyme has been characterized by cellulose acetate electrophoresis and by isoelectric focusing. It is proposed that this isozyme be called CAR-2C and that its encoding allele be designated Car-2c. Fertile hybrids of Mus spretus and C57BL/6J (Car-2a) show both CAR-2A and CAR-2C bands of approximately equal intensity. The CAR-2C isozyme is readily identified by electrophoresis on 75-mm cellulose acetate strips because it migrates significantly faster than the isozymes of inbred mice, the CAR-2A and CAR-2B that do not separate from one another under standard conditions. Isoelectric focusing cleanly resolves all three of these CAR-2 forms. Mus hortulanus, although closely related to Mus spretus in other biochemical-genetic characteristics, has a CAR-2-homologous isozyme that is distinctly different from the CAR-2C of Mus spretus and from the isozymes of the common inbred strains. PMID:6440531

Whitney, J B

1984-10-01

293

Microsatellite allele dose and configuration establishment (MADCE): an integrated approach for genetic studies in allopolyploids  

PubMed Central

Background Genetic studies in allopolyploid plants are challenging because of the presence of similar sub-genomes, which leads to multiple alleles and complex segregation ratios. In this study, we describe a novel method for establishing the exact dose and configuration of microsatellite alleles for any accession of an allopolyploid plant species. The method, named Microsatellite Allele Dose and Configuration Establishment (MADCE), can be applied to mapping populations and pedigreed (breeding) germplasm in allopolyploids. Results Two case studies are presented to demonstrate the power and robustness of the MADCE method. In the mapping case, five microsatellites were analysed. These microsatellites amplified 35 different alleles based on size. Using MADCE, we uncovered 30 highly informative segregating alleles. A conventional approach would have yielded only 19 fully informative and six partially informative alleles. Of the ten alleles that were present in all progeny (and thereby ignored or considered homozygous when using conventional approaches), six were found to segregate by dosage when analysed with MADCE. Moreover, the full allelic configuration of the mapping parents could be established, including null alleles, homozygous loci, and alleles that were present on multiple homoeologues. In the second case, 21 pedigreed cultivars were analysed using MADCE, resulting in the establishment of the full allelic configuration for all 21 cultivars and a tracing of allele flow over multiple generations. Conclusions The procedure described in this study (MADCE) enhances the efficiency and information content of mapping studies in allopolyploids. More importantly, it is the first technique to allow the determination of the full allelic configuration in pedigreed breeding germplasm from allopolyploid plants. This enables pedigree-based marker-trait association studies the use of algorithms developed for diploid crops, and it may increase the effectiveness of LD-based association studies. The MADCE method therefore enables researchers to tackle many of the genotyping problems that arise when performing mapping, pedigree, and association studies in allopolyploids. We discuss the merits of MADCE in comparison to other marker systems in polyploids, including SNPs, and how MADCE could aid in the development of SNP markers in allopolyploids. PMID:22340438

2012-01-01

294

The Scientific CouncilThe Scientific Council to the European Research Councilto the European Research Council  

E-print Network

1 The Scientific CouncilThe Scientific Council to the European Research Councilto the European;2 The Scientific CouncilThe Scientific Council to the European Research Councilto the European Research CouncilThe Scientific Council to the European Research Councilto the European Research Council Challenges for

De Cindio, Fiorella

295

EUROPEAN INDUSTRIAL AND COMPETITION POLICY  

Microsoft Academic Search

This article discusses alternative perspectives on competition and industrial policies (IP) in theory and in practice and critically assesses recent European IP in this context. It develops a new framework for IP that emphasises the sustainability of value creation at the firm, meso and national levels, and explores its implications for IP in general and European IP in particular. It

Christos N. Pitelis

2007-01-01

296

Quantifying the transcriptional output of single alleles in single living mammalian cells  

PubMed Central

Transcription kinetics of actively transcribing genes in vivo have generally been measured using tandem gene arrays. However, tandem arrays do not reflect the endogenous state of genome organization where genes appear as single alleles. We present here a robust technique for the quantification of mRNA synthesis from a single allele in real-time, in single living mammalian cells. The protocol describes how to generate cell clones harboring a tagged allele and how to detect in vivo transcription from this tagged allele at high spatial and temporal resolution throughout the cell cycle. Quantification of nascent mRNAs produced from the single tagged allele is performed using RNA fluorescence in situ hybridization (FISH) and live-cell imaging. Subsequent analyses and data modeling detailed in the protocol include measurements of: transcription rates of RNA polymerase II; determining the number of polymerases recruited to the tagged allele; and measuring the spacing between polymerases. Generating the cells containing the single tagged alleles should take up to a month; RNA FISH or live-cell imaging will require an additional week. PMID:23424748

Yunger, Sharon; Rosenfeld, Liat; Garini, Yuval; Shav-Tal, Yaron

2013-01-01

297

S-allele diversity in Sorbus aucuparia and Crataegus monogyna (Rosaceae: Maloideae).  

PubMed

RT-PCR was used to obtain the first estimates from natural populations of allelic diversity at the RNase-based gametophytic self-incompatibility locus in the Rosaceae. A total of 20 alleles were retrieved from 20 Sorbus aucuparia individuals, whereas 17 alleles were found in 13 Crataegus monogyna samples. Estimates of population-level allele numbers fall within the range observed in the Solanaceae, the only other family with RNase-based incompatibility for which estimates are available. The nucleotide diversity of S-allele sequences was found to be much lower in the two Rosaceae species as compared with the Solanaceae. This was not due to a lower sequence divergence among most closely related alleles. Rather, it is the depth of the entire genealogy that differs markedly in the two families, with Rosaceae S-alleles exhibiting more recent apparent coalescence. We also investigated patterns of selection at the molecular level by comparing nucleotide diversity at synonymous and nonsynonymous sites. Stabilizing selection was inferred for the 5' region of the molecule, while evidence of diversifying selection was present elsewhere. PMID:12180088

Raspé, O; Kohn, J R

2002-06-01

298

Investigation of Japanese-specific alleles: Most are of Jomon lineage.  

PubMed

Japanese-specific alleles are expected to be powerful markers for the differentiation of the Japanese from other people. In this study, three single nucleotide polymorphisms (SNPs) in the GALNT11, H19, and PLA2G12A genes were analyzed in 2396 DNA samples from 25 global populations, and the derived alleles suggested that Japanese-specific alleles exist on autosomes. To identify new Japanese-specific alleles, candidate SNPs obtained from the HapMap database were investigated using 875 DNA samples from nine populations. A total of 67 (nearly) Japanese-specific derived alleles were observed. Of them, 57 showed higher frequencies in the Ryukyuans, living in the southernmost part of the Japanese Archipelago, than in the Wajins living in mainland Japan, and 43 were also present in Koreans at low frequencies. Jomon skeletons excavated from Hokkaido, the northernmost island of Japan, showed higher frequencies of the three derived alleles in the GALNT11, H19, and PLA2G12A genes than the Ryukyuans, suggesting that most of the 57 derived alleles observed at the high frequencies in the Ryukyuans originated from the Jomon lineage. These novel markers will be useful in the field of forensics. PMID:25239165

Yuasa, Isao; Umetsu, Kazuo; Adachi, Noboru; Matsusue, Aya; Nakayashiki, Nori; Fujihara, Junko; Akane, Atsushi; Harihara, Shinji; Jin, Feng; Ishikawa, Takaki

2015-01-01

299

Novel cause of hereditary obstructive azoospermia: a T2 allele in the CFTR gene.  

PubMed

Congenital bilateral absence of the vas deferens (CBAVD) is a frequent cause of obstructive azoospermia, and caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. A novel TG(13)T(2) allele was identified in a CBAVD patient with no clinical cystic fibrosis phenotype, normal pancreatic function, normal sweat chloride concentrations and no Y chromosome microdeletions. This case was studied for CFTR mutations, IVS8-poly(T), and M470V exon 10 missense polymorphism. One novel allele was detected in the (TG)(m)(T)(n) loci that had not been reported previously. This patient carried a [TG(11)T(9); R117H; p.Met470Val] haplotype on the other chromosome. Since the TG(13)T(2) allele was a compound heterozygote with R117H mutation, it was difficult to judge the severity of this allele. To better understand the complex regulation of exon 9 splicing, the levels of correctly spliced CFTR transcripts in CFTR-expressing epithelial cells derived from vas deferens and epididymis were analysed. These data emphasize the role of the T2 allele in CBAVD, and identify the T2 allele as a severe CBAVD disease-causing mutation. According to the data, the longer (TG)(m) polymorphic tract increases the proportion of transcripts with exon 9 deletion (9-), but only when activated by the short T allele. PMID:19298730

Radpour, Ramin; Taherzadeh-Fard, Elahe; Gourabi, Hamid; Aslani, Sahar; Vosough Dizaj, Ahmad; Aslani, Ali

2009-03-01

300

Genome-wide association study of subtype-specific epithelial ovarian cancer risk alleles using pooled DNA.  

PubMed

Epithelial ovarian cancer (EOC) is a heterogeneous cancer with both genetic and environmental risk factors. Variants influencing the risk of developing the less-common EOC subtypes have not been fully investigated. We performed a genome-wide association study (GWAS) of EOC according to subtype by pooling genomic DNA from 545 cases and 398 controls of European descent, and testing for allelic associations. We evaluated for replication 188 variants from the GWAS [56 variants for mucinous, 55 for endometrioid and clear cell, 53 for low-malignant potential (LMP) serous, and 24 for invasive serous EOC], selected using pre-defined criteria. Genotypes from 13,188 cases and 23,164 controls of European descent were used to perform unconditional logistic regression under the log-additive genetic model; odds ratios (OR) and 95 % confidence intervals are reported. Nine variants tagging six loci were associated with subtype-specific EOC risk at P < 0.05, and had an OR that agreed in direction of effect with the GWAS results. Several of these variants are in or near genes with a biological rationale for conferring EOC risk, including ZFP36L1 and RAD51B for mucinous EOC (rs17106154, OR = 1.17, P = 0.029, n = 1,483 cases), GRB10 for endometrioid and clear cell EOC (rs2190503, P = 0.014, n = 2,903 cases), and C22orf26/BPIL2 for LMP serous EOC (rs9609538, OR = 0.86, P = 0.0043, n = 892 cases). In analyses that included the 75 GWAS samples, the association between rs9609538 (OR = 0.84, P = 0.0007) and LMP serous EOC risk remained statistically significant at P < 0.0012 adjusted for multiple testing. Replication in additional samples will be important to verify these results for the less-common EOC subtypes. PMID:24190013

Earp, Madalene A; Kelemen, Linda E; Magliocco, Anthony M; Swenerton, Kenneth D; Chenevix-Trench, Georgia; Lu, Yi; Hein, Alexander; Ekici, Arif B; Beckmann, Matthias W; Fasching, Peter A; Lambrechts, Diether; Despierre, Evelyn; Vergote, Ignace; Lambrechts, Sandrina; Doherty, Jennifer A; Rossing, Mary Anne; Chang-Claude, Jenny; Rudolph, Anja; Friel, Grace; Moysich, Kirsten B; Odunsi, Kunle; Sucheston-Campbell, Lara; Lurie, Galina; Goodman, Marc T; Carney, Michael E; Thompson, Pamela J; Runnebaum, Ingo B; Dürst, Matthias; Hillemanns, Peter; Dörk, Thilo; Antonenkova, Natalia; Bogdanova, Natalia; Leminen, Arto; Nevanlinna, Heli; Pelttari, Liisa M; Butzow, Ralf; Bunker, Clareann H; Modugno, Francesmary; Edwards, Robert P; Ness, Roberta B; du Bois, Andreas; Heitz, Florian; Schwaab, Ira; Harter, Philipp; Karlan, Beth Y; Walsh, Christine; Lester, Jenny; Jensen, Allan; Kjær, Susanne K; Høgdall, Claus K; Høgdall, Estrid; Lundvall, Lene; Sellers, Thomas A; Fridley, Brooke L; Goode, Ellen L; Cunningham, Julie M; Vierkant, Robert A; Giles, Graham G; Baglietto, Laura; Severi, Gianluca; Southey, Melissa C; Liang, Dong; Wu, Xifeng; Lu, Karen; Hildebrandt, Michelle A T; Levine, Douglas A; Bisogna, Maria; Schildkraut, Joellen M; Iversen, Edwin S; Weber, Rachel Palmieri; Berchuck, Andrew; Cramer, Daniel W; Terry, Kathryn L; Poole, Elizabeth M; Tworoger, Shelley S; Bandera, Elisa V; Chandran, Urmila; Orlow, Irene; Olson, Sara H; Wik, Elisabeth; Salvesen, Helga B; Bjorge, Line; Halle, Mari K; van Altena, Anne M; Aben, Katja K H; Kiemeney, Lambertus A; Massuger, Leon F A G; Pejovic, Tanja; Bean, Yukie T; Cybulski, Cezary; Gronwald, Jacek; Lubinski, Jan; Wentzensen, Nicolas; Brinton, Louise A; Lissowska, Jolanta; Garcia-Closas, Montserrat; Dicks, Ed; Dennis, Joe; Easton, Douglas F; Song, Honglin; Tyrer, Jonathan P; Pharoah, Paul D P; Eccles, Diana; Campbell, Ian G; Whittemore, Alice S; McGuire, Valerie; Sieh, Weiva; Rothstein, Joseph H; Flanagan, James M; Paul, James; Brown, Robert; Phelan, Catherine M; Risch, Harvey A; McLaughlin, John R; Narod, Steven A; Ziogas, Argyrios; Anton-Culver, Hoda; Gentry-Maharaj, Aleksandra; Menon, Usha; Gayther, Simon A; Ramus, Susan J; Wu, Anna H; Pearce, Celeste L; Pike, Malcolm C; Dansonka-Mieszkowska, Agnieszka; Rzepecka, Iwona K; Szafron, Lukasz M; Kupryjanczyk, Jolanta; Cook, Linda S; Le, Nhu D; Brooks-Wilson, Angela

2014-05-01

301

European Training Foundation  

NSDL National Science Digital Library

Working in conjunction with a host of other inter-governmental agencies, the European Training Foundation (ETF) is committed to "developing a range of quality of education and training systems" across Europe and into Asia. First-time visitors to the site will want to take a look at their "About the ETF" area to learn more about their mission, and then proceed to the "Themes" area, which contains basic information about their work in such areas as adult learning and online education. As might be expected from such an organization, their publications area is a real treasure-trove for policy analysts and others, as it contains works on "best practices" and overviews of educational systems throughout the region. In keeping with the strong emphasis place on vocational education, the site also contains a number of related events and conferences that will be of great interest as well.

302

Quantification of allele-specific expression of a gene encoding strawberry polygalacturonase-inhibiting protein (PGIP) using Pyrosequencing((TM))  

Microsoft Academic Search

Recent studies indicate that allele-specific differences in gene expression are a common phenomenon. The extent to which differential allelic expression exists might be underestimated, due to the limited accuracy of the methods used so far. To demonstrate allele-specific expression, we investigated the transcript abundance of six individual, highly homologous alleles of a polygalacturonase-inhibiting protein gene (FaPGIP) from octoploid strawberry (Fragaria

J. G. Schaart; L. Mehli; H. J. Schouten

2005-01-01

303

HLA-DRB1*13:01 allele in the genetic susceptibility to colorectal carcinoma.  

PubMed

Increasing evidence suggests that HLA-DRB1 alleles reduce or increase the risk of developing ulcerative colitis-associated colorectal carcinoma (CRC) tumors. However, the role of HLA-DRB1 locus on the susceptibility to develop CRC tumor, in the absence of a history of inflammatory bowel diseases (IBDs), is unclear. The aim of our study was to determine whether HLA-DRB1 alleles are associated with IBD-independent CRC tumor. HLA-DRB1 allele polymorphisms were identified by sequence-based typing method in 53 CRC patients and 57 sex- and age-matched healthy Caucasian controls. Pearson's chi-squared analysis with Yate's correction or Fisher's exact test with Bonferroni's correction, as appropriate, were used to compare the allele frequency (AF) differences of HLA-DRB1 in patients and controls. A total of 29 HLA-DRB1 alleles were recognized. A detailed study of these alleles allowed to identify DRB1*13:01 and DRB1*11:01 alleles that were significantly associated with an increased and reduced risk to develop CRC tumor, respectively. AF of DRB1*13:01, in CRC patients, was significantly higher than that of healthy controls, even following Bonferroni's correction (p?=?0.029). In contrast, the presence of the DRB1*11:01 allele was negatively associated with CRC tumor as evidenced by the significantly lower AF in CRC patients than that of healthy controls (p?=?0.005). However, following Bonferroni's correction, the AF of DRB*11:01 lost its statistical significance. These results suggest that HLA-DRB1*13:01 allele could be a potential marker for predicting genetic susceptibility to CRC tumor. In contrast, the protective role of DRB1*11:01 remains unclear. PMID:25346274

Aureli, Anna; Canossi, Angelica; Del Beato, Tiziana; Franceschilli, Luana; Buonomo, Oreste; Papola, Franco; De Sanctis, Flavio; Lanzilli, Giulia; Sileri, Pierpaolo; Coppola, Andrea; Caratelli, Sara; Arriga, Roberto; Orlandi, Augusto; Lauro, Davide; Rossi, Piero; Sconocchia, Giuseppe

2014-10-23

304

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression.  

PubMed

A complex interplay between transcription factors (TFs) and the genome regulates transcription. However, connecting variation in genome sequence with variation in TF binding and gene expression is challenging due to environmental differences between individuals and cell types. To address this problem, we measured genome-wide differential allelic occupancy of 24 TFs and EP300 in a human lymphoblastoid cell line GM12878. Overall, 5% of human TF binding sites have an allelic imbalance in occupancy. At many sites, TFs clustered in TF-binding hubs on the same homolog in especially open chromatin. While genetic variation in core TF binding motifs generally resulted in large allelic differences in TF occupancy, most allelic differences in occupancy were subtle and associated with disruption of weak or noncanonical motifs. We also measured genome-wide differential allelic expression of genes with and without heterozygous exonic variants in the same cells. We found that genes with differential allelic expression were overall less expressed both in GM12878 cells and in unrelated human cell lines. Comparing TF occupancy with expression, we found strong association between allelic occupancy and expression within 100 bp of transcription start sites (TSSs), and weak association up to 100 kb from TSSs. Sites of differential allelic occupancy were significantly enriched for variants associated with disease, particularly autoimmune disease, suggesting that allelic differences in TF occupancy give functional insights into intergenic variants associated with disease. Our results have the potential to increase the power and interpretability of association studies by targeting functional intergenic variants in addition to protein coding sequences. PMID:22300769

Reddy, Timothy E; Gertz, Jason; Pauli, Florencia; Kucera, Katerina S; Varley, Katherine E; Newberry, Kimberly M; Marinov, Georgi K; Mortazavi, Ali; Williams, Brian A; Song, Lingyun; Crawford, Gregory E; Wold, Barbara; Willard, Huntington F; Myers, Richard M

2012-05-01

305

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression  

PubMed Central

A complex interplay between transcription factors (TFs) and the genome regulates transcription. However, connecting variation in genome sequence with variation in TF binding and gene expression is challenging due to environmental differences between individuals and cell types. To address this problem, we measured genome-wide differential allelic occupancy of 24 TFs and EP300 in a human lymphoblastoid cell line GM12878. Overall, 5% of human TF binding sites have an allelic imbalance in occupancy. At many sites, TFs clustered in TF-binding hubs on the same homolog in especially open chromatin. While genetic variation in core TF binding motifs generally resulted in large allelic differences in TF occupancy, most allelic differences in occupancy were subtle and associated with disruption of weak or noncanonical motifs. We also measured genome-wide differential allelic expression of genes with and without heterozygous exonic variants in the same cells. We found that genes with differential allelic expression were overall less expressed both in GM12878 cells and in unrelated human cell lines. Comparing TF occupancy with expression, we found strong association between allelic occupancy and expression within 100 bp of transcription start sites (TSSs), and weak association up to 100 kb from TSSs. Sites of differential allelic occupancy were significantly enriched for variants associated with disease, particularly autoimmune disease, suggesting that allelic differences in TF occupancy give functional insights into intergenic variants associated with disease. Our results have the potential to increase the power and interpretability of association studies by targeting functional intergenic variants in addition to protein coding sequences. PMID:22300769

Reddy, Timothy E.; Gertz, Jason; Pauli, Florencia; Kucera, Katerina S.; Varley, Katherine E.; Newberry, Kimberly M.; Marinov, Georgi K.; Mortazavi, Ali; Williams, Brian A.; Song, Lingyun; Crawford, Gregory E.; Wold, Barbara; Willard, Huntington F.; Myers, Richard M.

2012-01-01

306

Amyloid mediates the association of apolipoprotein E e4 allele to cognitive function in older people  

PubMed Central

Background: The neurobiological changes underlying the association of the apolipoprotein E (APOE) e4 allele with level of cognition are poorly understood. Objective: To test the hypothesis that amyloid load can account for (mediate) the association of the APOE e4 allele with level of cognition assessed proximate to death. Methods: There were 44 subjects with clinically diagnosed Alzheimer's disease and 50 without dementia, who had participated in the Religious Orders Study. They underwent determination of APOE allele status, had comprehensive cognitive testing in the last year of life, and brain autopsy at death. The percentage area of cortex occupied by amyloid beta and the density of tau positive neurofibrillary tangles were quantified from six brain regions and averaged to yield summary measures of amyloid load and neurofibrillary tangles. Multiple regression analyses were used to examine whether amyloid load could account for the effect of allele status on level of cognition, controlling for age, sex, and education. Results: Possession of at least one APOE e4 allele was associated with lower level of cognitive function proximate to death (p = 0.04). The effect of the e4 allele was reduced by nearly 60% and was no longer significant after controlling for the effect of amyloid load, whereas there was a robust inverse association between amyloid and cognition (p = 0.001). Because prior work had suggested that neurofibrillary tangles could account for the association of amyloid on cognition, we next examined whether amyloid could account for the effect of allele status on tangles. In a series of regression analyses, e4 was associated with density of tangles (p = 0.002), but the effect of the e4 allele was reduced by more than 50% and was no longer significant after controlling for the effect of amyloid load. Conclusion: These findings are consistent with a sequence of events whereby the e4 allele works through amyloid deposition and subsequent tangle formation to cause cognitive impairment. PMID:16107349

Bennett, D; Schneider, J; Wilson, R; Bienias, J; Berry-Kravis, E; Arnold, S

2005-01-01

307

Polarisation of Major Histocompatibility Complex II Host Genotype with Pathogenesis of European Brown Hare Syndrome Virus  

PubMed Central

A study was conducted in order to determine the occurrence of European Brown Hare Syndrome virus (EBHSV) in Denmark and possible relation between disease pathogenesis and Major Histocompatibility Complex (MHC) host genotype. Liver samples were examined from 170 brown hares (hunted, found sick or dead), collected between 2004 and 2009. Macroscopical and histopathological findings consistent with EBHS were detected in 24 (14.1%) hares; 35 (20.6%) had liver lesions not typical of the syndrome, 50 (29.4%) had lesions in other tissues and 61 (35.9%) had no lesions. Sixty five (38.2%) of 170 samples were found to be EBHSV-positive (RT-PCR, VP60 gene). In order to investigate associations between viral pathogenesis and host genotype, variation within the exon 2 DQA gene of MHC was assessed. DQA exon 2 analysis revealed the occurrence of seven different alleles in Denmark. Consistent with other populations examined so far in Europe, observed heterozygosity of DQA (Ho?=?0.1180) was lower than expected (He?=?0.5835). The overall variation for both nucleotide and amino acid differences (2.9% and 14.9%, respectively) were lower in Denmark than those assessed in other European countries (8.3% and 16.9%, respectively). Within the peptide binding region codons the number of nonsynonymous substitutions (dN) was much higher than synonymous substitutions (dS), which would be expected for MHC alleles under balancing selection. Allele frequencies did not significantly differ between EBHSV-positive and -negative hares. However, allele Leeu-DQA*30 was detected in significantly higher (P?=?0.000006) frequency among the positive hares found dead with severe histopathological lesions than among those found sick or apparently healthy. In contrast, the latter group was characterized by a higher frequency of the allele Leeu-DQA*14 as well as the proportion of heterozygous individuals (P?=?0.000006 and P?=?0.027). These data reveal a polarisation between EBHSV pathogenesis and MHC class II genotype within the European brown hare in Denmark. PMID:24069299

Iacovakis, Christos; Mamuris, Zissis; Moutou, Katerina A.; Touloudi, Antonia; Hammer, Anne Sofie; Valiakos, George; Giannoulis, Themis; Stamatis, Costas; Spyrou, Vassiliki; Athanasiou, Labrini V.; Kantere, Maria; Asferg, Tommy; Giannakopoulos, Alexios; Salomonsen, Charlotte M.; Bogdanos, Dimitrios; Birtsas, Periklis; Petrovska, Liljana; Hannant, Duncan; Billinis, Charalambos

2013-01-01

308

Clarifying the Relationship between Average Excesses and Average Effects of Allele Substitutions  

PubMed Central

Fisher’s concepts of average effects and average excesses are at the core of the quantitative genetics theory. Their meaning and relationship have regularly been discussed and clarified. Here we develop a generalized set of one locus two-allele orthogonal contrasts for average excesses and average effects, based on the concept of the effective gene content of alleles. Our developments help understand the average excesses of alleles for the biallelic case. We dissect how average excesses relate to the average effects and to the decomposition of the genetic variance. PMID:22509178

Álvarez-Castro, José M.; Yang, Rong-Cai

2012-01-01

309

Distribution of self-incompatibility alleles and breeding structure of open-pollinated cultivars of Brussels sprouts  

Microsoft Academic Search

Nineteen different S alleles were found in 488 plants representing 16 cultivars of Brussels sprouts. Twelve of these S alleles have previously been found in kale, and 7 are known only from Brussels sprouts. The number of S alleles per cultivar varied from 4 to 13, but for most cultivars the number fell in the range 7–10. Relatively unselected cultivars

D J Ockendon

1974-01-01

310

PCSK9 polymorphism in a Tunisian cohort: Identification of a new allele, L8, and association of allele L10 with reduced coronary heart disease risk.  

PubMed

The c.61_63dupCTG (L10) allele of rs72555377 polymorphism in PCSK9 has been reported to be associated with low-density lipoprotein-cholesterol (LDL-C) levels and with a decreased risk of coronary artery disease (CAD). We investigated the effect of two known alleles for rs72555377, L10 and L11, on the risk of CAD in a Tunisian cohort (218 patients diagnosed by angiography and 125 control subjects). Two subgroups of patients were defined by their level of stenosis: ?50% for CAD and <50% for no-CAD. The genotypes were obtained by the size measurement of fluorescent-labeled PCR products. We identified a novel allele for the rs72555377 polymorphism: an in-frame deletion, c.61_63delCTG (L8). The frequency of the L10 allele was significantly higher in the no-CAD subgroup than in the CAD subgroup (0.210 vs 0.114, p = 0.045), and than in the subgroup of CAD patients presenting a stenosis ?50% in two or three major coronary arteries (0.210 vs 0.125, p = 0.028). Multiple regression analysis showed that the L10 allele was significantly associated with a reduced risk of CAD (p = 0.049, OR = 0.51[0.26-1.00]), and with its reduced severity (p = 0.045, OR = 0.44[0.20-0.98]). The L10 allele is associated with a reduced risk and severity of CAD, seemingly independently of its LDL-lowering effect, suggesting a direct effect of PCSK9 on atherogenesis. PMID:25239117

Slimani, Afef; Hrira, Mohamed Yahia; Najah, Mohamed; Jomaa, Walid; Maatouk, Faouzi; Hamda, Khaldoun Ben; Abifadel, Marianne; Rabès, Jean-Pierre; Boileau, Catherine; Rouis, Mustapha; Slimane, Mohamed Naceur; Varret, Mathilde

2014-09-18

311

A Novel Simple Method for Determining CYP2D6 Gene Copy Number and Identifying Allele(s) with Duplication/Multiplication  

PubMed Central

Background Cytochrome P450 2D6 (CYP2D6) gene duplication and multiplication can result in ultrarapid drug metabolism and therapeutic failure or excessive response in patients. Long range polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP) and sequencing are usually used for genotyping CYP2D6 duplication/multiplications and identification, but are labor intensive, time consuming, and costly. Methods We developed a simple allele quantification-based Pyrosequencing genotyping method that facilitates CYP2D6 copy number variation (CNV) genotyping while also identifying allele-specific CYP2D6 CNV in heterozygous samples. Most routine assays do not identify the allele containing a CNV. A total of 237 clinical and Coriell DNA samples with different known CYP2D6 gene copy numbers were genotyped for CYP2D6 *2, *3, *4, *6, *10, *17, *41 polymorphisms and CNV determination. Results The CYP2D6 gene allele quantification/identification were determined simultaneously with CYP2D6*2, *3, *4, *6, *10, *17, *41 genotyping. We determined the exact CYP2D6 gene copy number, identified which allele had the duplication or multiplication, and assigned the correct phenotype and activity score for all samples. Conclusions Our method can efficiently identify the duplicated CYP2D6 allele in heterozygous samples, determine its copy number in a fraction of time compared to conventional methods and prevent incorrect ultrarapid phenotype calls. It also greatly reduces the cost, effort and time associated with CYP2D6 CNV genotyping. PMID:25625348

Langaee, Taimour; Hamadeh, Issam; Chapman, Arlene B.; Gums, John G.; Johnson, Julie A.

2015-01-01

312

Differences in the ability to suppress interferon ? production between allele A and allele B NS1 proteins from H10 influenza A viruses  

PubMed Central

Background In our previous study concerning the genetic relationship among H10 avian influenza viruses with different pathogenicity in mink (Mustela vison), we found that these differences were related to amino acid variations in the NS1 protein. In this study, we extend our previous work to further investigate the effect of the NS1 from different gene pools on type I IFN promoter activity, the production of IFN-?, as well as the expression of the IFN-? mRNA in response to poly I:C. Results Using a model system, we first demonstrated that NS1 from A/mink/Sweden/84 (H10N4) (allele A) could suppress an interferon-stimulated response element (ISRE) reporter system to about 85%. The other NS1 (allele B), from A/chicken/Germany/N/49 (H10N7), was also able to suppress the reporter system, but only to about 20%. The differences in the abilities of the two NS1s from different alleles to suppress the ISRE reporter system were clearly reflected by the protein and mRNA expressions of IFN-? as shown by ELISA and RT-PCR assays. Conclusions These studies reveal that different non-structural protein 1 (NS1) of influenza viruses, one from allele A and another from allele B, show different abilities to suppress the type I interferon ? expression. It has been hypothesised that some of the differences in the different abilities of the alleles to suppress ISRE were because of the interactions and inhibitions at later stages from the IFN receptor, such as the JAK/STAT pathway. This might reflect the additional effects of the immune evasion potential of different NS1s. PMID:21194454

2010-01-01

313

Diversity of immune genes and associated gill microbes of European plaice Pleuronectes platessa  

NASA Astrophysics Data System (ADS)

Genetic variability of marine fish species is much higher than in most other vertebrates. Nevertheless, some species with large population sizes including flatfish such as European plaice Pleuronectes platessa show signs of population collapse and inbreeding. Taking plaice as a flagship example for fisheries-induced genetic changes also affecting the Wadden Sea, we determined the amount of genetic variability at antigen-presenting genes of the Major Histocompatibility Complex (MHC) and its potential interaction with the microbiota associated to gill tissue using a next-generation parallel tag sequencing approach. Genetic variation at MHC class IIB genes was extremely large, with 97 alleles found in 40 fish from different age cohorts. Although a strong signal of positive selection was present (dN/dS = 4.01) and we found significantly higher allelic diversity in 0+ fish than in older age classes, the amount of genetic variation maintained within the population may not have exceeded neutral expectations derived from mitochondrial markers. Associated microbes revealed significant spatiotemporal structure with 0+ fish displaying the highest microbial diversity as well as the highest diversity of potentially pathogenic genera. Overall the correlation between MHC genotypes and bacterial abundance was weak, and only few alleles significantly correlated with certain bacterial genera. These associations all conferred susceptibility (i.e. presence of an allele correlated to higher number of bacteria), either suggesting age-dependent selection on common alleles or weak selection on resistance against these bacterial genera. Taken together, our data suggest that selection coefficients of balancing selection maintaining immunogenetic diversity may be relatively small in large marine populations. However, if population sizes are further reduced by overharvesting, the response to increasing balancing selection coefficients will be largely unpredictable and may also negatively influence the adaptive potential of populations.

Wegner, K. Mathias; Shama, Lisa N. S.; Kellnreitner, Florian; Pockberger, Moritz

2012-08-01

314

Null alleles of ABCG2 encoding the breast cancer resistance protein define the new blood group system Junior  

PubMed Central

The breast cancer resistance protein, also known as ABCG2, is one of the most studied ATP-binding cassette (ABC) transporters, due to its ability to confer multidrug resistance1,2. The lack of information on the physiological roles of ABCG2 in humans severely limits cancer chemotherapeutic approaches targeting this transporter. We report here that ABCG2 comprises the molecular basis of a new blood group system (Junior, Jr), and that individuals of the Jr(a?) blood type have inherited two null alleles of ABCG2. We thus identified 5 frameshift and 3 nonsense mutations in ABCG2. Furthermore, we show that the prevalence of the Jr(a?) blood type in the Japanese and European Gypsy populations is related to the mutations p.Q126X and p.R236X, respectively. The identification of ABCG2?/? (Jr(a?)) individuals, who appear phenotypically normal, is an essential step towards targeting ABCG2 in cancer, but also understanding the physiological and pharmacological roles of this promiscuous transporter in humans. PMID:22246505

Saison, Carole; Helias, Virginie; Ballif, Bryan A.; Peyrard, Thierry; Puy, Hervé; Miyazaki, Toru; Perrot, Sébastien; Vayssier-Taussat, Muriel; Waldner, Mauro; Pennec, Pierre-Yves Le; Cartron, Jean-Pierre; Arnaud, Lionel

2013-01-01

315

The ADA*2 allele of the adenosine deaminase gene (20q13.11) and recurrent spontaneous abortions: an age-dependent association  

PubMed Central

OBJECTIVE: Adenosine deaminase acts on adenosine and deoxyadenosine metabolism and modulates the immune response. The adenosine deaminase G22A polymorphism (20q.11.33) influences the level of adenosine deaminase enzyme expression, which seems to play a key role in maintaining pregnancy. The adenosine deaminase 2 phenotype has been associated with a protective effect against recurrent spontaneous abortions in European Caucasian women. The aim of this study was to investigate whether the G22A polymorphism of the adenosine deaminase gene is associated with recurrent spontaneous abortions in Brazilian women. METHODS: A total of 311 women were recruited to form two groups: G1, with a history of recurrent spontaneous abortions (N?=?129), and G2, without a history of abortions (N?=?182). Genomic DNA was extracted from peripheral blood with a commercial kit and PCR-RFLP analysis was used to identify the G22A genetic polymorphism. Fisher's exact test and odds ratio values were used to compare the proportions of adenosine deaminase genotypes and alleles between women with and without a history of recurrent spontaneous abortion (p<0.05). The differences between mean values for categorical data were calculated using unpaired t tests. The Hardy-Weinberg equilibrium was assessed with a chi-square test. RESULTS: Statistically significant differences were identified for the frequencies of adenosine deaminase genotypes and alleles between the G1 and G2 groups when adjusted for maternal age. CONCLUSIONS: The results suggest that the adenosine deaminase *2 allele is associated with a low risk for recurrent spontaneous abortions, but this association is dependent on older age. PMID:22086524

Nunes, Daniela Prudente Teixeira; Spegiorin, Lígia Cosentino Junqueira Franco; de Mattos, Cinara Cássia Brandão; Oliani, Antonio Helio; Vaz-Oliani, Denise Cristina Mós; de Mattos, Luiz Carlos

2011-01-01

316

Characterization of microsatellite loci in the European pond turtle Emys orbicularis.  

PubMed

A set of eight highly polymorphic microsatellite markers was isolated and characterized from a genomic library enriched for dinucleotide repeats in the European pond turtle, Emys orbicularis. The markers were tested for polymorphism in a total of 33 turtles sampled in two natural ponds in the nature reserve of Kerkini, northern Greece. Number of alleles varied from 10 to 18, and expected heterozygosity ranged between 0.738 and 0.921. This novel set of loci will be particularly useful to assess fine-scale population structure and for parentage analysis in E. orbicularis. PMID:21564599

Ciofi, Claudio; Tzika, Athanasia C; Natali, Chiara; Chelazzi, Guido; Naziridis, Theodorus; Milinkovitch, Michel C

2009-01-01

317

Pyrophosphorylases in potato. V. Allelic polymorphism of UDP-glucose pyrophosphorylase in potato cultivars and its association with tuber resistance to sweetening in the cold.  

PubMed

UDP-glucose pyrophosphorylase (UGPase) was cloned from six American and nine European potato (Solanum tuberosum L.) cultivars. Restriction mapping of the different UGPase-cDNAs with BamHI, HindIII, and EcoRI revealed that at least two mRNA populations were present in most cultivars. Staining for UGPase activity in nondenaturing gels of proteins extracted from developing potato tubers yielded two major isozymes that were highly active and appeared to be dimeric in nature. Following sodium dodecyl sulfate-polyacrylamide gel electrophoresis, all isozymes were disassociated into a single subunit with a molecular mass of 53 kD. Since UGPase has been demonstrated to be a single-copy gene in the haploid genome of potato (A.Y. Borovkov, P.E. McClean, J.R. Sowokinos, S.H. Ruud, G.A. Secor [1995] J Plant Physiol 147: 644-652), there must be allelic differences at the UGPase locus (chromosome 11). The two alleles, designated ugpA and ugpB, were identified by the absence and presence of a BamHI site, respectively. The relative band intensities of the two cDNA populations following polymerase chain reaction amplification and agarose gel electrophoresis were related to a potato cultivar's ability to resist sweetening when exposed to cold temperatures. PMID:9046597

Sowokinos, J R; Thomas, C; Burrell, M M

1997-02-01

318

Identification of low penetrance alleles for lung cancer: The GEnetic Lung CAncer Predisposition Study (GELCAPS)  

E-print Network

Abstract Background Part of the inherited risk to lung cancer is likely to include common, low risk alleles. The identification of this class of susceptibility is contingent on association-based analyses. We established GEnetic Lung CAncer...

Eisen, Tim; Matakidou, Athena; Consortium, Gelcaps; Houlston, Richard

2008-08-20

319

Evidence for a genetic association between alleles of monoamine oxidase A gene and bipolar affective disorder  

SciTech Connect

We present evidence of a genetic association between bipolar disorder and alleles at 3 monoamine oxidase A (MAOA) markers, but not with alleles of a monoamine oxidase B (MAOB) polymorphism. The 3 MAOA markers, including one associated with low MAOA activity, show strong allelic association with each other but surprisingly not with MAOB. Our results are significantly only for females, though the number of males in our sample is too small to draw any definite conclusions. Our data is consistent with recent reports of reduced MAOA activity in patients with abnormal behavioral phenotypes. The strength of the association is weak, but significant, which suggests that alleles at the MAOA locus contribute to susceptibility to bipolar disorder rather than being a major determinant. 58 refs., 1 fig., 3 tabs.

Lim, L.C.C.; Sham, P.; Castle, D. [Institute of Psychiatry, London (United Kingdom)] [and others

1995-08-14

320

Genomic Analysis of Parent-of-Origin Allelic Expression in Arabidopsis thaliana Seeds  

E-print Network

Differential expression of maternally and paternally inherited alleles of a gene is referred to as gene imprinting, a form of epigenetic gene regulation common to flowering plants and mammals. In plants, imprinting primarily ...

Gehring, Mary

321

Random monoallelic expression: regulating gene expression one allele at a time.  

PubMed

Monoallelic gene expression is a remarkable process in which transcription occurs from only one of two homologous alleles in a diploid cell. Interestingly, between 0.5% and 15% of autosomal genes exhibit random monoallelic gene expression, in which different cells express only one allele independently of the underlying genomic sequence, in a cell type-specific manner. Recently, genome-wide studies have increased our understanding of the cell type-specific incidence of random monoallelic gene expression, and how the imbalance in allelic expression is distinguished within the cell and potentially maintained across cell generations. Monoallelic gene expression is likely generated through stochastic independent regulation of the two alleles upon differentiation, and has varied implications for the cell and organism, in particular with respect to disease. PMID:24780084

Eckersley-Maslin, Mélanie A; Spector, David L

2014-06-01

322

Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars  

PubMed Central

Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium. PMID:25368628

Shahin, Arwa; Smulders, Marinus J. M.; van Tuyl, Jaap M.; Arens, Paul; Bakker, Freek T.

2014-01-01

323

Class II MHC alleles in rheumatoid arthritis in Tamilnadu, India: is there an association?  

PubMed

Rheumatoid arthritis (RA) was reported to be associated with class II MHC alleles in different ethnic populations. A similar study was undertaken to determine the association of class II MHC with RA patients of Tamilnadu (Tamil-speaking Hindus), India. Thirty patients with RA and 39 healthy controls were included. Polymorphic second exons of the DRB1, DQA1, and DQB1 genes were amplified and subjected to SSOP typing. No allele was found to be significantly associated with RA. However DRB1*11 (P = 0.01) and DQB1*0302 (P = 0.02) were significantly associated with rheumatoid factor-positive RA patients. (All the DRB1*11-positive RA patients had either *04 or *10 allele as their second allele. This study is first of its kind in this population. PMID:12021152

Parthiban, M; Madhavan, Radha; Porkodi, R; Rajendran, C Panchapakesa; Zake, L; Sanjeevi, C B; Chandrasekaran, A N

2002-04-01

324

SNP-specific array-based allele-specific expression analysis  

PubMed Central

We have developed an optimized array-based approach for customizable allele-specific gene expression (ASE) analysis. The central features of the approach are the ability to select SNPs at will for detection, and the absence of need to PCR amplify the target. A surprisingly long probe length (39–49 nt) was needed for allelic discrimination. Reconstitution experiments demonstrate linearity of ASE over a broad range. Using this approach, we have discovered at least two novel imprinted genes, NLRP2, which encodes a member of the inflammasome, and OSBPL1A, which encodes a presumed oxysterol-binding protein, were both preferentially expressed from the maternal allele. In contrast, ERAP2, which encodes an aminopeptidase, did not show preferential parent-of-origin expression, but rather, cis-acting nonimprinted differential allelic control. The approach is scalable to the whole genome and can be used for discovery of functional epigenetic modifications in patient samples. PMID:18369178

Bjornsson, Hans T.; Albert, Thomas J.; Ladd-Acosta, Christine M.; Green, Roland D.; Rongione, Michael A.; Middle, Christina M.; Irizarry, Rafael A.; Broman, Karl W.; Feinberg, Andrew P.

2008-01-01

325

Balancing Selection at a Frog Antimicrobial Peptide Locus: Fluctuating Immune Effector Alleles?  

E-print Network

Balancing Selection at a Frog Antimicrobial Peptide Locus: Fluctuating Immune Effector Alleles such as antimicrobial peptides (AMPs). We describe genetic diversity at a brevinin-1 AMP locus in three species

Blouin, Michael S.

326

Phenotypic instability of Arabidopsis alleles affecting a disease Resistance gene cluster  

PubMed Central

Background Three mutations in Arabidopsis thaliana strain Columbia – cpr1, snc1, and bal – map to the RPP5 locus, which contains a cluster of disease Resistance genes. The similar phenotypes, gene expression patterns, and genetic interactions observed in these mutants are related to constitutive activation of pathogen defense signaling. However, these mutant alleles respond differently to various conditions. Exposure to mutagens, such as ethyl methanesulfonate (EMS) and ?-irradiation, induce high frequency phenotypic instability of the bal allele. In addition, a fraction of the bal and cpr1 alleles segregated from bal × cpr1 F1 hybrids also show signs of phenotypic instability. To gain more insight into the mechanism of phenotypic instability of the bal and cpr1 mutations, we systematically compared the behavior of these unusual alleles with that of the missense gain-of-function snc1 allele in response to DNA damage or passage through F1 hybrids. Results We found that the cpr1 allele is similar to the bal allele in its unstable behavior after EMS mutagenesis. For both the bal and cpr1 mutants, destabilization of phenotypes was observed in more than 10% of EMS-treated plants in the M1 generation. In addition, exceptions to simple Mendelian inheritance were identified in the M2 generation. Like cpr1 × bal F1 hybrids, cpr1 × snc1 F1 hybrids and bal × snc1 F1 hybrids exhibited dwarf morphology. While only dwarf F2 plants were produced from bal × snc1 F1 hybrids, about 10% wild-type F2 progeny were produced from cpr1 × snc1 F1 hybrids, as well as from cpr1 × bal hybrids. Segregation analysis suggested that the cpr1 allele in cpr1 × snc1 crosses was destabilized during the late F1 generation to early F2 generation. Conclusion With exposure to EMS or different F1 hybrid contexts, phenotypic instability is induced for the bal and cpr1 alleles, but not for the snc1 allele. Our results suggest that the RPP5 locus can adopt different metastable genetic or epigenetic states, the stability of which is highly susceptible to mutagenesis and pairing of different alleles. PMID:18410684

Yi, Hankuil; Richards, Eric J

2008-01-01

327

A human-specific allelic group of the MHC DRB1 gene in primates  

PubMed Central

Background Diversity among human leukocyte antigen (HLA) molecules has been maintained by host-pathogen coevolution over a long period of time. Reflecting this diversity, the HLA loci are the most polymorphic in the human genome. One characteristic of HLA diversity is long-term persistence of allelic lineages, which causes trans-species polymorphisms to be shared among closely related species. Modern humans have disseminated across the world after their exodus from Africa, while chimpanzees have remained in Africa since the speciation event between humans and chimpanzees. It is thought that modern humans have recently acquired resistance to novel pathogens outside Africa. In the present study, we investigated HLA alleles that could contribute to this local adaptation in humans and also studied the contribution of natural selection to human evolution by using molecular data. Results Phylogenetic analysis of HLA-DRB1 genes identified two major groups, HLA Groups A and B. Group A formed a monophyletic clade distinct from DRB1 alleles in other Catarrhini, suggesting that Group A is a human-specific allelic group. Our estimates of divergence time suggested that seven HLA-DRB1 Group A allelic lineages in humans have been maintained since before the speciation event between humans and chimpanzees, while chimpanzees possess only one DRB1 allelic lineage (Patr-DRB1*03), which is a sister group to Group A. Experimental data showed that some Group A alleles bound to peptides derived from human-specific pathogens. Of the Group A alleles, three exist at high frequencies in several local populations outside Africa. Conclusions HLA Group A alleles are likely to have been retained in human lineages for a long period of time and have not expanded since the divergence of humans and chimpanzees. On the other hand, most orthologs of HLA Group A alleles may have been lost in the chimpanzee due to differences in selective pressures. The presence of alleles with high frequency outside of Africa suggests these HLA molecules result from the local adaptations of humans. Our study helps elucidate the mechanism by which the human adaptive immune system has coevolved with pathogens over a long period of time. PMID:24928070

2014-01-01

328

Interrogation of allelic chromatin states in human cells by high-density ChIP-genotyping.  

PubMed

Allele-specific (AS) assessment of chromatin has the potential to elucidate specific cis-regulatory mechanisms, which are predicted to underlie the majority of the known genetic associations to complex disease. However, development of chromatin landscapes at allelic resolution has been challenging since sites of variable signal strength require substantial read depths not commonly applied in sequencing based approaches. In this study, we addressed this by performing parallel analyses of input DNA and chromatin immunoprecipitates (ChIP) on high-density Illumina genotyping arrays. Allele-specificity for the histone modifications H3K4me1, H3K4me3, H3K27ac, H3K27me3, and H3K36me3 was assessed using ChIP samples generated from 14 lymphoblast and 6 fibroblast cell lines. AS-ChIP SNPs were combined into domains and validated using high-confidence ChIP-seq sites. We observed characteristic patterns of allelic-imbalance for each histone-modification around allele-specifically expressed transcripts. Notably, we found H3K4me1 to be significantly anti-correlated with allelic expression (AE) at transcription start sites, indicating H3K4me1 allelic imbalance as a marker of AE. We also found that allelic chromatin domains exhibit population and cell-type specificity as well as heritability within trios. Finally, we observed that a subset of allelic chromatin domains is regulated by DNase I-sensitive quantitative trait loci and that these domains are significantly enriched for genome-wide association studies hits, with autoimmune disease associated SNPs specifically enriched in lymphoblasts. This study provides the first genome-wide maps of allelic-imbalance for five histone marks. Our results provide new insights into the role of chromatin in cis-regulation and highlight the need for high-depth sequencing in ChIP-seq studies along with the need to improve allele-specificity of ChIP-enrichment. PMID:25055051

Light, Nicholas; Adoue, Véronique; Ge, Bing; Chen, Shu-Huang; Kwan, Tony; Pastinen, Tomi

2014-09-01

329

No evidence for allelic association between bipolar disorder and monoamine oxidase A gene polymorphisms  

SciTech Connect

We have tested the hypothesis that DNA markers in the MAOA gene show allelic association with bipolar affective disorder. Eighty-four unrelated Caucasian patients with DSM III-R bipolar disorder and 84 Caucasian controls were typed for three markers in MAOA: a dinucleotide repeat in intron 2, a VNTR in intron 1, and an Fnu4HI RFLP in exon 8. No evidence for allelic association was observed between any of the markers and bipolar disorder. 9 refs., 1 tab.

Craddock, N.; Daniels, J.; Roberts, E. [Univ. of Wales, College of Medicine, Cardiff (United Kingdom)] [and others

1995-08-14

330

Two different primate species express an identical functional MHC class I allele  

Microsoft Academic Search

The products of the highly polymorphic and variable major histocompatibility complex (MHC) class I loci play a crucial role\\u000a in host defenses against infectious disease. While similar alleles have been found in closely related species, sharing of\\u000a a functional MHC class I allele between two species has never been reported. Here we show that an identical functional MHC\\u000a class I

David T. Evans; Marian S. Piekarczyk; Luis Cadavid; Virginia S. Hinshaw; D. I. Watkins

1998-01-01

331

Breast cancer susceptibility alleles and ovarian cancer risk in 2 study populations.  

PubMed

Recent genome-wide scans identified several novel breast cancer risk alleles, including variants of the FGFR2, MAP3K1 and LSP1 genes, and a study of associations between these alleles and characteristics of breast cancer patients reported a borderline significant correlation between the number of FGFR2 minor alleles and family history of breast/ovarian cancer. Given these results and similarities in the etiology of breast and ovarian cancer, we examined the association between 7 novel breast cancer susceptibility alleles and epithelial ovarian cancer risk in 2 large study populations. Our analysis included 1,173 cases and 1,201 controls from a New England-based Case-Control study and 210 cases and 603 controls from the prospective Nurses' Health Study. We used logistic regression to estimate the odds ratio (OR) for individuals heterozygous or homozygous for the minor allele at each locus, compared to individuals with the wild-type genotype. We examined the associations separately in each population and, after testing for heterogeneity in the results, pooled the estimates using a random effects model. There was no clear association between these polymorphisms and ovarian cancer risk in either population. The pooled per allele OR for FGFR2 was 1.06 (95% confidence interval (CI)=0.95-1.18) for rs1219648 and 1.04 (95% CI=0.93-1.15) for rs2981582. We had more than 80% power to detect a log-additive OR of 1.16-1.18 per allele at the alpha=0.05 level in the pooled analysis. Our results do not provide strong support for an association between these breast cancer susceptibility alleles and epithelial ovarian cancer risk. PMID:18973230

Gates, Margaret A; Tworoger, Shelley S; Terry, Kathryn L; De Vivo, Immaculata; Hunter, David J; Hankinson, Susan E; Cramer, Daniel W

2009-02-01

332

The effect of Ph gene alleles on synaptonemal complex formation in Triticum aestivum × T. kotschyi hybrids  

Microsoft Academic Search

Chromosome pairing at zygotene-pachytene was studied in Triticum aestivum × T. kotschyi hybrids (2n=5x=35, genomic constitution ABDCUSv) by electron microscopy of synaptonemal complexes in spread microsporocyte nuclei. Hybrids carrying either the Ph allele or the ph allele, which differ markedly in metaphase I pairing, are both capable of greater than 90% pachytene pairing, although pairing in the Ph hybrids appeared

C. B. Gillies

1987-01-01

333

Analysis of FBN1 allele expression by dermal fibroblasts from Marfan syndrome patients  

SciTech Connect

Screening for mutations in the FBN1 cDNA from Marfan patient cell strains has detected mutations in only 10-15% of patients. In an attempt to explain this poor detection rate, we examined FBN1 allele expression and fibrillin synthesis by 26 cell strains from Marfan patients. DNA from the patients and 10 controls was assessed for the presence of a polymorphic Rsa I restriction site in the 3{prime} untranslated region of the FBN1 gene. Twelve of 26 patient and 5 of 10 control DNAs were heterozygous. Fibroblast RNA from the heterozygous cell strains was reverse-transcribed and subsequently PCR amplified using a [{sup 32}P]-labelled primer, digested with Rsa I and analyzed. Although 3 samples showed no transcript from one allele by ethidium bromide staining, a Betagen scanner detected low levels (10-15%) of that allele. In addition, there was unequal expression of the two alleles in three other patients; for example, only 30% expression from one allele. The remaining patients and the controls had equal expression of each allele. Fibrillin protein synthesis by fibroblasts from these heterozygous patients was also examined. After a 30 minute pulse with [{sup 35}S]-cysteine, cell lysates were collected and proteins analyzed by SDS-PAGE. The amount of fibrillin produced relative to a reference protein was determined using a Betagen scanner. Fibrillin protein synthesis was reduced in 2 of the 3 patients with very low RNA production from one of the FBN1 alleles. All other Marfan and control cell strains showed normal amounts of fibrillin synthesized. The low expression levels from one allele may contribute to, but not fully account for, the low detection rate of FBN1 mutations. Interestingly, protein synthesis levels were not affected in 4 of 6 cell strains demonstrating low levels of RNA expression.

Putman, E.A.; Cao, S.N.; Milewicz, D.M. [Univ. of Texas Medical School, Houston, TX (United States)

1994-09-01

334

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

PubMed

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

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

2013-04-01

335

A novel allelic variant of the human serotonin transporter gene regulatory polymorphism  

Microsoft Academic Search

Allelic variation of the human serotonin transporter gene (SLC6A4) has recently been shown to modulate anxiety-related traits. A tandemly repeated sequence in close proximity to the promoter was found to be represented by a long (L) and short (S) variant, differentially modulating gene expression in vitro. Specifically, allele S, generated by a deletion of 44 bp involving repeats VI to

S. J. W. Delbrück; B. Wendel; I. Grunewald; T. Sander; D. Morris-Rosendahl; M. A. Crocq; W. H. Berrettini; M. R. Hoehe

1997-01-01

336

Development of a standard set of microsatellite reference alleles for identification of grape cultivars  

Microsoft Academic Search

In order to investigate the comparability of microsatellite profiles obtained in different laboratories, ten partners in seven countries analyzed 46 grape cultivars at six loci (VVMD5, VVMD7, VVMD27, VVS2, VrZAG62, and VrZAG79). No effort was made to standardize equipment or protocols. Although some partners obtained very similar results, in other cases different absolute allele sizes and, sometimes, different relative allele

P. This; A. Jung; P. Boccacci; J. Borrego; R. Botta; L. Costantini; M. Crespan; G. S. Dangl; C. Eisenheld; F. Ferreira-Monteiro; S. Grando; J. Ibáñez; T. Lacombe; V. Laucou; R. Magalhães; C. P. Meredith; N. Milani; E. Peterlunger; F. Regner; L. Zulini; E. Maul

2004-01-01

337

CONTROL OF ANTHOCYANIN SYNTHESIS IN PETUNIA HYBRIDA BY MULTIPLE ALLELIC SERIES OF THE GENES  

Microsoft Academic Search

A mutable allele of the An1 locus in Petunia hybrida has given rise to a multiple series of stable derivative alleles. Anthocyanin concentration in mature flowers of these mutants (anI+lP\\/anl) decreases from the wild-type red to the recessive white in a continuous series. Anthocyanin composition changes reg- ularly: the ratio of peonidin to cyanidin is 3.5 for an anl+'+\\/anl and

ANTON G. M. GERATS; ELIANE FARCY; ANDRE SCHRAM

338

Geographic distribution of vacA allelic types of Helicobacter pylori  

Microsoft Academic Search

Background & Aims: Distinct allelic types of Helicobacter pylori vacA have been defined. The geographic distribution of vacA alleles and cagA was assessed in this study. Methods: A total of 735 cultures from patients in 24 countries were analyzed by polymerase chain reaction and reverse hybridization on a line probe assay (LiPA). Results: In 124 (16.9%) of the 735 cultures,

Céu Figueiredo; Francis Mégraud; Salvador Pena; Peter Midolo; Dulciene Maria De Magalhães Queiroz; Fátima Carneiro; Bart Vanderborght; Maria Da Glória F. Pegado; Ricardo Sanna; Wink De Boer; Peter M. Schneeberger; Pelayo Correa; Enders K. W. Ng; John Atherton; Martin J. Blaser; Wim G. V. Quint

1999-01-01

339

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

Microsoft Academic Search

At intron 40 of the von Willebrand factor (vWF) gene, two GATA-repeat polymorphic sites exist that are physically separated by 212 bp. At the first site (vWF1 locus), seven segregating repeat alleles were observed in a Brazilian Caucasian population, and at the second (vWF2 locus) there were eight alleles, detected through PCR amplifications of this DNA region. Haplotype analysis of

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

1994-01-01

340

BGMUT Database of Allelic Variants of Genes Encoding Human Blood Group Antigens  

PubMed Central

Summary The Blood group antigen Gene MUTation (BGMUT) database documents variations in genes of human blood group systems. In March 2014, the database, accessible at www.ncbi.nlm.nih.gov/gv/mhc/xslcgi.cgi?cmd=bgmut, listed 1,545 alleles of 44 genes of 34 blood group systems. Besides allelic information, the BGMUT resource also presents comprehensive and current information on blood group systems. This review describes the database and notes its utility for the transfusion medicine and human genetics communities.

Patnaik, Santosh Kumar; Helmberg, Wolfgang; Blumenfeld, Olga O.

2014-01-01

341

Gene-Based Rare Allele Analysis Identified a Risk Gene of Alzheimer’s Disease  

PubMed Central

Alzheimer’s disease (AD) has a strong propensity to run in families. However, the known risk genes excluding APOE are not clinically useful. In various complex diseases, gene studies have targeted rare alleles for unsolved heritability. Our study aims to elucidate previously unknown risk genes for AD by targeting rare alleles. We used data from five publicly available genetic studies from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) and the database of Genotypes and Phenotypes (dbGaP). A total of 4,171 cases and 9,358 controls were included. The genotype information of rare alleles was imputed using 1,000 genomes. We performed gene-based analysis of rare alleles (minor allele frequency?3%). The genome-wide significance level was defined as meta P<1.8×10–6 (0.05/number of genes in human genome?=?0.05/28,517). ZNF628, which is located at chromosome 19q13.42, showed a genome-wide significant association with AD. The association of ZNF628 with AD was not dependent on APOE ?4. APOE and TREM2 were also significantly associated with AD, although not at genome-wide significance levels. Other genes identified by targeting common alleles could not be replicated in our gene-based rare allele analysis. We identified that rare variants in ZNF628 are associated with AD. The protein encoded by ZNF628 is known as a transcription factor. Furthermore, the associations of APOE and TREM2 with AD were highly significant, even in gene-based rare allele analysis, which implies that further deep sequencing of these genes is required in AD heritability studies. PMID:25329708

Kim, Jong Hun; Song, Pamela; Lim, Hyunsun; Lee, Jae-Hyung; Lee, Jun Hong; Park, Sun Ah

2014-01-01

342

Molecular genetics of MHC class II alleles in Chinese patients with IgA nephropathy.  

PubMed

We have studied the restriction fragment length polymorphism (RFLP) of the major histocompatibility complex (MHC) class II DQ and DR regions of 79 Chinese patients with IgA nephropathy (IgAN) and compared it with 104 normal Chinese controls. The DR and DQ alleles were confirmed by polymerase chain reaction using sequence specific primers. There was a significantly higher frequency of homozygous DQ beta 3b (DQ7) in patients with IgAN (16.4%) compared with controls (5.7%). Seventy-one IgAN patients had their renal biopsies graded according to histopathological severity: grades I, II or III. There was no statistical difference in the DR and DQ alleles among the three grades. Seventy-three patients were classified into group A with normal and stable renal function (serum creatinine < or = 150 mumol/liter) and group B with chronic renal failure (serum creatinine > 150 mumol/liter). There was a significant increase in frequency of DQA2 U (DX alpha U) allele in group B (66.9%) compared with group A (26.9%). Also, there was an increased frequency of DQ alpha 2 allele in the group A (40.4%) compared with group B (14.3%). Out of the 24 patients carrying the DQ alpha 2 allele, 17 were DQA2 U allele-negative and they all had normal renal function, suggesting that DQA2 U allele is associated with a poor prognostic factor in IgAN. The study shows that DQ alleles are probably the important genetic loci or are close markers for the disease susceptibility and prognostic index for IgAN in Chinese people. PMID:7933837

Li, P K; Poon, A S; Lai, K N

1994-07-01

343

Allelic variants of ovine prion protein gene (PRNP) in Oklahoma sheep  

Microsoft Academic Search

1,144 sheep belonging to 21 breeds and known crosses were sequence analyzed for polymorphisms in the ovine PRNP gene. Genotype and allele frequencies of polymorphisms in PRNP known to confer resistance to scrapie, a fatal neurodegenerative disease of sheep, are reported. Known polymorphisms at codons 136 (A\\/V), 154 (H\\/R) and 171 (Q\\/R\\/H\\/K) were identified. The frequency of the171R allele known

U. DeSilva; X. Guo; D. M. Kupfer; S. C. Fernando; A. T. V. Pillai; F. Z. Najar; S. So; G. Q. Fitch; B. A. Roe

2003-01-01

344

European Southern Observatory  

NSDL National Science Digital Library

The European Southern Observatory (ESO) is an intergovernmental organization comprised of 14 member countries. Its headquarters are in Germany, but they have three observatories in Chile as well. Their website is loaded with information and visitors shouldn't miss going on the "Virtual Tours", on the far right side of the homepage. The tours are of the three observatories in Chile, and offer almost 360 degree views of beautiful, yet sparse landscapes. The tour of La Silla has two particularly beautiful views, "La Silla Moonlight" and "La Silla Sunset". Visitors interested in seeing a panning of an artist's 3D rendering of the Orion Nebula must go to the "Video" link on the left hand menu on the homepage. There are over 1400 videos to choose from, so for those not into the Orion Nebula, never fear, there are plenty of other video choices. Finally, visitors must go to the "Top 100 Images" link on the right side of the homepage to see amazing and gorgeous images taken from the ESO's various observatories.

345

Genetic backgrounds of the Plasmodium falciparum chloroquine resistant transporter (pfcrt) alleles in Pakistan.  

PubMed

Chloroquine (CQ) resistance in Plasmodium falciparum has been associated with point mutations in the P. falciparum CQ resistance transporter gene (pfcrt). Previous studies have shown 4-5 independent origins for CQ resistant pfcrt alleles globally, two in South America, one each in Southeast Asia, Papua New Guinea (PNG) and Philippines. In Asia, at least two different alleles corresponding to amino acids 72-76 (CVIET and SVMNT) have been found. The CVIET allele originated in Southeast Asia and then spread to Asia and Africa as well. The SVMNT allele, originating from PNG, has been found in India. This study was undertaken to investigate the genetic background of the CQ resistant pfcrt haplotypes in Pakistan. We genotyped microsatellite markers surrounding the pfcrt gene (six different markers at -12.3, -4.8, -1, 1.5, 3.9, 18.8 kb) in 114 clinical isolates of P. falciparum collected from different regions in Pakistan. Microsatellite analysis showed a significant reduction in genetic variation among the mutant SVMNT pfcrt alleles when compared to wild type alleles. The predominant SVMNT haplotype found in this study shared the same microsatellite haplotype found in both PNG and India. Two isolates with CVIET haplotypes showed similar microsatellite background to those found in Africa and Asia. In conclusion, this study suggests that CQ resistant SVMNT haplotypes in India and Pakistan have a common ancestral origin similar to that of Papua New Guinean isolates. PMID:22138496

Rawasia, Wasiq Faraz; Sridaran, Sankar; Patel, Jaymin C; Abdallah, Joseph; Ghanchi, Najia Karim; Barnwell, John W; Escalante, Ananias A; Udhayakumar, Venkatachalam; Beg, Mohammad Asim

2012-03-01

346

Nepalese populations show no association between the distribution of malaria and protective alleles  

PubMed Central

Malaria is perhaps the most important parasitic infection and strongest known force for selection in the recent evolutionary history of the human genome. Genetically-determined resistance to malaria has been well-documented in some populations, mainly from Africa. The disease is also endemic in South Asia, the world's second most populous region, where resistance to malaria has also been observed, for example in Nepal. The biological basis of this resistance, however, remains unclear. We have therefore investigated whether known African resistance alleles also confer resistance in Asia. We typed seven single nucleotide polymorphisms (SNPs) from the genes HBB, FY, G6PD, TNFSF5, TNF, NOS2 and FCGR2A in 928 healthy individuals from Nepal. Five loci were found to be fixed for the non-resistant allele (HBB, FY, G6PD, TNFSF5 and NOS2). The remaining two (rs1800629 and rs1801274) showed the presence of the resistant allele at a frequency of 93% and 27% in TNF and FCGR2A, respectively. However, the frequencies of these alleles did not differ significantly between highland (susceptible) and lowland (resistant) populations. The observed differences in allele and genotype frequencies in Nepalese populations therefore seem to reflect demographic processes or other selective forces in the Himalayan region, rather than malaria selection pressure acting on these alleles. PMID:19461987

Caetano, Cátia P; Kraaijenbrink, Thirsa; Tuladhar, Nirmal M; van Driem, George L; de Knijff, Peter; Tyler-Smith, Chris; Carvalho-Silva, Denise R

2006-01-01

347

How Old Is the Most Recent Ancestor of Two Copies of an Allele?  

PubMed Central

An important clue to the evolutionary history of an allele is the structure of the neighboring region of the genome, which we term the genomic background of the allele. Consider two copies of the allele. How similar we expect their genomic background to be is strongly influenced by the age of their most recent common ancestor (MRCA). We apply diffusion theory, first used by Motoo Kimura as a tool for predicting the changes in allele frequencies over time and developed by him in many articles in this journal, to prove a variety of new results on the age of the MRCA under the simplest demographic assumptions. In particular, we show that the expected age of the MRCA of two copies of an allele with population frequency f is just 2Nf generations, where N is the effective population size. Our results are a first step in running exact coalescent simulations, where we also simulate the history of the population frequency of an allele. PMID:15520271

Patterson, Nick J.

2005-01-01

348

Multiple and independent origins of short seeded alleles of GS3 in rice  

PubMed Central

GRAIN SIZE 3 (GS3) is a cloned gene that is related to seed length. Here we report the discovery of new deletion alleles at the GS3 locus, each of which confer short seed. We selected ten short seeded cultivars from a collection of 282 diverse cultivars. Sequence analysis across the GS3 gene in these ten cultivars identified three novel alleles and a known allele that contain several independent deletion(s) in the fifth exon of GS. These independent deletion variants each resulted in a frameshift mutation that caused a premature stop codon, and they were functionally similar to one another. Each coded for a truncated gene product that behaved as an incomplete dominant allele and conferred a short seeded phenotype. Haplotype analysis of these sequence variants indicated that two of the variants were of japonica origin, and two were from indica. Transformation experiments demonstrated that one of the deletion alleles of GS3 decrease the cell number in the upper epidermis of the glume, resulting in a significant reduction in seed length. The multiple and independent origins of these short seeded alleles indicate that farmers and early breeders imposed artificial selection favoring short seeds. PMID:23641184

Takano-Kai, Noriko; Jiang, Hui; Powell, Adrian; McCouch, Susan; Takamure, Itsuro; Furuya, Naruto; Doi, Kazuyuki; Yoshimura, Atsushi

2013-01-01

349

Frequency of alleles and haplotypes of the human leukocyte antigen system in Bauru, São Paulo, Brazil  

PubMed Central

Background: HLA allele identification is used in bone marrow transplant programs as HLA compatibility between the donor and recipient may prevent graft rejection. Objective: This study aimed to estimate the frequency of alleles and haplotypes of the HLA system in the region of Bauru and compare these with the frequencies found in other regions of the country. Methods: HLA-A*, HLA-B*, and HLA-DRB1* allele frequencies and haplotypes were analyzed in a sample of 3542 volunteer donors at the National Registry of Voluntary Bone Marrow Donors (REDOME) in Bauru. HLA low resolution typing was performed using reverse line blot with the Dynal Reli(tm) SSO-HLA Typing Kit and automated Dynal AutoReli(tm)48 device (Invitrogen, USA). Results: Twenty, 36, and 13 HLA-A*, HLA-B*, and HLA-DRB1* allele groups, respectively, were identified. The most common alleles for each locus were HLA-A*02, HLA-B*35, and HLA-DRB1*07. The most frequent haplotype was A*01-B*08-DRB1*03. Allele and haplotype frequencies were compared to other regions in Brazil and the similarities and differences among populations are shown. Conclusion: The knowledge of the immunogenic profile of a population contributes to the comprehension of the historical and anthropological aspects of different regions. Moreover, this helps to find suitable donors quickly, thereby shortening waiting lists for transplants and thus increasing survival rates among recipients. PMID:24790535

Salvadori, Luana de Cassia; Santana, Fabiana Covolo de Souza; Marcos, Elaine Valim Camarinha

2014-01-01

350

ACE-II genotype and I allele predicts ischemic stroke among males in south India  

PubMed Central

Two hundred ischemic stroke patients and 193 age and sex matched healthy controls were studied for the presence of Angiotensin Converting Enzyme Insertion/Deletion (ACE I/D) gene polymorphism. The PCR studies revealed that ACE ‘II’ (OR = 2.055; p = 0.004) genotype and ‘I’ (OR = 1.411; p = 0.018) alleles were significantly associated with IS patients. Gender specific analysis revealed a strong association of ‘II’ (OR = 2.044; p = 0.014) genotype and ‘I’ (OR = 1.531; p = 0.011) allele with male sex. Classification of patients based on TOAST criteria, revealed a significant association for ‘II’ genotype (OR = 1.713; p = 0.043) and ‘I’ (OR = 1.382; p = 0.039) allele in LVD patients only. When the data was stratified based on age and sex, a statistically significant association was observed for ACE ‘II’ genotype (OR = 2.288; p = 0.006) and ‘I’ allele (OR = 1.395; p = 0.054) in IS male patients of > 50 years of age. The ACE ‘D’ allele was found to be increased in controls (OR = 0.709; p = 0.018) than IS patients. Multivariate logistic regression analysis showed that smoking and diabetes were the most powerful independent risk factor in LVD type of stroke. Thus, we presented here an evidence for a strong association of ACE ‘II’ genotype and ‘I’ allele compounded by factors such as smoking and diabetes among south Indian IS patients. PMID:25606450

Vijayan, Murali; Chinniah, Rathika; Ravi, Padma Malini; Mosses Joseph, Arun Kumar; Vellaiappan, Neethi Arasu; Krishnan, Jeyaram Illiayaraja; Karuppiah, Balakrishnan

2014-01-01

351

ACE-II genotype and I allele predicts ischemic stroke among males in south India.  

PubMed

Two hundred ischemic stroke patients and 193 age and sex matched healthy controls were studied for the presence of Angiotensin Converting Enzyme Insertion/Deletion (ACE I/D) gene polymorphism. The PCR studies revealed that ACE 'II' (OR = 2.055; p = 0.004) genotype and 'I' (OR = 1.411; p = 0.018) alleles were significantly associated with IS patients. Gender specific analysis revealed a strong association of 'II' (OR = 2.044; p = 0.014) genotype and 'I' (OR = 1.531; p = 0.011) allele with male sex. Classification of patients based on TOAST criteria, revealed a significant association for 'II' genotype (OR = 1.713; p = 0.043) and 'I' (OR = 1.382; p = 0.039) allele in LVD patients only. When the data was stratified based on age and sex, a statistically significant association was observed for ACE 'II' genotype (OR = 2.288; p = 0.006) and 'I' allele (OR = 1.395; p = 0.054) in IS male patients of > 50 years of age. The ACE 'D' allele was found to be increased in controls (OR = 0.709; p = 0.018) than IS patients. Multivariate logistic regression analysis showed that smoking and diabetes were the most powerful independent risk factor in LVD type of stroke. Thus, we presented here an evidence for a strong association of ACE 'II' genotype and 'I' allele compounded by factors such as smoking and diabetes among south Indian IS patients. PMID:25606450

Vijayan, Murali; Chinniah, Rathika; Ravi, Padma Malini; Mosses Joseph, Arun Kumar; Vellaiappan, Neethi Arasu; Krishnan, Jeyaram Illiayaraja; Karuppiah, Balakrishnan

2014-12-01

352

Limited efficacy of hydroxyurea in lowering of the JAK2 V617F allele burden.  

PubMed

Besides being an invaluable marker of clonal disease in chronic myeloproliferative disorders (CMPDs), the JAK2 V617F mutation and the mutated allele burden have an impact on disease phenotype and may provide information on prognosis. Recently, hydroxyurea (HU) has been shown to induce a rapid decline in the JAK2 V617F allele burden. The aim of the present study was to assess the dynamics of the JAK2 V617F allele burden during long-term treatment with HU in a series of patients with CMPDs. The JAK2 V617F allele burden was determined by quantitative PCR in 24 patients of whom 17 received HU, four received anagrelide and three were followed without any cytoreductive therapy. During a median follow-up of 24.2 months, no significant reductions in the JAK2 V617F allele burden were seen in patients treated with HU. We conclude that HU has only a limited effect on the JAK2 V617F allele burden in CMPD. PMID:19154659

Larsen, Thomas Stauffer; Pallisgaard, Niels; de Stricker, Karin; Møller, Michael Boe; Hasselbalch, Hans Carl

2009-02-01

353

Rapid Microarray-Based Identification of Different mecA Alleles in Staphylococci  

PubMed Central

To screen isolates and to identify mecA alleles, published mecA sequences were analyzed, and a microarray for the rapid discrimination of mecA alleles was designed. A GenBank analysis yielded 135 full-length gene sequences annotated as mecA. These sequences clustered into 32 different alleles corresponding to 28 unique amino acid sequences and to 15 distinct hybridization patterns on this microarray. A collection of 78 clinical and veterinary isolates of Staphylococcus spp. was characterized using this assay. Nine of the 15 expected patterns, as well as one as-yet-unknown pattern, were identified. These patterns were detected in various epidemic methicillin-resistant Staphylococcus aureus strains, in S. pseudintermedius, and in coagulase-negative species such as S. epidermidis, S. fleurettii, or S. haemolyticus. There was no correlation between the different mecA hybridization patterns and the SCCmec type. Determination of MICs showed that mecA alleles corresponding to only four of these nine patterns were associated with ?-lactam resistance. The mecA alleles that did not confer ?-lactam resistance were largely restricted to coagulase-negative staphylococci of animal origin, such as S. sciuri and S. vitulinus. Because of the diversity of sequences and the different impact on ?-lactam susceptibility, the existence of different mecA alleles needs to be taken into account when designing diagnostic assays for the detection of mecA. PMID:22890767

Müller, Elke; Schwarz, Stefan; Hotzel, Helmut; Ehricht, Ralf

2012-01-01

354

Distribution of AB0 and RH blood group alleles in different populations of southern Punjab, Pakistan.  

PubMed

The analysis of a sample of 1632 individuals from patients of the Nishtar Teaching Hospital, Multan, suggests that different ethnic groups (Araeen, Mughals, Syed, Jat, Rajputs, Baloch and Pathan) are not significantly different from another with regard to the distribution of RH blood group alleles (RH*d around 0.30). The distributions of the AB0 blood group alleles suggest that different ethnic groups are not significantly different from the average alele frequencies (AB0*A = 0.23, AB0*B = 0.33, AB0*0 = 0.47) except for the Pathan ethnic group (AB0*A = 0.35, AB0*B = 0.47, AB0*0 = 0.27). The populations of different geographic areas are not significantly different from the average allele frequencies, except for the southern district of Rahim Yar Khan (AB0*A = 0.12) and the northern district of Sahiwal (AB0*A = 0.19). The populations of Sahiwal (RH*d = 0.35) and Muzaffargarh (RH*d = 0.36) yield significantly different allele frequencies at the RH locus. The interpopulation differences can be explained by the geographic distance. There is a significant difference in the frequencies of the AB0 alleles between rural and urban populations, suggesting that rural populations maintain their isolation from urban populations. Rural and urban populations are not significantly different from one another concerning the allele frequencies at the RH locus. PMID:10320923

Mian, A; Farooq, A

1999-03-01

355

Allelic diversity and molecular characterization of puroindoline genes in five diploid species of the Aegilops genus.  

PubMed

Grain hardness is an important quality trait in wheat. This trait is related to the variation in, and the presence of, puroindolines (PINA and PINB). This variation can be increased by the allelic polymorphism present in the Aegilops species that are related to wheat. This study evaluated allelic Pina and Pinb gene variability in five diploid species of the Aegilops genus, along with the molecular characterization of the main allelic variants found in each species. This polymorphism resulted in 16 alleles for the Pina gene and 24 alleles for the Pinb gene, of which 10 and 17, respectively, were novel. Diverse mutations were detected in the deduced mature proteins of these alleles, which could influence the hardness characteristics of these proteins. This study shows that the diploid species of the Aegilops genus could be a good source of genetic variability for both Pina and Pinb genes, which could be used in breeding programmes to extend the range of different textures in wheat. PMID:24058161

Cuesta, Susana; Guzmán, Carlos; Alvarez, Juan B

2013-11-01

356

Interleukin-1beta+3953 allele 2: association with disease status in adult periodontitis.  

PubMed

Adult periodontitis is a complex multifactorial disease whose etiology is not well defined. The pro-inflammatory and bone resorptive properties of interleukin-1 beta (IL-1beta) strongly suggest a role for this cytokine in the pathogenesis of periodontal disease. In the study reported here, the frequency of IL-1beta genotypes including allele 2 of the IL-1beta+3953 restriction fragment length bi-allelic polymorphism was significantly increased in patients with advanced adult periodontitis compared to those with early and moderate disease. Furthermore, allele 2 was associated with increased production of IL-1beta by activated peripheral blood polymorphonuclear cells of patients with advanced disease, although this increase failed to reach statistical significance. Finally, the data obtained revealed significant linkage disequilibrium between allele 2 of the IL-1beta+3953 polymorphism and allele 2 of the bi-allelic IL-1alpha-889 polymorphism in both patients and orally healthy controls. These findings provide new insight into the possible role of IL-1alpha and beta gene polymorphisms in the susceptibility to adult periodontitis. PMID:9797049

Gore, E A; Sanders, J J; Pandey, J P; Palesch, Y; Galbraith, G M

1998-10-01

357

Quantification of allele-specific expression of a gene encoding strawberry polygalacturonase-inhibiting protein (PGIP) using Pyrosequencing.  

PubMed

Recent studies indicate that allele-specific differences in gene expression are a common phenomenon. The extent to which differential allelic expression exists might be underestimated, due to the limited accuracy of the methods used so far. To demonstrate allele-specific expression, we investigated the transcript abundance of six individual, highly homologous alleles of a polygalacturonase-inhibiting protein gene (FaPGIP) from octoploid strawberry (Fragaria x ananassa). We applied the highly quantitative Pyrosequencing method which, for the gene under study, detected allele frequency differences as small as 4.0 +/- 2.8%. Pyrosequencing of RT-PCR products showed that one FaPGIP allele was preferentially expressed in leaf tissue, while two other alleles were expressed in a fruit-specific way. For fruits that were inoculated with Botrytis cinerea a strong increase in overall FaPGIP gene expression was observed. This upregulation was accompanied by a significant change in FaPGIP allele frequencies when compared with non-treated fruits. Remarkably, in the five cultivars tested, the allele frequency in cDNA from the inoculated fruits was similar to that in genomic DNA, suggesting uniform upregulation of all FaPGIP alleles present as a result of pathogenesis-related stress. The results demonstrate that when Pyrosequencing of RT-PCR products is performed, novel allele-specific gene regulation can be detected and quantified. PMID:15659106

Schaart, Jan G; Mehli, Lisbeth; Schouten, Henk J

2005-02-01

358

The IPD and IMGT/HLA database: allele variant databases.  

PubMed

The Immuno Polymorphism Database (IPD) was developed to provide a centralized system for the study of polymorphism in genes of the immune system. Through the IPD project we have established a central platform for the curation and publication of locus-specific databases involved either directly or related to the function of the Major Histocompatibility Complex in a number of different species. We have collaborated with specialist groups or nomenclature committees that curate the individual sections before they are submitted to IPD for online publication. IPD consists of five core databases, with the IMGT/HLA Database as the primary database. Through the work of the various nomenclature committees, the HLA Informatics Group and in collaboration with the European Bioinformatics Institute we are able to provide public access to this data through the website http://www.ebi.ac.uk/ipd/. The IPD project continues to develop with new tools being added to address scientific developments, such as Next Generation Sequencing, and to address user feedback and requests. Regular updates to the website ensure that new and confirmatory sequences are dispersed to the immunogenetics community, and the wider research and clinical communities. PMID:25414341

Robinson, James; Halliwell, Jason A; Hayhurst, James D; Flicek, Paul; Parham, Peter; Marsh, Steven G E

2015-01-28

359

papG Alleles among Escherichia coli Strains Causing Urosepsis: Associations with Other Bacterial Characteristics and Host Compromise  

PubMed Central

Alleles I, II, and III of the P adhesin gene papG were sought by PCR among 75 Escherichia coli blood isolates from adults with urosepsis, and the papG genotype was compared with associated bacterial characteristics and host compromise status. Allele II predominated over allele III in the total population (71% of the strains versus 7% for allele III; P?Allele I was not encountered. In comparison with allele II, allele III was significantly associated with the presence of hly and the absence of iuc (which encode hemolysin and aerobactin biosynthesis), nonagglutination of digalactoside-coated beads, absence of aerobactin production, membership in serogroups O6 and O18, and host compromise, particularly cancer and upper urinary tract abnormalities. PMID:9712823

Johnson, James R.

1998-01-01

360

European Solar Engineering School Homepage  

NSDL National Science Digital Library

The European Solar Engineering School (ESES) provides courses in advanced solar energy engineering for well qualified master's level engineering students. The following are offered: advanced solar thermal engineering, advanced photovoltaic engineering, applied solar energy engineering, and utilization of solar energy.

2007-02-12

361

Yahoo! Groups: EuropeanArchaeology  

NSDL National Science Digital Library

This moderated mailing list is intended for a discussion of European prehistoric and historic archaeology, from the Early Paleolithic period through the 1800s. EuropeanArchaeology is a general purpose academic list that is designed to include book and article announcements, field school announcements, discuss new discoveries, theories and interpretations, and related topics. At the site, users can subscribe to the list and read the discussion logs.

362

European Union enlargement A historic opportunity  

E-print Network

European Union enlargement A historic opportunity #12;"Enlargement is both a historical opportunity and an obligation for the European Union and therefore one of its highest priorities. My aim is to strike the right European Council 46 Table of contents European Union enlargement A historic opportunity TABLE OF CONTENTS

Bilbao Arrese, Jesús Mario

363

information & research skills programme European Union Resources  

E-print Network

informED information & research skills programme European Union Resources © European Community and politics 4 The Budget - Financing the European Union 5 Economic and monetary policy 6 Single market. Culture 18 External Relations 19 Law EUROPA ­ Gateway to the European Union http

Hickman, Mark

364

Autumn 2009-Spring 2010 EUROPEAN BULLETIN  

E-print Network

. The subjects we cover range from geography and economics to anthropology, sociology, philology, history, art35-36 Autumn 2009-Spring 2010 EBHR EUROPEAN BULLETIN OF HIMALAYAN RESEARCH Special double issue: Nepalese migrations #12;European Bulletin of Himalayan ResearchEuropean Bulletin of Himalayan ResearchEuropean

Richner, Heinz

365

North European Transect  

NASA Astrophysics Data System (ADS)

A nearly continuous, 3600 km long, NE-running North European Transect (NET) is combined from the existing deep seismic reflection data sets in the Baltic Sea (BABEL, 1600 km), Northern Finland (FIRE 4-4A, 580 km) and Barents Sea (1-AR, 1440 km;). The reflective image of the deep crust is highly dependent on the thickness of the sedimentary cover. The cover is few hundred meters in the Baltic sea, few tens of meters in the land areas and few kilometers in the Barents Sea area. In the Barents Sea area, the seismic image is dominated by the layered structure of the sedimentary basins and the middle and lower crust are poorly imaged. Therefore the Moho boundary in the Barents Sea has been determined from wide-angle reflections. Geologically the transect covers the transition from Phanerozoic Europe to Precambrian Europe and back to the Phanerozoic Barents Sea Shelf. It displays how Northern Europe grew around Baltica in several tectonic episodes involving the formation and destruction of Columbia/Hudsonland, Rodinia and Pangea supercontinents. The paleo plateboundaries are traversed by subvertical transparent zones suggesting transpressional and trantensional environments. The BABEL lines image how the core of Baltica was formed by sequential accretion of microcontinents and arc terranes at the old continental margin during the Svecofennian Orogeny ~1.9-1.8 Ga .When Baltica joined the Columbia supercontinent, new terranes were added to its southern edge in the Sveocbaltic Orogeny (~1.8 Ga). During the dispersal of the Columbia, the Baltic Sea failed rift was formed, rapakivi granitoids were intruded and sedimentary basins were developed. An extended plate margin structure has been imposed on the Rodinian (Sveconorwegian) and Pangean additions (Variscan-Caledonian). Major crustal thinning takes place along a series of subvertical faults across the Trans-European Suture Zone marking the transition from Phanerozoic to Proterozoic Europe. The FIRE lines in Northen Finland image a collage of older continental fragments and intervening basins that have been welded together in Svecofennian and Lapland-Kola orogenies. The Lapland-Kola orogen record the collision of Baltica and Laurentia during the compilation of the Columbia supercontinent. The collisional structures were overprinted by extension associated with the dispersal of Columbia. The Russian Arctic line 1-AR focuses on the Phanerozoic sedimentary cover of the Barents Sea Basin. The line images the transition from Paleoproterozoic Baltica to Neoproterozoic Barentsia. As part of the Rodinia supercontinent formation, Baltica collided with Barentsia resulting in Timanide orogeny. During the break-up of Rodinia an aborted rift was formed within the Barentsia. Later peripheral tectonic events modified the interior parts of Barentsia that acted first as a back arc basin and later as a foreland basin to the Uralian and Caledonian orogen during the formation of the Pangea supercontinent.

Korja, Annakaisa; Heikkinen, Pekka J.; Roslov, Yuri; Ivanova, Nina; Verba, Marc; Sakoulina, Tamara

2010-05-01

366

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

PubMed Central

Recently, the observation of a high-frequency private allele, the 9-repeat allele at microsatellite D9S1120, in all sampled Native American and Western Beringian populations has been interpreted as evidence that all modern Native Americans descend primarily from a single founding population. However, this inference assumed that all copies of the 9-repeat allele were identical by descent and that the geographic distribution of this allele had not been influenced by natural selection. To investigate whether these assumptions are satisfied, we genotyped 34 single nucleotide polymorphisms across ?500 kilobases (kb) around D9S1120 in 21 Native American and Western Beringian populations and 54 other worldwide populations. All chromosomes with the 9-repeat allele share the same haplotypic background in the vicinity of D9S1120, suggesting that all sampled copies of the 9-repeat allele are identical by descent. Ninety-one percent of these chromosomes share the same 76.26 kb haplotype, which we call the “American Modal Haplotype” (AMH). Three observations lead us to conclude that the high frequency and widespread distribution of the 9-repeat allele are unlikely to be the result of positive selection: 1) aside from its association with the 9-repeat allele, the AMH does not have a high frequency in the Americas, 2) the AMH is not unusually long for its frequency compared with other haplotypes in the Americas, and 3) in Latin American mestizo populations, the proportion of Native American ancestry at D9S1120 is not unusual compared with that observed at other genomewide microsatellites. Using a new method for estimating the time to the most recent common ancestor (MRCA) of all sampled copies of an allele on the basis of an estimate of the length of the genealogy descended from the MRCA, we calculate the mean time to the MRCA of the 9-repeat allele to be between 7,325 and 39,900 years, depending on the demographic model used. The results support the hypothesis that all modern Native Americans and Western Beringians trace a large portion of their ancestry to a single founding population that may have been isolated from other Asian populations prior to expanding into the Americas. PMID:19221006

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

2009-01-01

367

HLA B27 allele types in homogeneous groups of juvenile idiopathic arthritis patients in Latvia  

PubMed Central

Juvenile idiopathic arthritis (JIA) is a heterogeneous condition and therapeutic strategies vary in different JIA types. The routinely accepted practice to start with Sulphasalazine (SS) as the first line treatment in patients with HLA B27 positive JIA proves to be ineffective in a large proportion of children. Objective to investigate HLA B27 positive JIA patients clinical characteristics, determined HLA B27 allele types and their connection with antirheumatic treatment in homogenous patient groups. Materials and methods 56 patients diagnosed with JIA and observed over the period 2006 to 2009 included in the study. HLAB27 allele types were determined using PCR method. Results In HLA B27 positive JIA patients mean disease onset was 12.34 ± 3.3 years. Most common (44%) JIA type was enthesitis related arthritis. Positive response to the treatment with SS was found in 32% of patients, Methotrexate (MTX) - in 43%, combined treatment - SS with MTX was effective in 12.5%. 12.5% of patients required combination MTX with Enbrel. Eight HLA B27 allele types were found in JIA patients in Latvia: *2702, *2703, *2704, *2705, *2710, *2715, *2717, *2728. The most common was *2705 - in 55% of cases. Among all the patients enthesitis related arthritis most commonly occurred in patients with HLAB*2705 allele (OR = 2.01, p < 0.02), oligoarthritis in patients with *2710 allele (OR = 3.0, p < 0.04) and polyarthritis with *2717 allele (OR = 3.0, p < 0.05). In patients with *2705 allele effective treatment was MTX (OR = 1.13, p < 0.03) and MTX with SS (OR = 2.02, p < 0.05), but in patients having *2703 allele - MTX with Enbrel (OR = 2.94, p < 0.02). Conclusions There are 8 different HLA B27 alleles in JIA patients in Latvia and the most common is *2705, but in order to assert them to be disease associated alleles, more extensive studies are needed, including control group of HLA B27 positive healthy individuals. Standard treatment approach with SS proves to be unsatisfactory in the majority of JIA patients. To improve children's quality of life achieving rapid disease control, the first line treatment in HLA B27 positive patients should be MTX. In order to start with the most appropriate drug it is necessary to determine HLAB 27 type at the onset of disease. PMID:20946671

2010-01-01

368

The Burden of JAK2V617F Mutated Allele in Turkish Patients With Myeloproliferative Neoplasms  

PubMed Central

Background Studies regarding the impact of JAK2V617F allele burden on phenotypic properties and clinical course in Philadelphia-negative myeloproliferative neoplasms (Ph-negative MPNs) have reported variable results. We aimed to analyze the association of mutated JAK2V617F allele burden with laboratory characteristics and clinical phenotype in Turkish patients (107 essential thrombocythemia (ET) and 77 primary myelofibrosis (PMF)). Methods Peripheral blood samples of 184 patients with Ph-negative MPNs were analyzed for JAK2V617F allele status and burden. JAK2 MutaScreen assay (Ipsogen, Luminy Biotech, Marseille, France) was used to detect the JAK2V617F status and quantitative JAK2V617F allele burdens in genomic DNA using TaqMan allelic discrimination. Results Frequency of JAK2V617F-positive patients with high mutation load (allele burden > 50%) was higher in PMF compared to ET (23.4% and 4.7%, respectively; P = 0.001). We found significant association between ET patients with high JAK2V617F allele burden and lower hemoglobin (Hgb) and hematocrit (Hct), higher LDH levels and more prevalent massive splenomegaly (P = 0.001, P = 0.001, P = 0.012 and P = 0.015, respectively). ET patients with high mutation load displayed higher prevalence of bleeding compared to low mutation load and wild-type mutational status (P = 0.003). Rate of DVT was significantly higher in ET patients with mutant allele burden in upper half compared to lower half and wild-type (P = 0.029). We observed significant association between PMF patients with high JAK2V617F allele burden and higher Hgb, Hct levels and leukocyte counts (P = 0.003, P = 0.021 and P = 0.001, respectively). Conclusions Our study demonstrated JAK2V617F allele burden correlates with clinical features in ET and PMF. We conclude quantification of JAK2V617F mutation contributes to the workup of Ph-negative MPNs. PMID:25584101

Yonal-Hindilerden, Ipek; Daglar-Aday, Aynur; Akadam-Teker, Basak; Yilmaz, Ceylan; Nalcaci, Meliha; Yavuz, Akif Selim; Sargin, Deniz

2015-01-01

369

Mixed allele malaria vaccines: host protection and within-host selection.  

PubMed

Malaria parasites are frequently polymorphic at the antigenic targets of many candidate vaccines, presumably as a consequence of selection pressure from protective immune responses. Conventional wisdom is therefore that vaccines directed against a single variant could select for non-target variants, rendering the vaccine useless. Many people have argued that a solution is to develop vaccines containing the products of more than one variant of the target. However, we are unaware of any evidence that multi-allele vaccines better protect hosts against parasites or morbidity. Moreover, selection of antigen-variants is not the only evolution that could occur in response to vaccination. Increased virulence could also be favored if more aggressive strains are less well controlled by vaccine-induced immunity. Virulence and antigenic identity have been confounded in all studies so far, and so we do not know formally from any animal or human studies whether vaccine failure has been due to evasion of protective responses by variants at target epitopes, or whether vaccines are just less good at protecting against more aggressive strains. Using the rodent malaria model Plasmodium chabaudi and recombinant apical membrane antigen-1 (AMA-1), we tested whether a bi-allelic vaccine afforded greater protection from parasite infection and morbidity than did vaccination with the component alleles alone. We also tested the effect of mono- and bi-allelic vaccination on within-host selection of mixed P. chabaudi infections, and whether parasite virulence mediates pathogen titres in immunized hosts. We found that vaccination with the bi-allelic AMA-1 formulation did not afford the host greater protection from parasite infection or morbidity than did mono-allelic AMA-1 immunization. Mono-allelic immunization increased the frequency of heterologous clones in mixed clone infections. There was no evidence that any type of immunization regime favored virulence. A single AMA-1 variant is a component of candidate malaria vaccines current in human trials; our results suggest that adding extra AMA-1 alleles to these vaccines would not confer clinical benefits, but that that mono-allelic vaccines could alter AMA-1 allele frequencies in natural populations. PMID:18804509

Barclay, Victoria C; Chan, Brian H K; Anders, Robin F; Read, Andrew F

2008-11-11

370

Factors Influencing Ascertainment Bias of Microsatellite Allele Sizes: Impact on Estimates of Mutation Rates  

PubMed Central

Microsatellite loci play an important role as markers for identification, disease gene mapping, and evolutionary studies. Mutation rate, which is of fundamental importance, can be obtained from interspecies comparisons, which, however, are subject to ascertainment bias. This bias arises, for example, when a locus is selected on the basis of its large allele size in one species (cognate species 1), in which it is first discovered. This bias is reflected in average allele length in any noncognate species 2 being smaller than that in species 1. This phenomenon was observed in various pairs of species, including comparisons of allele sizes in human and chimpanzee. Various mechanisms were proposed to explain observed differences in mean allele lengths between two species. Here, we examine the framework of a single-step asymmetric and unrestricted stepwise mutation model with genetic drift. Analysis is based on coalescent theory. Analytical results are confirmed by simulations using the simuPOP software. The mechanism of ascertainment bias in this model is a tighter correlation of allele sizes within a cognate species 1 than of allele sizes in two different species 1 and 2. We present computations of the expected average allele size difference, given the mutation rate, population sizes of species 1 and 2, time of separation of species 1 and 2, and the age of the allele. We show that when the past demographic histories of the cognate and noncognate taxa are different, the rate and directionality of mutations affect the allele sizes in the two taxa differently from the simple effect of ascertainment bias. This effect may exaggerate or reverse the effect of difference in mutation rates. We reanalyze literature data, which indicate that despite the bias, the microsatellite mutation rate estimate in the ancestral population is consistently greater than that in either human or chimpanzee and the mutation rate estimate in human exceeds or equals that in chimpanzee with the rate of allele length expansion in human being greater than that in chimpanzee. We also demonstrate that population bottlenecks and expansions in the recent human history have little impact on our conclusions. PMID:23525076

Li, Biao; Kimmel, Marek

2013-01-01

371

Allele loss, replication errors and loss of expression of E-cadherin in colorectal cancers.  

PubMed Central

BACKGROUND: Loss of E-cadherin expression has been implicated in the development of invasive characteristics in colorectal carcinomas. Failure to express E-cadherin may result from mutations of the E-cadherin gene (HSECAD). AIMS: To examine the correlation between E-cadherin expression and genetic changes at HSECAD; and to examine differences in E-cadherin expression and genetic changes at HSECAD between three different groups of colorectal cancer--replication error positive (RER+) sporadic cancers, RER--sporadic cancers and ulcerative colitis associated cancers. SUBJECTS AND METHODS: Sixty eight colorectal cancers (22 RER+ sporadic cancers, 32 RER- sporadic cancers and 14 ulcerative colitis associated cancers) were studied using immunohistochemistry and for allele loss at the HSECAD locus. Exon 16 of HSECAD contains several mononucleotide repeat tracts which are very similar to microsatellite repeats and which may be susceptible to replication errors (manifest as new alleles). All cases were also examined for new alleles in exon 16. RESULTS: Absent or decreased E-cadherin protein expression was found in 27 (38%) of 68 colorectal cancers and the pattern of expression did not differ significantly among the three tumour groups. Allele loss occurred at HSECAD in four (10%) of 40 informative cancers and there were no differences between the three subgroups. New alleles at exon 16 were detected in three (14%) of 22 RER+ tumours; no new alleles were detected in RER- or ulcerative colitis associated cancers. Overall, there was no correlation between allelic loss or exon 16 replication errors and immunohistochemical E-cadherin expression. CONCLUSIONS: (1) Loss of E-cadherin expression probably does not occur as a result of mutation at the HSECAD locus in colorectal cancers. (2) There is no difference in the frequency of loss of heterozygosity at HSECAD among RER+, RER- and ulcerative colitis associated colorectal cancers. Images PMID:9203946

Ilyas, M; Tomlinson, I P; Hanby, A; Talbot, I C; Bodmer, W F

1997-01-01

372

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

PubMed

The epsilon4 allele of the apolipoprotein E (APOE) gene is associated with increased cholesterol levels and heart disease. Population allele frequencies of APOE have previously been shown to vary, with epsilon4 frequencies generally increasing with latitude. We hypothesize that this trend resulted from natural selection protecting against low-cholesterol levels. In high-latitude cold environments and low-latitude hot environments, metabolic rate is elevated, which could require higher cholesterol levels. To explore this hypothesis, we compiled APOE allele frequencies, latitude, temperature, and elevation from populations around the world. epsilon4 allele frequencies show a curvilinear relationship with absolute latitude, with lowest frequencies found in the mid-latitudes where temperatures generally require less expenditure on cooling/thermogenesis. Controlling for population structure in a subset of populations did not appreciably change this pattern of association, consistent with selection pressures that vary by latitude shaping epsilon4 allele frequencies. Temperature records also predict APOE frequency in a curvilinear fashion, with lowest epsilon4 frequencies at moderate temperatures. The model fit between historical temperatures and epsilon4 is less than between latitude and epsilon4, but strengthened after correcting for estimated temperature differences during the Paleolithic. Contrary to our hypothesis, we find that elevation did not improve predictive power, and an integrated measure of the cholesterol effect of multiple APOE alleles was less related to latitude than was epsilon4 alone. Our results lend mixed support for a link between past temperature and human APOE allele distribution and point to the need to develop better models of past climate in future analyses. PMID:20734437

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

2010-09-01

373

Active alleles of the human XIST gene replicate late in S phase  

SciTech Connect

The XIST gene is a strong candidate for controlling X chromosome inactivation. It has been mapped to the X inactivation control region (Xic) and is transcribed exclusively from the inactive X chromosome. XIST expression during development appears to be controlled by epigenetic modulation. Replication timing is an epigenetic modification implicated in transcriptional control and chromosomal imprinting. We have studied the replication timing of human XIST alleles on active and inactive X chromosomes present in somatic cell hybrids and fibroblast cultures. The replication timing method was based on the isolation of newly-replicated DNA from cells pulse-labeled with bromodexyuridine and separated by flow cytometry into different fractions of the cell cycle. Two human x hamster hybrid cell lines that contain active X chromosomes were found to replicate the inactive XIST allele early in S, similar to the active MIC2 gene. Active XIST alleles replicated late in S for three different hybrids containing inactive X chromosomes. MIC2 is expressed from both active and inactive X chromosomes and was found to replicate early in both active and inactive X hybrids. Male fibroblasts replicated XISt early in S, while both early and late peaks of replication were observed in female cells. The unusual replication patterns of active and inactive X alleles of XIST are similar to that of the autosomal H19 gene: late replication for active alleles and early replication for inactive alleles. This pattern of replication is a dramatic exception to the general rule that active genes replicate early in S phase. In addition to similar replication patterns, both H19 and XIST are subject to genomic imprinting and encode functional RNA products. Late replication timing for the active alleles of these genes may have functional significance. Further studies at these loci may help to eluidate the role of replication timing in the epigenetic control of imprinting, gene activity, and gene function.

Hansen, R.S.; Gartler, S.M. [Univ. of Washington, Seattle, WA (United States)

1994-09-01

374

Allele-Specific Deletions in Mouse Tumors Identify Fbxw7 as Germline Modifier of Tumor Susceptibility  

PubMed Central

Genome-wide association studies (GWAS) have been successful in finding associations between specific genetic variants and cancer susceptibility in human populations. These studies have identified a range of highly statistically significant associations between single nucleotide polymorphisms (SNPs) and susceptibility to development of a range of human tumors. However, the effect of each SNP in isolation is very small, and all of the SNPs combined only account for a relatively minor proportion of the total genetic risk (5–10%). There is therefore a major requirement for alternative routes to the discovery of genetic risk factors for cancer. We have previously shown using mouse models that chromosomal regions harboring susceptibility genes identified by linkage analysis frequently exhibit allele-specific genetic alterations in tumors. We demonstrate here that the Fbxw7 gene, a commonly mutated gene in a wide range of mouse and human cancers, shows allele-specific deletions in mouse lymphomas and skin tumors. Lymphomas from three different F1 hybrids show 100% allele-specificity in the patterns of allelic loss. Parental alleles from 129/Sv or Spretus/Gla mice are lost in tumors from F1 hybrids with C57BL/6 animals, due to the presence of a specific non-synonymous coding sequence polymorphism at the N-terminal portion of the gene. A specific genetic test of association between this SNP and lymphoma susceptibility in interspecific backcross mice showed a significant linkage (p?=?0.001), but only in animals with a functional p53 gene. These data therefore identify Fbxw7 as a p53-dependent tumor susceptibility gene. Increased p53-dependent tumor susceptibility and allele-specific losses were also seen in a mouse skin model of skin tumor development. We propose that analysis of preferential allelic imbalances in tumors may provide an efficient means of uncovering genetic variants that affect mouse and human tumor susceptibility. PMID:22348067

Perez-Losada, Jesus; Wu, Di; DelRosario, Reyno; Balmain, Allan; Mao, Jian-Hua

2012-01-01

375

Apolipoprotein E ?4 allele decreases functional connectivity in Alzheimer's disease as measured by EEG coherence  

PubMed Central

OBJECTIVES—The ?4 allele of apolipoprotein E (APOE) represents a major biological risk factor for late onset Alzheimer's disease. However, it is still not known whether the APOE genotype affects the progression of the disease, assessed by different functional methods.?METHODS—The study sample included 41 patients with probable Alzheimer's disease. Subjects had similar severity of disease, age of onset, and duration of illness, and were subcategorised according to their APOE genotypes: 17 with no ?4 allele, 14 with one ?4 allele, and 10 with two ?4 alleles. The control group consisted of 18 healthy subjects comparable with the patients in age and education. Analysed quantitive EEG (qEEG) variables were the ratio of alpha and theta absolute power and EEG coherence in alpha frequency band, representing major cortical association pathways.?RESULTS—There was pronounced EEG slowing in all three patient subgroups compared with the controls for the alpha/theta ratio, but there was no significant difference across the patient subgroups. Patients homozygous for the APOE ?4 allele had reduced right and left temporoparietal, right temporofrontal, and left occipitoparietal coherence. Patients without and with one ?4 allele showed an overlap between the control group and group with two ?4 alleles in coherence measures.?CONCLUSIONS—APOE ?4 does not influence EEG slowing, an index which reflects severity of the disease in patients with Alzheimer's disease, but seems to be associated with selective decreases in functional connectivity as assessed by EEG coherence. This finding might be of clinical importance when considering different pathogenetic mechanisms.?? PMID:9221969

Jelic, V.; Julin, P.; Shigeta, M.; Nordberg, A.; Lannfelt, L.; Winblad, B.; Wahlund, L.

1997-01-01

376

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

PubMed

At intron 40 of the von Willebrand factor (vWF) gene, two GATA-repeat polymorphic sites exist that are physically separated by 212 bp. At the first site (vWF1 locus), seven segregating repeat alleles were observed in a Brazilian Caucasian population, and at the second (vWF2 locus) there were eight alleles, detected through PCR amplifications of this DNA region. Haplotype analysis of individuals revealed 36 different haplotypes in a sample of 338 chromosomes examined. Allele frequencies between generations and gender at each locus were not significantly different, and the genotype frequencies were consistent with their Hardy-Weinberg expectations. Linkage disequilibrium between loci is highly significant with positive allele size association; that is, large alleles at the loci tend to occur together, and so do the small alleles. Variability at each locus appeared to have arisen in a stepwise fashion, suggesting replication slippage as a possible mechanism of production of new alleles. However, we observed an increased number of haplotypes, in contrast with the predictions of a stepwise production of variation in the entire region, suggesting some form of "cooperative" changes between loci that could be due to either gene conversion, or a common control mechanism of production of new variation at these repeat polymorphism sites. The high degree of polymorphism (gene diversity values of 72% and 78% at vWF1 and vWF2, respectively, and of 93% at the haplotype level) makes these markers informative for paternity testing, genetic counseling, and individual-identification purposes. PMID:8290589

Pena, S D; de Souza, K T; de Andrade, M; Chakraborty, R

1994-01-18

377

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

SciTech Connect

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

Pena, S.D.J.; De Souza, K.T. (Nucleo de Genetica Medica de Minas Gerais, Belo Horizonte (Brazil)); De Andrade, M.; Chakraborty, R. (Univ. of Texas Graduate School of Biomedical Sciences, Houston, TX (United States))

1994-01-18

378

Fine Mapping of Dominant X-Linked Incompatibility Alleles in Drosophila Hybrids  

PubMed Central

Sex chromosomes have a large effect on reproductive isolation and play an important role in hybrid inviability. In Drosophila hybrids, X-linked genes have pronounced deleterious effects on fitness in male hybrids, which have only one X chromosome. Several studies have succeeded at locating and identifying recessive X-linked alleles involved in hybrid inviability. Nonetheless, the density of dominant X-linked alleles involved in interspecific hybrid viability remains largely unknown. In this report, we study the effects of a panel of small fragments of the D. melanogaster X-chromosome carried on the D. melanogaster Y-chromosome in three kinds of hybrid males: D. melanogaster/D. santomea, D. melanogaster/D. simulans and D. melanogaster/D. mauritiana. D. santomea and D. melanogaster diverged over 10 million years ago, while D. simulans (and D. mauritiana) diverged from D. melanogaster over 3 million years ago. We find that the X-chromosome from D. melanogaster carries dominant alleles that are lethal in mel/san, mel/sim, and mel/mau hybrids, and more of these alleles are revealed in the most divergent cross. We then compare these effects on hybrid viability with two D. melanogaster intraspecific crosses. Unlike the interspecific crosses, we found no X-linked alleles that cause lethality in intraspecific crosses. Our results reveal the existence of dominant alleles on the X-chromosome of D. melanogaster which cause lethality in three different interspecific hybrids. These alleles only cause inviability in hybrid males, yet have little effect in hybrid females. This suggests that X-linked elements that cause hybrid inviability in males might not do so in hybrid females due to differing sex chromosome interactions. PMID:24743238

Matute, Daniel R.; Gavin-Smyth, Jackie

2014-01-01

379

Characterizing HMW-GS alleles of decaploid Agropyron elongatum in relation to evolution and wheat breeding  

PubMed Central

Bread wheat quality is mainly correlated with high molecular weight glutenin subunits (HMW-GS) of endosperm. The number of HMW-GS alleles with good processing quality is limited in bread wheat cultivars, while there are plenty of HMW-GS alleles in wheat-related grasses to exploit. We report here on the cloning and characterization of HMW-GS alleles from the decaploid Agropyron elongatum. Eleven novel HMW-GS alleles were cloned from the grass. Of them, five are x-type and six y-type glutenin subunit genes. Three alleles Aex4, Aey7, and Aey9 showed high similarity with another three alleles from the diploid Lophopyrum elongatum, which provided direct evidence for the Ee genome origination of A. elongatum. It was noted that C-terminal regions of three alleles of the y-type genes Aey8, Aey9, and Aey10 showed more similarity with x-type genes than with other y-type genes. This demonstrates that there is a kind of intermediate state that appeared in the divergence between x- and y-type genes in the HMW-GS evolution. One x-type subunit, Aex4, with an additional cysteine residue, was speculated to be correlated with the good processing quality of wheat introgression lines. Aey4 was deduced to be a chimeric gene from the recombination between another two genes. How the HMW-GS genes of A. elongatum may contribute to the improvement of wheat processing quality are discussed. PMID:17992503

Liu, Shuwei; Gao, Xin

2007-01-01

380

Characterizing HMW-GS alleles of decaploid Agropyron elongatum in relation to evolution and wheat breeding.  

PubMed

Bread wheat quality is mainly correlated with high molecular weight glutenin subunits (HMW-GS) of endosperm. The number of HMW-GS alleles with good processing quality is limited in bread wheat cultivars, while there are plenty of HMW-GS alleles in wheat-related grasses to exploit. We report here on the cloning and characterization of HMW-GS alleles from the decaploid Agropyron elongatum. Eleven novel HMW-GS alleles were cloned from the grass. Of them, five are x-type and six y-type glutenin subunit genes. Three alleles Aex4, Aey7, and Aey9 showed high similarity with another three alleles from the diploid Lophopyrum elongatum, which provided direct evidence for the Ee genome origination of A. elongatum. It was noted that C-terminal regions of three alleles of the y-type genes Aey8, Aey9, and Aey10 showed more similarity with x-type genes than with other y-type genes. This demonstrates that there is a kind of intermediate state that appeared in the divergence between x- and y-type genes in the HMW-GS evolution. One x-type subunit, Aex4, with an additional cysteine residue, was speculated to be correlated with the good processing quality of wheat introgression lines. Aey4 was deduced to be a chimeric gene from the recombination between another two genes. How the HMW-GS genes of A. elongatum may contribute to the improvement of wheat processing quality are discussed. PMID:17992503

Liu, Shuwei; Gao, Xin; Xia, Guangmin

2008-02-01

381

[Allele polymorphism of the DNA loci MET, D7S8, D7S23, linked to the cystic fibrosis gene in some populations of the USSR, in high risk families and in cystic fibrosis patients].  

PubMed

RELP analysis of DNA loci MET, D7S8 and D7S23 was carried out in Leningrad population and partially in populations of Moscow, Azerbaijan, Ukraine, Buryatia as well as in individuals from high risk families and in cystic fibrosis (CF) patients by means of blot hybridization and polymerase chain reaction. Allelic polymorphism of all loci studied in these three groups was found to be quite similar to that in the North-Western Europe and in whites of the North America. Linkage disequilibrium of the alleles studied with the CF gene was especially pronounced for alleles of the D7S23 locus and gradually decreases from KM-19 through CS-7 to XV-2c DNA probes. The data witness genetic homogeneity of the CF mutation in European populations of the USSR and its similarity to this mutation in Western Europe. The significance of these data for potential diagnosis of CF and for heterozygous carrier detection is discussed. PMID:2037248

Baranov, V S; Ivashchenko, T E; Gorbunova, V N; Voronina, O V; Ga?tskhoki, V S; Gol'tsov, A A; Kaboev, O K; Shvarts, E I; Berlin, Iu A; Livshits, L A

1991-01-01

382

Range-Wide Sex-Chromosome Sequence Similarity Supports Occasional XY Recombination in European Tree Frogs (Hyla arborea)  

PubMed Central

In contrast with mammals and birds, most poikilothermic vertebrates feature structurally undifferentiated sex chromosomes, which may result either from frequent turnovers, or from occasional events of XY recombination. The latter mechanism was recently suggested to be responsible for sex-chromosome homomorphy in European tree frogs (Hyla arborea). However, no single case of male recombination has been identified in large-scale laboratory crosses, and populations from NW Europe consistently display sex-specific allelic frequencies with male-diagnostic alleles, suggesting the absence of recombination in their recent history. To address this apparent paradox, we extended the phylogeographic scope of investigations, by analyzing the sequences of three sex-linked markers throughout the whole species distribution. Refugial populations (southern Balkans and Adriatic coast) show a mix of X and Y alleles in haplotypic networks, and no more within-individual pairwise nucleotide differences in males than in females, testifying to recurrent XY recombination. In contrast, populations of NW Europe, which originated from a recent postglacial expansion, show a clear pattern of XY differentiation; the X and Y gametologs of the sex-linked gene Med15 present different alleles, likely fixed by drift on the front wave of expansions, and kept differentiated since. Our results support the view that sex-chromosome homomorphy in H. arborea is maintained by occasional or historical events of recombination; whether the frequency of these events indeed differs between populations remains to be clarified. PMID:24892652

Brelsford, Alan; Perrin, Nicolas

2014-01-01

383

Range-wide sex-chromosome sequence similarity supports occasional XY recombination in European tree frogs (Hyla arborea).  

PubMed

In contrast with mammals and birds, most poikilothermic vertebrates feature structurally undifferentiated sex chromosomes, which may result either from frequent turnovers, or from occasional events of XY recombination. The latter mechanism was recently suggested to be responsible for sex-chromosome homomorphy in European tree frogs (Hyla arborea). However, no single case of male recombination has been identified in large-scale laboratory crosses, and populations from NW Europe consistently display sex-specific allelic frequencies with male-diagnostic alleles, suggesting the absence of recombination in their recent history. To address this apparent paradox, we extended the phylogeographic scope of investigations, by analyzing the sequences of three sex-linked markers throughout the whole species distribution. Refugial populations (southern Balkans and Adriatic coast) show a mix of X and Y alleles in haplotypic networks, and no more within-individual pairwise nucleotide differences in males than in females, testifying to recurrent XY recombination. In contrast, populations of NW Europe, which originated from a recent postglacial expansion, show a clear pattern of XY differentiation; the X and Y gametologs of the sex-linked gene Med15 present different alleles, likely fixed by drift on the front wave of expansions, and kept differentiated since. Our results support the view that sex-chromosome homomorphy in H. arborea is maintained by occasional or historical events of recombination; whether the frequency of these events indeed differs between populations remains to be clarified. PMID:24892652

Dufresnes, Christophe; Stöck, Matthias; Brelsford, Alan; Perrin, Nicolas

2014-01-01

384

Duponchelia fovealisDuponchelia fovealis (Zeller)(Zeller) European Pepper MothEuropean Pepper Moth  

E-print Network

Duponchelia fovealisDuponchelia fovealis (Zeller)(Zeller) European Pepper MothEuropean Pepper Moth Agriculture Pest Survey program). The photographs of the European pepper moth were used with permission from

Watson, Craig A.

385

German and British labour law in a European context following European Union enlargement   

E-print Network

This thesis examines and compares German and British trade union responses in a European context following the recent European enlargements which are unprecedented in the history of the European Union. In terms of labour ...

Zahn, Rebecca Lisa

2011-07-01

386

Rare SERINC2 variants are specific for alcohol dependence in subjects of European descent  

PubMed Central

Objectives We previously reported a top-ranked risk gene [i.e., serine incorporator 2 gene (SERINC2)] for alcohol dependence in the subjects of European descent by analyzing the common variants in a genome-wide association study. In the present study, we comprehensively examined the rare variants [minor allele frequency (MAF) < 0.05] in the NKAIN1-SERINC2 region, in order to confirm our previous finding. Methods A discovery sample (1,409 European-American cases with alcohol dependence and 1,518 European-American controls) and a replication sample (6,438 European-Australian family subjects with 1,645 alcohol dependent probands) underwent association analysis. A total of 39,903 subjects from 19 other cohorts with 11 different neuropsychiatric and neurological disorders served as contrast groups. The entire NKAIN1-SERINC2 region was imputed in all cohorts using the same reference panels of genotypes that included rare variants from the whole-genome sequencing data. We stringently cleaned the phenotype and genotype data, and obtained a total of about 220 SNPs in the subjects with European descent and about 450 SNPs in the subjects with African descent with 0European-Americans (Fp: overall p=1.8×10?4; VT: overall p=1.4×10?4; Collapsing p=6.5×10?5) and European-Australians (Fp: overall p=0.028; Collapsing p=0.025), but not African-Americans, and not associated with any other disorder examined. Association signals in this region came mainly from SERINC2, a gene that codes for an activity-regulated protein expressed in brain that incorporates serine into lipids. Additionally, 26 individual rare variants were nominally associated with alcohol dependence in European-Americans (p<0.05). The associations of 5 of these rare variants that lay within SERINC2 exhibited region-wide significance (pEuropean-Australians (p<0.05). Conclusion We concluded that SERINC2 was a replicable and significant risk gene specific for alcohol dependence in the subjects of European descent. PMID:23778322

Zuo, Lingjun; Wang, Ke-Sheng; Zhang, Xiang-Yang; Li, Chiang-Shan R.; Zhang, Fengyu; Wang, Xiaoping; Chen, Wenan; Gao, Guimin; Zhang, Heping; Krystal, John H.; Luo, Xingguang

2015-01-01

387

Lack of association between allelic status and myostatin content in lambs with the myostatin g+6723G>A allele.  

PubMed

Lambs with the myostatin (MSTN) g+6723G>A mutation have a greater muscle mass, which is believed to be associated with reduced myostatin protein abundance. This experiment was designed to determine if differences in allelic frequency of the MSTN g+6723G>A mutation affected abundance of myostatin protein from birth to 24 wk of age. A Poll Dorset cross White Suffolk ram (MSTN A/G) was mated to 35 White Suffolk cross Border Leicester cross Merino ewes (MSTN A/G, n=21, and MSTN G/G, n=14). The progeny of these matings delivered 44 lambs with MSTN A/A (n=9), MSTN A/G (n=21), and MSTN G/G (n=14) genotypes. At approximately 1, 4, and 12 wk of age, a biopsy sample was collected and a blood sample was taken to measure the abundance of myostatin protein in muscle and plasma. At approximately 24 wk of age, the wether lambs were slaughtered to determine carcass characteristics and muscle samples were taken from the bicep femoris. The abundance of mature myostatin protein in muscle from 1 wk old lambs was less (P=0.05) in MSTN A/A and MSTN A/G compared with MSTN G/G lambs. However, at 4 and 24 wk the MSTN A/A lambs had a greater (P=0.04) abundance of myostatin protein compared with the MSTN A/G and MSTN G/G lambs. The abundance of mature myostatin did not differ between genotypes in plasma but the myostatin protein did increase as the lambs aged. At slaughter the MSTN A/A wether lambs had greater dressing percentages (P=0.04), shortloin (P=0.01), topside (P<0.001), and round (P=0.01) weights but did not differ in final BW or HCW (P>0.05). The MSTN A/A lambs had more muscle fibers (P=0.02) in the cross-section of LM between the 12th and 13th rib. The MSTN A/A lambs also had greater lean (P=0.002), less fat (P=0.009), and reduced organ (heart, liver, spleen, and kidneys) mass as determined by computed tomography scanning than MSTN G/G lambs. The results of this study demonstrated that lambs homozygous for the MSTN g+6723G>A mutation have changes in carcass characteristics (dressing and total lean), organ weights, and muscle fiber number. This may be due to reduced myostatin protein early in utero, but after 4 wk of age there was no difference in the abundance of mature myostatin protein in muscle or plasma among MSTN A/A, MSTN A/G, and MSTN G/G genotypes. PMID:23048142

Haynes, F E M; Greenwood, P L; McDonagh, M B; McMahon, C D; Nicholas, G D; Berry, C J; Oddy, V H

2013-01-01

388

Association of the interleukin 1 receptor antagonist gene with ulcerative colitis in Northern European Caucasians  

PubMed Central

BACKGROUND AND AIMS—An association between the allele 2 of the interleukin 1 receptor antagonist gene variable number tandem repeats polymorphism in intron 2 and ulcerative colitis was first reported in 1994. Subsequent studies in Caucasian Northern European patients have not confirmed this, although trends towards an association were observed. The lack of statistical significance could reflect inadequate power. In this study the association was reassessed in a large independent set of well characterised Caucasian patients and a meta-analysis of reported patient series was performed.?PATIENTS AND METHODS—A total of 320 patients with endoscopically and histologically confirmed ulcerative colitis (124 pancolitis, 196 left sided and distal disease) and 827 ethnically matched controls were genotyped at polymorphic sites in the interleukin 1 receptor antagonist gene. Carriage rates were compared using ?2 statistics. A meta-analysis of this and seven previous studies in North European Caucasian patients was performed using the Mantel-Haenszel ?2 test.?RESULTS—Patients had a significantly increased carriage rate of allele 2 compared with controls (52% v 45%; odds ratio 1.3 (95% confidence interval (CI) 1.01-1.7); p=0.04). The allele 2 carriage rate was highest in extensive colitis (carriage rate 56%; odds ratio 1.5 (95% CI 1.1-2.3) p=0.02) and in individuals who had undergone colectomy (carriage rate 55%; odds ratio 1.5 (95% CI 0.95-2.4); p=0.08). Meta-analysis of all eight studies showed a significant association between carriage of allele 2 and ulcerative colitis (odds ratio 1.23 (95% CI 1.04-1.45); p=0.01).?CONCLUSIONS—The association of the interleukin 1 receptor antagonist gene polymorphism with ulcerative colitis is confirmed. The association is minor and confers only a small risk to an individual but will contribute a high attributable risk in a population due to the high allelic frequency. Accurate phenotypic characterisation defines more homogeneous subsets of patients, such as those with extensive disease, in whom the association is greater.???Keywords: ulcerative colitis; cytokine gene polymorphisms; interleukin 1 receptor antagonist; interleukin 1; inflammatory bowel disease; genetics PMID:11247888

Carter, M; di, G; Jones, S; Mee, J; Camp, N; Lobo, A; Duff, G

2001-01-01

389

Human Leukocyte Antigen Class I and II Alleles and Cervical Adenocarcinoma  

PubMed Central

Background: Associations between human leukocyte antigens (HLA) alleles and cervical cancer are largely representative of squamous cell carcinoma (SCC), the major histologic subtype. We evaluated the association between HLA class I (A, B, and C) and class II (DRB1 and DQB1) loci and risk of cervical adenocarcinoma (ADC), a less common but aggressive histologic subtype. Methods: We pooled data from the Eastern and Western US Cervical Cancer studies, and evaluated the association between individual alleles and allele combinations and ADC (n?=?630 ADC; n?=?775 controls). Risk estimates were calculated for 11 a priori (based on known associations with cervical cancer regardless of histologic type) and 38 non a priori common alleles, as odds ratios (OR) and 95% confidence intervals (CI), adjusted for age and study. In exploratory analysis, we compared the risk associations between subgroups with HPV16 or HPV18 DNA in ADC tumor tissues in the Western US study cases and controls. Results: Three of the a priori alleles were significantly associated with decreased risk of ADC [DRB1*13:01 (OR?=?0.61; 95% CI: 0.41–0.93), DRB1*13:02 (OR?=?0.49; 95% CI: 0.31–0.77), and DQB1*06:03 (OR?=?0.64; 95% CI: 0.42–0.95)]; one was associated with increased risk [B*07:02 (OR?=?1.39; 95% CI: 1.07–1.79)]. Among alleles not previously reported, DQB1*06:04 (OR?=?0.46; 95% CI: 0.27–0.78) was associated with decreased risk of ADC and remained significant after correction for multiple comparisons, and C*07:02 (OR?=?1.41; 95% CI: 1.09–1.81) was associated with increased risk. We did not observe a difference by histologic subtype. ADC was most strongly associated with increased risk with B*07:02/C*07:02 alleles (OR?=?1.33; 95% CI: 1.01–1.76) and decreased risk with DRB1*13:02/DQB1*06:04 (OR?=?0.41; 95% CI: 0.21–0.80). Conclusion: Results suggest that HLA allele associations with cervical ADC are similar to those for cervical SCC. An intriguing finding was the difference in risk associated with several alleles restricted to HPV16 or HPV18-related tumors, consistent with the hypothesis that HLA recognition is HPV type-specific. PMID:24995157

Safaeian, Mahboobeh; Johnson, Lisa G.; Yu, Kai; Wang, Sophia S.; Gravitt, Patti E.; Hansen, John A.; Carrington, Mary; Schwartz, Stephen M.; Gao, Xiaojiang; Hildesheim, Allan; Madeleine, Margaret M.

2014-01-01

390

European Ancestry Predominates in Neuromyelitis Optica and Multiple Sclerosis Patients from Brazil  

PubMed Central

Background Neuromyelitis optica (NMO) is considered relatively more common in non-Whites, whereas multiple sclerosis (MS) presents a high prevalence rate, particularly in Whites from Western countries populations. However, no study has used ancestry informative markers (AIMs) to estimate the genetic ancestry contribution to NMO patients. Methods Twelve AIMs were selected based on the large allele frequency differences among European, African, and Amerindian populations, in order to investigate the genetic contribution of each ancestral group in 236 patients with MS and NMO, diagnosed using the McDonald and Wingerchuck criteria, respectively. All 128 MS patients were recruited at the Faculty of Medicine of Ribeirão Preto (MS-RP), Southeastern Brazil, as well as 108 healthy bone marrow donors considered as healthy controls. A total of 108 NMO patients were recruited from five Neurology centers from different Brazilian regions, including Ribeirão Preto (NMO-RP). Principal Findings European ancestry contribution was higher in MS-RP than in NMO-RP (78.5% vs. 68.7%) patients. In contrast, African ancestry estimates were higher in NMO-RP than in MS-RP (20.5% vs. 12.5%) patients. Moreover, principal component analyses showed that groups of NMO patients from different Brazilian regions were clustered close to the European ancestral population. Conclusions Our findings demonstrate that European genetic contribution predominates in NMO and MS patients from Brazil. PMID:23527051

Santos, Antônio Carlos; Lana-Peixoto, Marco Aurélio; Rocha, Cristiane Franklin; Brito, Maria Lucia; de Oliveira, Enedina Maria Lobato; Bichuetti, Denis Bernardi; Gabbai, Alberto Alan; Diniz, Denise Sisterolli; Kaimen-Maciel, Damacio Ramon; Comini-Frota, Elizabeth Regina; Vieira Wiezel, Claudia E.; Muniz, Yara Costa Netto; da Silva Costa, Roberta Martins; Mendes-Junior, Celso Teixeira; Donadi, Eduardo Antônio; Barreira, Amilton Antunes; Simões, Aguinaldo Luiz

2013-01-01

391

Sex-chromosome differentiation parallels postglacial range expansion in European tree frogs (Hyla arborea).  

PubMed

Occasional XY recombination is a proposed explanation for the sex-chromosome homomorphy in European tree frogs. Numerous laboratory crosses, however, failed to detect any event of male recombination, and a detailed survey of NW-European Hyla arborea populations identified male-specific alleles at sex-linked loci, pointing to the absence of XY recombination in their recent history. Here, we address this paradox in a phylogeographic framework by genotyping sex-linked microsatellite markers in populations and sibships from the entire species range. Contrasting with postglacial populations of NW Europe, which display complete absence of XY recombination and strong sex-chromosome differentiation, refugial populations of the southern Balkans and Adriatic coast show limited XY recombination and large overlaps in allele frequencies. Geographically and historically intermediate populations of the Pannonian Basin show intermediate patterns of XY differentiation. Even in populations where X and Y occasionally recombine, the genetic diversity of Y haplotypes is reduced below the levels expected from the fourfold drop in copy numbers. This study is the first in which X and Y haplotypes could be phased over the distribution range in a species with homomorphic sex chromosomes; it shows that XY-recombination patterns may differ strikingly between conspecific populations, and that recombination arrest may evolve rapidly (<5000 generations). PMID:25209463

Dufresnes, Christophe; Bertholet, Youna; Wassef, Jérôme; Ghali, Karim; Savary, Romain; Pasteur, Baptiste; Brelsford, Alan; Rozenblut-Ko?cisty, Beata; Ogielska, Maria; Stöck, Matthias; Perrin, Nicolas

2014-12-01

392

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

PubMed Central

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

1993-01-01

393

Allelic imbalance of HER2 variant in sporadic breast and ovarian cancer.  

PubMed

Both breast and ovarian cancers are associated with HER2 receptor activation, which usually results from receptor overexpression and/or gene amplification. The HER-2 gene harbors a polymorphism at codon 655 (GTC/valine to ATC/isoleucine) in the transmembrane domain region, which has been associated with an elevated risk of breast cancer. The objective of this study was to determine whether the polymorphism is under a selection pressure during breast and ovarian carcinogenesis. The Ile/Val genotype was present in 41% (9/22) of the normal DNA of breast cancer patients. An allelic imbalance in the tumor tissue was found in three breast tumors, with overrepresentation of the Val allele. HER-2 was amplified and overexpressed in these tumors. Half of the eight ovarian tumor patients carried heterozygous Ile/Val genotypes. In contrast to breast tumors, all these ovarian cancer specimens showed the presence of the Ile allele. In our selected set of tumors, the Val allele was overrepresented in the subset of HER2-positive breast cancers and the Ile allele in serous ovarian cancer. Further analyses of tumors with known gene amplifications and overexpression may reveal novel associations between germline polymorphisms and development of sporadic tumors. PMID:16682283

Puputti, Marjut; Sihto, Harri; Isola, Jorma; Butzow, Ralf; Joensuu, Heikki; Nupponen, Nina N

2006-05-01

394

Distribution of an allele associated with blond hair color across Northern Island Melanesia.  

PubMed

Pigmentation of the skin, hair, and eyes is a complex trait controlled by multiple genetic loci. Recently a non-synonymous mutation in the pigmentation candidate gene TYRP1 was shown to be significantly associated with a blond-hair phenotype in populations from the Solomon Islands. The distribution of this mutation in the islands of Northern Island Melanesia, where the blondism phenotype is also prevalent, was unknown. Here, we present data describing the distribution of this allele in 550 individuals sampled from across this region, and test for associations between genotype at this locus and quantitatively measured skin and hair pigmentation phenotype. We report that the frequency of the 93C allele is notably lower than observed in the Solomons (0.12 vs. 0.26). The allele exhibits significant geographic heterogeneity across the islands sampled (?(2) ?=?108.4, P?allele is significantly associated with a decrease in hair pigmentation but not skin pigmentation. We discuss the distribution of the 93C allele across the Southwest Pacific in light of its possible place of origin and dispersal. PMID:24449225

Norton, Heather L; Correa, Elena A; Koki, George; Friedlaender, Jonathan S

2014-04-01

395

Allele-specific genetic interactions between Mitf and Kit affect melanocyte development  

PubMed Central

Summary The tyrosine kinase receptor KIT and the transcription factor MITF, each required for melanocyte development, have been shown to interact functionally both in vitro and in vivo. In vitro, KIT signaling leads to MITF phosphorylation, affecting MITF activity and stability. In vivo, the presence of the MitfMi-wh allele exacerbates the spotting phenotype associated with heterozygosity for Kit mutations. Here we show that among a series of other Mitf alleles, only the recessive Mitfmi-bws mimics the effect of MitfMi-wh on Kit. Intriguingly, Mitfmi-bws is characterized by a splice defect that leads to a reduction of RNAs containing MITF exon 2B which encodes serine-73, a serine phosphorylated upon KIT signaling. Nevertheless, other Mitf alleles that generally affect Mitf RNA levels, or carry a serine-73-to-alanine mutation that specifically reduces exon 2B-containing RNAs, do not show interactions with Kit in vivo. We conclude that the recessive Mitfmi-bws is a complex allele that can display a semi-dominant effect when present in a Kit-sensitized background. We suggest that human disease variability may equally be due to complex, allele-specific interactions between different genes. PMID:20374522

Wen, Bin; Chen, Yu; Li, Huirong; Wang, Jin; Shen, Jie; Ma, Aobo; Qu, Jia; Bismuth, Keren; Debbache, Julien; Arnheiter, Heinz; Hou, Ling

2010-01-01

396

Interaction of MC1R and PMEL alleles on solid coat colors in Highland cattle.  

PubMed

Six solid colors occur in Highland cattle: black, dun, silver dun and red, yellow, and white. These six coat colors are explained by a non-epistatic interaction of the genotypes at the MC1R and PMEL genes. A three base pair deletion in the PMEL gene leading to the deletion of a leucine from the signal peptide is observed in dilute-colored Highland cattle (c.50_52delTTC, p.Leu18del). The mutant PMEL allele acts in a semi-dominant manner. Dun Galloway cattle also have one copy of the deletion allele, and silver dun Galloway cattle have two copies. The presence of two adjacent leucine residues at the site of this deletion is highly conserved in human, horse, mouse and chicken as well as in cattle with undiluted coat colors. Highland and Galloway cattle thus exhibit a similar dose-dependent dilution effect based on the number of PMEL :c.50_51delTTC alleles, as Charolais cattle with PMEL :c.64G>A alleles. The PMEL :c.64G>A allele was not found in Highland or Galloway cattle. PMID:22524257

Schmutz, Sheila M; Dreger, Dayna L

2013-02-01

397

Osteogensis imperfecta type I is commonly due to a COLIAI null allel of type I collagen  

SciTech Connect

Dermal fibroblasts from most individuals with osteogenesis imperfecta (OI) type I produce about half the normal amount of type I procollagen, as a result of decreased synthesis of one of its constituent chains, pro[alpha](I). To test the hypothesis that decreased synthesis of pro[alpha](I) chains results from mutations in the COL1A1 gene, the authors used primer extension with nucleotide-specific chain termination to measure the contribution of individual COL1A1 alleles to the mRNA pool in fibroblasts from affected individuals. A polymorphic Mn/I restriction endonuclease site in the 3'-untranslated region of COL1A1 was used to distinguish the transcripts of the two alleles in heterozygous individuals. Twenty-three individuals from 21 unrelated families were studied. In each case there was marked diminution in steady-state mRNA levels from one COL1A2 allele. Loss of an allele through deletion or rearrangement was not the cause of the diminished COL1A1 mRNA levels. Primer extension with nucleotide-specific chain termination allows identification of the mutant COL1A1 allele in cell strains that are heterozygous for an expressed polymorphism. It is applicable to sporadic cases, to small families, and to large families in whom key individuals are uninformative at the polymorphic sites used in linkage analysis, making it a useful adjunct to the biochemical screening of collagenous proteins for OI. 40 refs., 3 figs., 1 tab.

Willing, M.C.; Pruchno, C.J. (Univ. of Iowa, Iowa City, IA (United States)); Atkinson, M.; Byers, P.H. (Univ. of Washington, Seattle, WA (United States))

1992-09-01

398

Allele-specific copy number profiling by next-generation DNA sequencing.  

PubMed

The progression and clonal development of tumors often involve amplifications and deletions of genomic DNA. Estimation of allele-specific copy number, which quantifies the number of copies of each allele at each variant loci rather than the total number of chromosome copies, is an important step in the characterization of tumor genomes and the inference of their clonal history. We describe a new method, falcon, for finding somatic allele-specific copy number changes by next generation sequencing of tumors with matched normals. falcon is based on a change-point model on a bivariate mixed Binomial process, which explicitly models the copy numbers of the two chromosome haplotypes and corrects for local allele-specific coverage biases. By using the Binomial distribution rather than a normal approximation, falcon more effectively pools evidence from sites with low coverage. A modified Bayesian information criterion is used to guide model selection for determining the number of copy number events. Falcon is evaluated on in silico spike-in data and applied to the analysis of a pre-malignant colon tumor sample and late-stage colorectal adenocarcinoma from the same individual. The allele-specific copy number estimates obtained by falcon allows us to draw detailed conclusions regarding the clonal history of the individual's colon cancer. PMID:25477383

Chen, Hao; Bell, John M; Zavala, Nicolas A; Ji, Hanlee P; Zhang, Nancy R

2014-12-01

399

The role of double-strand break-induced allelic homologous recombination in somatic plant cells.  

PubMed

During meiosis, homologous recombination occurs between allelic sequences. To evaluate the biological significance of such a pathway in somatic cells, we used transgenic tobacco plants with a restriction site for the rare cutting endonuclease I-SceI within a negative selectable marker gene. These plants were crossed with two tobacco lines containing, in allelic position, either a deletion or an insertion within the marker gene that rendered both marker gene and restriction site inactive. After the double-strand break induction, we selected for repair events resulting in a loss of marker gene function. This loss was mostly due to deletions. We were also able to detect double strand break-induced allelic recombination in which the break was repaired by a faithful copying process from the homologue carrying the shortened transgene. The estimated frequency indicates that homologous recombination in somatic cells between allelic sites appears to occur at the same order of magnitude as between ectopic sites, and is thus far too infrequent to act as major repair pathway. As somatic changes can be transferred to the germ line, the prevalence of intrachromatid rearrangements over allelic recombination might be an indirect prerequisite for the enhanced genome plasticity postulated for plants. PMID:12410807

Gisler, Brigitte; Salomon, Siegfried; Puchta, Holger

2002-11-01

400

Stepwise arms race between AvrPik and Pik alleles in the rice blast pathosystem.  

PubMed

A stepwise mutation that occurred in both pathogens and their respective hosts has played a seminal role in the co-evolutionary arms race evolution in diverse pathosystems. The process driven by rice blast AvrPik and Pik alleles was investigated through population genetic and evolutionary approaches. The genetic diversity of the non-signal domain of AvrPik was higher than that in its signal peptide domain. Positive selection for particular AvrPik alleles in the northeastern region of China was stronger than in the south. The perfect relationship between the functional lineages and AvrPik allele-specific pathotypes was established by ruling out the nonfunctional lineages derived from additional copies. Only four alleles conditioning stepwise pathotypes were detected in natural populations, which were likely created by only one evolutionary pathway with three recognizable mutation steps. Two non-stepwise pathotypes were determined by two blocks in a network constructed by all 16 possible alleles, indicating that a natural evolution process can be artificially changed by a combination of specific single-nucleotide polymorphisms. Assuming that AvrPik evolution has been largely driven by host selection, the co-evolutionary stepwise relationships between AvrPik and Pik was established. The experimental validation of stepwise mutation is required for the development of sustainable management strategies against plant disease. PMID:24742074

Wu, Weihuai; Wang, Ling; Zhang, Shu; Li, Zekang; Zhang, Yu; Lin, Fei; Pan, Qinghua

2014-08-01

401

Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles  

PubMed Central

The genomic basis of adaptation to novel environments is a fundamental problem in evolutionary biology that has gained additional importance in the light of the recent global change discussion. Here, we combined laboratory natural selection (experimental evolution) in Drosophila melanogaster with genome-wide next generation sequencing of DNA pools (Pool-Seq) to identify alleles that are favourable in a novel laboratory environment and traced their trajectories during the adaptive process. Already after 15 generations, we identified a pronounced genomic response to selection, with almost 5000 single nucleotide polymorphisms (SNP; genome-wide false discovery rates < 0.005%) deviating from neutral expectation. Importantly, the evolutionary trajectories of the selected alleles were heterogeneous, with the alleles falling into two distinct classes: (i) alleles that continuously rise in frequency; and (ii) alleles that at first increase rapidly but whose frequencies then reach a plateau. Our data thus suggest that the genomic response to selection can involve a large number of selected SNPs that show unexpectedly complex evolutionary trajectories, possibly due to nonadditive effects. PMID:22726122

Orozco-terWengel, Pablo; Kapun, Martin; Nolte, Viola; Kofler, Robert; Flatt, Thomas; Schlötterer, Christian

2012-01-01

402

Europages: The European Business Directory  

NSDL National Science Digital Library

Europages is a pan-European purchaser's guide featuring a selection of 150,000 companies from 25 European countries. Published in collaboration with the major European telecom companies for 13 years, it is now available online. Europages can be searched in 5 languages, and additional languages will be available in the near future. Europages' Economic Info Service provides an economic indicators for all the industrial, commercial and service sectors driving Europe's economy. A selection of tables, maps and graphs presents the key figures and main short- and medium-term trends for each of the 18 Europages sectors can be viewed with Adobe Acrobat. (A link to Adobe is provided to download the Acrobat reader.)

1998-01-01

403

Guide to European Legal Databases  

NSDL National Science Digital Library

The New York University (NYU) Law School Reference Librarian For International and Foreign Law, Mirela Roznovschi, has prepared this excellent Guide to European Legal Databases. The Guide offers recommendations for search engines and search tips/strategies for researching foreign law topics. Visitors will find the annotated list of European Websites useful for finding constitutional, copyright, and environmental laws (many laws listed by country). Also referenced in the Guide are sites covering the laws of Austria, Belgium, Denmark, England, France, Germany, Italy, Norway, Russia, Spain, Sweden, Switzerland, the Council of Europe, and the European Union. A section entitled Indices, Guides, Journals, Dictionaries, Library Catalogs covers consolidated resource guides and notable collections, to facilitate further research efforts.

404

European Register of Marine Species  

NSDL National Science Digital Library

This website presents the European Register of Marine Species, an EU-funded marine biodiversity research consortium involving research groups in nine European nations. An ultimate goal of the project was to "produce a register of marine species in Europe, linked with a bibliography of identification guides, register of taxonomic experts, locations of collections of reference specimens, and an Information Pack on European marine biodiversity (based on this project's results)." The site links to brief and full checklists for numerous taxa including information on genus, higher taxon, authority, specific epithet, distribution, and more. From the species pages, site users can link to information about the checklists, identification guides, and taxonomic hierarchy. The homepage provides links to information about project participants, project background, and a simple map illustrating the geographic scope of the project. This site is also reviewed in the April 2, 2004 _NSDL Life Sciences Report_.

405

European Economic and Social Committee  

NSDL National Science Digital Library

The European Economic and Social Committee (EESC) is a "consultative body of the European Union." The EESC is meant to serve as "a bridge between European and organized civil society", and their work includes networking with other governmental organization, adopting policy resolutions and suggestions, and researching energy issues, among other things. The materials on the site are divided into seven primary sections, including "Documents", "Themes", and "Events & Activities". A good place to get started is the "Themes" area, which features information about their recent activities in areas like civil society, consumers, economics, and agriculture and environment. Along the left-side of this page, visitors can look at the latest events and conferences related to each separate theme. Moving along, the "Documents" area includes opinion pieces and working papers such as "EU-Canada Relations" and "Higher Education and Entrepreneurship". Lastly, the "Press & Media" area includes videos, interviews, and photo galleries.

406

Divergent allele advantage at MHC-DRB through direct and maternal genotypic effects and its consequences for allele pool composition and mating  

PubMed Central

It is still debated whether main individual fitness differences in natural populations can be attributed to genome-wide effects or to particular loci of outstanding functional importance such as the major histocompatibility complex (MHC). In a long-term monitoring project on Galápagos sea lions (Zalophus wollebaeki), we collected comprehensive fitness and mating data for a total of 506 individuals. Controlling for genome-wide inbreeding, we find strong associations between the MHC locus and nearly all fitness traits. The effect was mainly attributable to MHC sequence divergence and could be decomposed into contributions of own and maternal genotypes. In consequence, the population seems to have evolved a pool of highly divergent alleles conveying near-optimal MHC divergence even by random mating. Our results demonstrate that a single locus can significantly contribute to fitness in the wild and provide conclusive evidence for the ‘divergent allele advantage’ hypothesis, a special form of balancing selection with interesting evolutionary implications. PMID:23677346