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DNA Polymorphism (dna + polymorphism)
Selected AbstractsOptimisation of AP,PCR fingerprinting discriminatory power for clinical isolates of Pseudomonas aeruginosaFEMS MICROBIOLOGY LETTERS, Issue 1 2003Waldemar Da, browski Abstract Recently methods based on analysis of arbitrarily amplified target sites of microorganism genomes have been extensively applied in microbiological studies. The range of their applications is limited by problems with discrimination and reproducibility resulting from lack of standardised and reliable methods of optimisation. By orthogonal-array optimisation most advantageous and optimal parameters for highly discriminatory primers (CagA2+CMVin2) were selected and efficient AP,PCR (arbitrarily primed-polymerase chain reaction) fingerprinting conditions for Pseudomonas aeruginosa isolates were set up. Stable and multiplex amplicon profiles obtained in this study revealed high level of intraspecies DNA polymorphism among 20 analysed clinical strains of P. aeruginosa proving optimised AP,PCR fingerprinting to be useful in epidemiological typing of the species. [source] Morphometric and genetic variation of small dwarf honeybees Apis andreniformis Smith, 1858 in ThailandINSECT SCIENCE, Issue 6 2007ATSALEK RATTANAWANNEE Abstract The small dwarf honey bee, Apis andreniformis, is a rare and patchily distributed Apis spp. and is one of the native Thai honey bees, yet little is known about its biodiversity. Thirty (27 Thai and 3 Malaysian) and 37 (32 Thai and 5 Malaysian) colonies of A. andreniformis were sampled for morphometric and genetic analysis, respectively. For morphometric analysis, 20 informative characters were used to determine the variation. After plotting the factor scores, A. andreniformis from across Thailand were found to belong to one group, a notion further supported by a cluster analysis generated dendrogram. However, clinal patterns in groups of bee morphometric characters were revealed by linear regression analysis. The body size of bees increases from South to North but decreases from West to East, although this may reflect altitude rather than longitude. Genetic variation was determined by sequence analysis of a 520 bp fragment of the mitochondrial cytochrome oxidase subunit b (cytb). DNA polymorphism among bees from the mainland of Thailand is lower than that from Phuket Island and Chiang Mai. Although two main different groups of bees were obtained from phylogenetic trees constructed by neighbor-joining and unweighted pair-group method using arithmetic averages programs, no clear geographic signal was present. Thus, while the minor group (B) contained all of the samples from the only island sampled (Phuket in the south), but not the southern mainland colonies, it also contained samples from the far northern inland region of Chiang Mai, other samples of which were firmly rooted in the major group (A). [source] A new HpaII PCR-RFLP within the porcine prolactin receptor (PRLR) gene and study of its effect on litter size and number of teatsJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 1 2002L. PUTNOVÁ DNA polymorphism of the porcine prolactin receptor gene (PRLR) was investigated and used to study its effect on litter size and number of teats in pigs. By means of PRLR gene sequence homology in pig, human and other species, primers were designed for PCR amplification within 5, unknown (to date) part of the prolactin receptor gene in pigs. In this part of the gene, a new polymorphism with HpaII restriction endonuclease was detected. AluI polymorphism described before and our new HpaII polymorphism were used to study the associations with reproduction traits. The PCR restriction fragment length polymorphism (PCR-RFLP) method was used to genotype AluI and HpaII loci of the PRLR gene in line A with 83 sows of Landrace breed and in two lines (B and C) with 75 and 86 Large White sows, respectively. Statistical analysis of 1020 litters showed that AluI locus was associated with litter size mainly in Landrace and affected the first parities, while HpaII locus of the gene was associated with the same traits in Landrace and Large White pigs and mainly affected numbers of weaned of pigs. The magnitude of the effect varied by population with the effects exceeding two pigs per litter in Landrace line and 1 pig per litter in Large White populations. Ein neuer HpaII PCR-RFLP innerhalb des porcinen Prolaktionrezeptorgens (PRLR), und Zusammenhänge zur Wurfgröße und Zitzenzahl DNA-Polymorphismen im porcinen Prolaktionrezeptorgen (PRLR) wurden untersucht und für die Analyse von Einflüssen auf Wurfgröße und Zitzenzahl bei Schweinen verwendet. Auf der Basis der PRLR -Gensequenzhomologie zwischen Schwein, Mensch und anderen Spezies wurden Primer für die PCR-Amplifikation aus dem 5, Bereich des Prolaktionrezeptorgens abgeleitet, der bisher beim Schwein noch unbekannt ist. In diesem Teil des Gens wurde mittels HpaII-Restriktionsendonuklease ein neuer Polymorphismus dargestellt. AluI Polymorphismus und der neue HpaII Polymorphismus wurden für Assoziationsstudien in Bezug auf Reproduktionsmerkmale verwendet. Mittels PCR-RFLP wurden in Linie A 83 Sauen der Landrasse und die Linien B und C mit 75 bzw. 86 Large White Sauen unter Verwendung von AluI und HpaII am PRLR -Gen genotypisiert. Die statistische Analyse von 1.020 Würfen zeigte, dass der AluI-Polymorphismus insbesondere in der Landrasse mit der Wurfgröße assoziiert ist, sowie die ersten Trächtigkeiten beeinflusst, während der HpaII Polymorphismus die gleichen Merkmale in der Landrasse und Large White Schweinen und insbesondere die Zahl an abgesetzten Ferkeln beeinflusste. Die Auswirkungen des Effekts variierten innerhalb Population, wobei der Effekt 2 Ferkel je Wurf in der Landrasse-Linie und 1 Ferkel je Wurf in der Large White Populationen überstieg. [source] Variation in synonymous codon use and DNA polymorphism within the Drosophila genomeJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 1 2006N. BIERNE Abstract A strong negative correlation between the rate of amino-acid substitution and codon usage bias in Drosophila has been attributed to interference between positive selection at nonsynonymous sites and weak selection on codon usage. To further explore this possibility we have investigated polymorphism and divergence at three kinds of sites: synonymous, nonsynonymous and intronic in relation to codon bias in D. melanogaster and D. simulans. We confirmed that protein evolution is one of the main explicative parameters for interlocus codon bias variation (r2, 40%). However, intron or synonymous diversities, which could have been expected to be good indicators of local interference [here defined as the additional increase of drift due to selection on tightly linked sites, also called ,genetic draft' by Gillespie (2000)] did not covary significantly with codon bias or with protein evolution. Concurrently, levels of polymorphism were reduced in regions of low recombination rates whereas codon bias was not. Finally, while nonsynonymous diversities were very well correlated between species, neither synonymous nor intron diversities observed in D. melanogaster were correlated with those observed in D. simulans. All together, our results suggest that the selective constraint on the protein is a stable component of gene evolution while local interference is not. The pattern of variation in genetic draft along the genome therefore seems to be instable through evolutionary times and should therefore be considered as a minor determinant of codon bias variance. We argue that selective constraints for optimal codon usage are likely to be correlated with selective constraints on the protein, both between codons within a gene, as previously suggested, and also between genes within a genome. [source] Genetic analysis of offspring from intra- and interspecific crosses of Carassius auratus gibelio by chromosome and RAPD analysisJOURNAL OF FISH BIOLOGY, Issue 3 2005B. Tóth The ploidy of silver crucian carp Carassius auratus gibelio individuals, originating from nine natural habitats of Hungary, was estimated by erythrocyte nucleus area analysis. On the basis of DNA polymorphism, the genetic homogeneity or heterogeneity and the chromosome number of different offspring derived from the crossing of triploid and diploid populations and of two types of silver crucian carp females with other cyprinid males (Cyprinus carpio, Carassius carassius, Carassius auratus and Barbus conchonius) were determined. The results of chromosome and RAPD analysis demonstrated that diploid females could reproduce sexually with silver crucian carp and other cyprinid males and that the offspring of intra- and interspecific crosses contained the paternal DNA. Triploid females usually reproduced by gynogenesis and their offspring were clones, however, in very rare cases paternal genes were actually transmitted (i.e. paternal leakage) to the offspring and the progeny were triploid interspecific hybrids. RAPD analysis showed that while the paternal DNA appeared in the offspring, the maternal phenotype was strongly expressed. [source] E-selectin and L-selectin polymorphisms in patients with periodontitisJOURNAL OF PERIODONTAL RESEARCH, Issue 1 2009B. Houshmand Background amd Objective:, Periodontitis is a multifactorial disease in which environmental and genetic determinant factors contribute to individual subject's susceptibility. A DNA polymorphism in the regulating region of adhesion molecule genes is suggested to modulate the molecule's physiological effects. The aim of this study was to investigate the genetic association between the E-selectin Ser128Arg and L-selectin Phe206Leu polymorphisms and periodontitis. Material and Methods:, DNA was isolated from the whole blood of 88 patients with periodontitis and 139 healthy individuals. All samples were genotyped for the E-selectin Ser128Arg and L-selectin Phe206Leu polymorphisms using the polymerase chain reaction with sequence specific primers. Results:, Our findings revealed a significant difference in the Ser128Arg polymorphism of E-selectin, but not in the L-selectin polymorphism, between periodontal patients and controls. The 128Arg allele was present more frequently in patients than in healthy individuals (31.25% vs. 12.2%, p < 0.0001). In addition, there was an association between the presence of the 128Arg allele and periodontitis (odds ratio 2.9; 95% confidence interval: 1.75,4.4, p < 0.0001). No significant association was found between the polymorphisms tested and the subgroups of periodontal disease (i.e. chronic periodontitis and aggressive periodontitis). Conclusion:, The findings of this study showed that the Ser128Arg polymorphism of E-selectin might contribute to the susceptibility of Iranian individuals to periodontitis. [source] Expression Profile During the Development of Appressoria Induced by Hydrophobic Surfaces in Magnaporthe grisea Y34JOURNAL OF PHYTOPATHOLOGY, Issue 3 2010Qingchao Jin Abstract To study the gene expression profile during appressorium developmental process of Magnaphorthe grisea strain Y34 isolated from the rich area of Asia cultivated rice resources, expressed sequence tags (ESTs) and cDNA array analysis were performed. A total of 4756 tentative unique transcripts (TUTs) were obtained from 13 057 ESTs of the 3, ends of the strain, which was approximately 25% of the total M. grisea EST sequences deposited in the GenBank database. Approximately 84% of these TUTs matched with the published draft genome sequences of strain 70-15. Southern analyses with 12 TUT probes revealed no obvious DNA polymorphism among strains 70-15, Guy11 and Y34. A cDNA array with 4108 TUTs was used to monitor gene expression patterns during appressorium development of M. grisea. Compared with ungerminated conidia, the number of up-regulated and down-regulated genes was almost consistent at any time-points of 2, 8, 20 and 30 h during appressorium development. More genes were differentially expressed during appressorium maturation (20 and 30 h) than during appressorium induction (2 h) and formation (8 h). During appressorium maturation (20,30 h), genes generally seemed to be most actively expressed. [source] Analysis of Mycelial Growth Rates and RAPD-PCR Profiles in a Population of Gaeumannomyces graminis var. tritici Originating from Wheat Plants Grown from Fungicide-treated SeedJOURNAL OF PHYTOPATHOLOGY, Issue 6 2005Z. Weber Abstract Linear mycelial growth rates of 70 isolates of Gaeumannomyces graminis var. tritici on agar medium amended or unamended with the fungicide silthiofam were not correlated. Mycelial growth rate was not influenced by the fungicide applied to the seed of the plants from, which the isolates originated. DNA polymorphism determined by randomly amplified polymorphic DNA (RAPD) polymerase chain reaction was used to assess genetic variation among isolates. Thirty RAPD markers generated with five arbitrary 10-mer primers revealed DNA polymorphism suitable for assessing variability in this fungal population. Cluster analysis of RAPD data identified two groups at the 54% similarity level. There was a significant relationship between the presence of 11 markers and sensitivity to silthiofam. [source] Molecular Variability of Mycosphaerella graminicola as Detected by RAPD MarkersJOURNAL OF PHYTOPATHOLOGY, Issue 10 2004M. Razavi Abstract A total of 90 isolates of Mycosphaerella graminicola, the cause of septoria tritici leaf blotch of wheat, were tested for DNA polymorphism using 15 decamer random primers. There was a high level of genetic variability among isolates. In 131 random amplified polymorphic DNA (RAPD) fragments, which were produced, 96% were polymorphic. Based on multilocus analysis, 40 different molecular phenotypes were detected. These molecular phenotypes were randomly distributed among sampling sites, suggesting that no clonal structure existed in the population. Cluster analysis showed that the maximum similarity value among isolates was approximately 81% and no identical isolates were detected, indicating that every isolate was a unique genotype. The high degree of DNA polymorphism, the large number of different molecular phenotypes, their random distribution and the results of the cluster analysis all suggested that sexual reproduction has a major role in the genetic structure of M. graminicola in western Canada. The presence of sexual reproduction provides the opportunity for development of new virulent genotypes in the population and suggests that the pathogen may adapt rapidly to any race-specific sources of resistance. Therefore, when breeding for resistance to M. graminicola, emphasis should be placed on use of non-race-specific resistance. [source] High population differentiation and unusual haplotype structure in a shade-intolerant pioneer tree species, Zanthoxylum ailanthoides (Rutaceae) revealed by analysis of DNA polymorphism at four nuclear lociMOLECULAR ECOLOGY, Issue 10 2008K. KAMIYA Abstract Differences in demographic history, life-history traits, and breeding systems affect nucleotide variation patterns. It is expected that shade-intolerant pioneer tree species have different patterns of genetic polymorphism and population structure than climax species. We studied patterns of nucleotide polymorphism at four putative starch pathway loci (agpSA, agpSB, agpL, and GBSSI) in Zanthoxylum ailanthoides, a shade-intolerant pioneer tree species that occupies forest gaps in warm-temperate forests of East Asia. Genetic diversity was lower within each population than among populations, and differentiation among populations was high across the loci (FST = 0.32,0.64), as expected from the insect-pollinated breeding system and the metapopulation structure of this pioneer species. Numbers of haplotypes were smaller than those expected from the observed numbers of segregating sites. Single haplotypes accounted for more than 47% of all the sampled genes at the respective loci. These variation patterns were incompatible with neutral predictions for populations of a finite island model. Complex population dynamics, such as bottleneck and/or admixture, in the history of this pioneer tree species might have resulted in the observed patterns of genetic variation and population structure, which are different from those of climax wind-pollinated tree species, such as conifers. In contrast to the other loci investigated in this study, agpL showed nearly no variation in Z. ailanthoides (one singleton only), but there was some extent of variation in a closely related species, Zanthoxylum schinifolium. This suggests possibly a recent selective sweep at or near the locus in Z. ailanthoides. [source] INVITED REVIEW: Using genome scans of DNA polymorphism to infer adaptive population divergenceMOLECULAR ECOLOGY, Issue 3 2005JAY F. STORZ Abstract Elucidating the genetic basis of adaptive population divergence is a goal of central importance in evolutionary biology. In principle, it should be possible to identify chromosomal regions involved in adaptive divergence by screening genome-wide patterns of DNA polymorphism to detect the locus-specific signature of positive directional selection. In the case of spatially separated populations that inhabit different environments or sympatric populations that exploit different ecological niches, it is possible to identify loci that underlie divergently selected traits by comparing relative levels of differentiation among large numbers of unlinked markers. In this review I first address the question of whether diversifying selection on polygenic traits can be expected to produce predictable patterns of allelic variation at the underlying quantitative trait loci (QTL), and whether the locus-specific effects of selection can be reliably detected against the genome-wide backdrop of stochastic variability. I then review different approaches that have been developed to identify loci involved in adaptive population divergence and I discuss the relative merits of model-based approaches that rely on assumptions about population structure vs. model-free approaches that are based on empirical distributions of summary statistics. Finally, I consider the evolutionary and functional insights that might be gained by conducting genome scans for loci involved in adaptive population divergence. [source] Prion protein gene polymorphisms in Saccharomyces cerevisiaeMOLECULAR MICROBIOLOGY, Issue 4 2003Catarina G. Resende Summary The yeast Saccharomyces cerevisiae genome encodes several proteins that, in laboratory strains, can take up a stable, transmissible prion form. In each case, this requires the Asn/Gln-rich prion-forming domain (PrD) of the protein to be intact. In order to further understand the evolutionary significance of this unusual property, we have examined four different prion genes and their corresponding PrDs, from a number of naturally occurring strains of S. cerevisiae. In 4 of the 16 strains studied we identified a new allele of the SUP35 gene (SUP35,19) that contains a 19-amino-acid deletion within the N-terminal PrD, a deletion that eliminates the prion property of Sup35p. In these strains a second prion gene, RNQ1, was found to be highly polymorphic, with eight different RNQ1 alleles detected in the six diploid strains studied. In contrast, for one other prion gene (URE2) and the sequence of the NEW1 gene encoding a PrD, no significant degree of DNA polymorphism was detected. Analysis of the naturally occurring alleles of RNQ1 and SUP35 indicated that the various polymorphisms identified were associated with DNA tandem repeats (6, 12, 33, 42 or 57 bp) within the coding sequences. The expansion and contraction of DNA repeats within the RNQ1 gene may provide an evolutionary mechanism that can ensure rapid change between the [PRION+] and [prion,] states. [source] Familial fibronectin glomerulopathy: analysis of chromosome 1q32 and uteroglobin gene loci in a large New Zealand familyNEPHROLOGY, Issue 5 2001Robert Walker SUMMARY: Recently, a newly recognized familial glomerulopathy with predominant fibronectin deposits has been reported. This is the first report of a family with this condition in Australasia and spans two generations over a 30-year period, with the histologically confirmed glomerulopathy present in the father and five out of eight siblings. The clinical presentations have ranged from asymptomatic proteinuria, pregnancy-associated proteinuria and the nephrotic syndrome to hypertension and proteinuria with progressive renal failure. The time-course from presentation to renal failure was over a 20 years. Histology demonstrated global and diffuse thickening of capillary loops, but no cellular proliferation. Immunofluorescence demonstrated granular positivity for IgM in the capillary loops only. Electron microscopy demonstrated massive electron-dense subendothelial granular deposits with occasional small fibrils and unremarkable epithelial cell foot processes. Immunohistochemical staining was strongly positive for fibronectin and negative for type I or type IV collagen and transforming growth factor , in all biopsies. Genetic studies of familial fibronectin glomerulopathy have recently highlighted two genetic loci. Firstly, a large five-generation pedigree has been described with linkage of fibronectin glomerulopathy to chromosome 1q32. Secondly, fibronectin glomerulopathy has been reported in uteroglobin gene knockout mice. In our studies, DNA sequence analysis of the uteroglobin gene showed that it was normal in all family members, and a DNA polymorphism in the uteroglobin gene did not co-segregate with the disease. In addition, DNA microsatellite markers at the 1q32 locus did not co-segregate with the disease in our family. We presume that the underlying abnormality involves as yet undefined glomerular extracellular matrix regulation and is inherited as an autosomal dominant condition. These data favour genetic heterogeneity for the aetiology of fibronectin glomerulopathy. [source] Identification of S -alleles using polymerase chain reaction-cleaved amplified polymorphic sequence of the S -locus receptor kinase in inbreeding lines of Brassica oleraceaPLANT BREEDING, Issue 3 2002J. I. Park Abstract Identification and DNA polymorphism of the S -locus receptor kinasegene (SRK) was analysed by pollen tube tests, polymerase chain reaction-cleaved amplified polymorphic sequence (PCR-CAPS) and nucleotide sequencing. SRK -specific primers that can distinguish class and class II S haplotypes amplified single DNA fragments of 900-1050 bp. The DNA fragments of 22 inbred lines amplified with a class SRK -specific primer pair determined seven types with HinfI and EcoRII. In addition, the DNA fragments of 17 inbred lines amplified with a class II SRK -specific primer pair determined three types with Hinf1. Nucleotide sequencing of the DNA fragments amplified from 10S haplotypes showed that exons of the 3,-end in SRK are highly conserved, and that there is much variation of the introns, which produced polymorphism of the band pattern in PCR-CAPS profiles. The S haplotypes of the plants were determined by restriction analysis of PCR products and agreed with results based on pollen tube growth tests. The PCR-CAPS analysis using specific primer pairs of SRK is considered to be useful for S allele identification in breeding programmes. [source] Distinguishing characteristics and vegetative compatibility of Colletotrichum kahawe in comparison with other related species from coffeePLANT PATHOLOGY, Issue 2 2002V. M. P. Varzea On the basis of pathogenicity tests on green berries or hypocotyls of coffee and by morphological and biochemical characteristics in culture, 31 isolates of Colletotrichum were classified into C. kahawe (24 isolates), C. gloeosporioides (six isolates) or C. acutatum (one isolate). Within these groups of isolates, vegetative compatibility groups (VCGs) were determined by complementation tests with mutants in the nitrate assimilation pathway. There were distinct incompatibility barriers between the three species. Among the C. gloeosporioides group, the three isolates tested were self-compatible but incompatible with each other. Within C. kahawe, 18 isolates were self-compatible and only one main VCG was detected. However, partial compatibility in C. kahawe was also indicated by variation in the intensity of heterokaryon formation between different pairs of isolates and between different types of mutant. The existence of only one VCG in C. kahawe is consistent with the low level of variation found in previous work on DNA polymorphism. [source] Cattle Pathogen Tritrichomonas foetus (Riedmüller, 1928) and Pig Commensal Tritrichomonas suis (Gruby & Delafond, 1843) Belong to the Same SpeciesTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2002JAN TACHEZY ABSTRACT. A number of reports suggest that the sexually transmitted pathogen of cattle, Tritrichomonas foetus, and a gastrointestinal commensal of pigs, Tritrichomonas suis, are very similar and may be co-specific. A conclusive review of the taxonomic and nomenclatural status of these species has not been presented so far. Toward this end, we reexamined and compared porcine and bovine trichomonads with regard to their morphology, pathogenic potential, and DNA polymorphism. Using light and electron microscopy, no distinguishing features between T. foetus and T. suis strains were found in size, general morphology, and karyomastigont structure. Both bovine and porcine trichomonads showed pathogenic potential in the subcutaneous mouse assays and did not separate into distinct groups according to strain virulence. Three DNA fingerprinting methods (i.e. RFLP, RAPD, and PCR-based analysis of variable-length DNA repeats) that produce species-specific DNA fragment patterns did not distinguish between the bovine and porcine strains. Sequencing of a variable 502-bp DNA fragment as well as comparison of 16S rRNA gene sequences did not reveal species-specific differences between the cattle and porcine strains. Therefore, we conclude that T. foetus and T. suis belong to the same species. To prevent confusion that may arise from T. foetus-T. suis synonymy, we propose to suppress the older name suis and maintain its accustomed junior synonym foetus as a nomen protection for both cattle and porcine trichomonads. The case has been submitted to the International Commision on Zoological Nomenclature for ruling under its plenary power. [source] Heterogeneity in juvenile idiopathic arthritis: Impact of molecular profiling based on DNA polymorphism and gene expression patternsARTHRITIS & RHEUMATISM, Issue 9 2010Susan D. Thompson First page of article [source] DNA polymorphism of Pvu II site in the lipoprotein lipase gene in patients with non-insulin dependent diabetes mellitusCELL BIOCHEMISTRY AND FUNCTION, Issue 6 2005Belgin Süsleyici Duman Abstract We studied the effect of variation at the lipoprotein lipase (LPL) gene locus on the susceptibility of individuals with non-insulin dependent diabetes mellitus (NIDDM) in a population of 110 NIDDM patients and 91 controls. Our objective was to study the relationship between the LPL,Pvu II polymorphism and NIDDM and lipid metabolism. PCR-RFLP was used to determine the DNA polymorphism of the sixth intron of the LPL gene. The frequencies of the genotypes in case and control groups were 29.1 and 30.8% for P+/P+; 45.5 and 36.3% for P+/P,; 25.5 and 33% for P,/P, respectively. There was no significant difference in frequencies of genotypes between the two groups. Logistic regression analysis revealed that triacylglycerol (TAG) and apolipoprotein E levels were associated with NIDDM, whereas Pvu II genotypes were not found as independent risk factors for the disease. Overall this study demonstrates the role of the Pvu II polymorphism in the LPL gene in modulating plasma lipid/lipoprotein levels in patients with NIDDM. Copyright © 2004 John Wiley & Sons, Ltd. [source] Investigation of Adducin 2 (beta) DNA polymorphisms in genetic predisposition to diabetic nephropathy in Type 1 diabetesDIABETIC MEDICINE, Issue 8 2008D. Currie Abstract Aims Adducin 2 (beta) (ADD2) is a biological and positional candidate gene proposed to confer genetic risk for diabetic nephropathy. This study aimed to comprehensively investigate all common and putatively functional polymorphisms in the genomic region encompassing this gene. Methods Tag single nucleotide polymorphisms (n = 23) derived from phase II of the International HapMap Project and in silico functional variants (n = 2) were genotyped in 1467 White individuals from the British Isles (cases, n = 718; control subjects, n = 749) by a combination of Sequenom iPLEX and TaqMan technologies. Results ,2 analysis of genotype and allele frequencies in cases vs. control subjects revealed weak evidence for association of one variant at the 5% level of significance (rs10164951, P = 0.02). Adjusting for multiple testing in the present case,control collection negated this association. Conclusions We selected an appropriate subset of variants suitable for genetic investigations of the ADD2 gene and report the first investigation of polymorphisms in ADD2 with diabetic nephropathy. Our results suggest that common polymorphisms and putatively functional variants in the ADD2 gene do not strongly influence genetic susceptibility to diabetic nephropathy in this White population with Type 1 diabetes. [source] Evaluation of DNA polymorphisms amplified by arbitrary primers (RAPD) as genetically associated elements to differentiate virulent and non-virulent Paracoccidioides brasiliensis isolatesFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 3 2002Teresa R Motta Abstract Randomly amplified polymorphic DNA (RAPD) analysis of 35 Paracoccidioides brasiliensis isolates was carried out to evaluate the correlation of RAPD profiles with the virulence degree or the type of the clinical manifestations of human paracoccidioidomycosis. The dendrogram presented two main groups sharing 64% genetic similarity. Group A included two isolates from patients with chronic paracoccidioidomycosis; group B comprised the following isolates showing 65% similarity: two non-virulent, six attenuated, five virulent, eight from patients with chronic paracoccidioidomycosis and two from patients with acute paracoccidioidomycosis. The virulent Pb18 isolate and six attenuated or non-virulent samples derived from it were genetically indistinguishable (100% of similarity). Thus, in our study, RAPD patterns could not discriminate among 35 P. brasiliensis isolates according to their differences either in the degree of virulence or in the type of the clinical manifestation of this fungal infection. [source] The thymidylate synthase tandem repeat promoter polymorphism: A predictor for tumor-related survival in neoadjuvant treated locally advanced gastric cancerINTERNATIONAL JOURNAL OF CANCER, Issue 12 2006Katja Ott Abstract We evaluated DNA polymorphisms in the thymidylate synthase (TS) and 5,10- methylene-tetrahydrofolate reductase (MTHFR) genes for an association with response and survival in locally advanced gastric cancer treated with 5-FU based preoperative chemotherapy (CTx). DNA of 238 patients (CTx-group: total n = 135, completely resected (R0) n = 102; without CTx: R0 n = 103) was isolated from blood or from nontumorous tissues. In the CTx-group, genotyping of the tandem repeat and the G/C polymorphism in the triple repeat in the promoter region of the TS gene and of the C677T polymorphism of the MTHFR gene was performed. None of the TS or MTHFR genotypes were associated with histopathological response and only the TS tandem repeat polymorphism was significantly related to survival (all patients n = 135, p = 0.002; R0 resected patients n = 102, p = 0.007; log-rank test). Multivariate analysis revealed ypN (p < 0.001) and the TS tandem repeat polymorphism as independent prognostic factors in the CTx-R0-group (p = 0.003). Analyzing the prognostic significance of the TS polymorphisms in the R0-group without CTx, TS genotypes were not significantly associated with survival. Comparing survival between R0 patients with and without CTx in the respective TS genotype groups of the tandem repeat polymorphism, a significant survival benefit for the patients with CTx was found for the 2rpt/2rpt (n = 49; p = 0.002) and 2rpt/3rpt genotypes (n = 99; p = 0.004), but not for the 3rpt/3rpt genotype (n = 57; p = 0.93). Patients' survival after CTx was associated with the TS tandem repeat polymorphism. CTx did not improve survival of patients with the 3rpt/3rpt genotype. Thus, a different therapy might be more appropriate for these patients. © 2006 Wiley-Liss, Inc. [source] TCRBV3S1 and TCRBV18 gene segment polymorphisms in Brazilian Caucasoid and Black populationsINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 1 2002C. Dresch Summary The T-cell receptor (TCR) repertoire plays an important role in shaping specific immune responses. Genetic polymorphisms at the TCR locus, in both constant and variable regions, seem to represent an important mechanism for generating inter-individual and inter-population differences. Considering the scarcity of immune parameters characterized for normal human populations, we decided to determine the frequency of two TCRBV polymorphisms (located in the TCRBV3S1 and TCRBV18 gene segments) in two ethnically distinct groups of the general Brazilian population. Both polymorphisms are related to the expression of these segments at the T-cell surface and can consequently modulate the T-cell repertoire, potentially modifying the capacity of a given individual to develop an immune response. These DNA polymorphisms were analysed in material obtained from adult, normal South-American Caucasoid and Black individuals. A total of 139 individuals were analysed for the TCRBV3S1 and 141 for the TCRBV18 gene segment polymorphisms. The data indicated statistically significant differences in allelic frequencies for the two ethnic groups analysed, suggesting that any correlation between TCR usage or T-cell repertoire and development of a given disease should take in account the ethnic origin of the population studied. [source] End-stage renal disease , not an equal opportunity disease: the role of genetic polymorphismsJOURNAL OF INTERNAL MEDICINE, Issue 1 2005L. NORDFORS Abstract. Despite several decades of development in renal replacement therapy, end-stage renal disease (ESRD) patients continue to have markedly increased morbidity and mortality especially caused by cardiovascular disease (CVD). This shows that current strategies, e.g. the focus on dialysis adequacy, to improve the clinical outcome in ESRD patients have to be complemented by novel approaches. Although traditional risk factors are common in dialysis patients they cannot alone explain the unacceptably high prevalence of CVD in this patient group. Much recent interest has therefore focused on the role of various nontraditional cardiovascular risk factors, such as inflammation, vascular calcification and oxidative stress. Recent studies show that genetic factors, such as DNA single nucleotide polymorphisms, may significantly influence the immune response, the levels of inflammatory markers, as well as the prevalence of atherosclerosis in this patient group. To elucidate the respective roles of DNA polymorphisms in genes that encode inflammatory markers (such as IL-10, IL-6 and TNF- ,) and other factors that may affect the development of atherosclerosis (such as apolipoprotein E, transforming growth factor and fetuin-A), sufficiently powered studies are needed in which genotype, the protein product and the specific phenotype all are analysed in relation to outcome. The recent developments in the field of genetics have opened up entirely new possibilities to understand the impact of genotype on disease development and progress and thus offer new options and strategies for treatment. It seems conceivable that in the near future, prognostic or predictive multigene DNA assays will provide the nephrological community with a more precise approach for the identification of ,high-risk' ESRD patients and the development of accurate individual treatment strategies. For this purpose, integrative studies on genotype,phenotype associations and impact on clinical outcome are needed. [source] Molecular mapping of a fertility restorer gene for cytoplasmic male sterility in soybeanPLANT BREEDING, Issue 1 2010Y. Wang With 2 figures and 2 tables Abstract In this study, we report the mapping of the Rf locus in soybean by microsatellite simple sequence repeat (SSR) genetic markers. A cross was made between cytoplasmic male sterility (CMS) line JLCMS82A and restorer line JIHUI 1 based on the DNA polymorphisms revealed by 109 SSR markers. A F2 population derived from a single F1 plant containing 103 individuals was used for mapping the Rf locus. The Rf gene of JIHUI 1 gametophytically restores male fertility to JLCMS82A. Fertile and semi-fertile DNA bulks and parental DNAs were screened with 219 SSR markers, and Satt215 which was previously mapped to soybean LG J, was found linked to the Rf gene. Five additional polymorphic SSR markers from LG J were used for analysis and a regional linkage map around the Rf locus was established. SSR markers, Sctt011 and Satt547, flanked the Rf locus at 3.6 cM and 5.4 cM, respectively. The availability of these SSR markers will facilitate the selection of restorer lines in hybrid soybean breeding. [source] The utility of an erythroblast scoring system and gender-independent short tandem repeat (STR) analysis for the detection of aneuploid fetal cells in maternal bloodPRENATAL DIAGNOSIS, Issue 7 2005Dong Hyun Cha Abstract Objective The aim of this study was to determine whether fetal nucleated red blood cells (NRBCs) could be distinguished from maternal cells in peripheral blood using an erythroblast scoring system based on the unique morphological and hemoglobin staining characteristics of this cell type. Presumptive fetal NRBCs were further analyzed for the presence of paternally inherited DNA polymorphisms to prove fetal origin. Methods NRBCs were isolated by density gradient separation, CD15/45 depletion, and gamma hemoglobin positive selection from peripheral blood of nine women following termination of pregnancy for trisomy 21 (n = 4), 18 (n = 1), 13 (n = 2), and other genetic abnormalities (n = 2). Candidate fetal NRBCs, based on four discrete morphological and hemoglobin staining criteria, were then subjected to fluorescent PCR (polymerase chain reaction) amplification of chromosome 21 (D21S1411, D21S11) and chromosome 18 (D18S535) short tandem repeat (STR) DNA polymorphisms. Results In all cases, candidate fetal NRBCs were accurately identified on the basis of morphologic and hemoglobin staining characteristics and confirmed to be fetal in origin based on the presence of shared and nonshared polymorphic DNA alleles when compared to DNA isolated from maternal cells. Conclusions Using the erythroblast scoring system and subsequent analysis of inherited DNA polymorphisms, we were able to distinguish fetal NRBCs from maternal cells and prove fetal origin independent of gender. These results suggest that this novel combined approach to fetal cell isolation and genetic analysis is a promising method for noninvasive prenatal diagnostic applications. Copyright © 2005 John Wiley & Sons, Ltd. [source] Association of the G-2548A polymorphism in the 5, region of the LEP gene with overweightANNALS OF HUMAN GENETICS, Issue 5 2000O. MAMMÈS Mutations in the translated part of the leptin gene (LEP) have been found in only two families. Nevertheless DNA polymorphisms in the LEP region are linked to extreme obesity. We previously found in the 5, region of LEP a polymorphism, G-2548A, associated with a difference in BMI reduction following a low calorie diet in overweight women. Recently, this polymorphism was associated with extreme obesity in women. In this work, we genotyped a new sample from the general population including 314 normal weight (BMI < 27 kg/m2) and 109 overweight subjects (BMI , 27 kg/m2). The genotype and allele frequencies were significantly different between groups, with the G-2548 allele being more frequent in the overweight subjects (p < 0.01). In men, carriers of this allele had lower leptin concentrations adjusted for fat mass (p= 0.05). Our results indicate that variations at the leptin locus are associated with common obesity phenotypes, and not only with extreme obesity or the rare mendelian obesity syndromes. [source] Influence of parental origin of the X chromosome on physical phenotypes and GH responsiveness of patients with Turner syndromeCLINICAL ENDOCRINOLOGY, Issue 1 2010Jung Min Ko Summary Objective, Previous studies have reported the effects of parental origin of the X chromosome on specific phenotypic and cognitive profiles in Turner syndrome (TS). Here, we investigate the possible parent-of-origin effects on physical phenotypes and responsiveness to GH in Korean patients with TS. Design and patients, Thirty-three patients with TS with nonmosaic karyotype and their parents participated in this study. The parental origin of the normal X chromosome was determined by comparing parental DNA polymorphisms using nine highly polymorphic microsatellite markers on the X chromosome. For the evaluation of parent-of-origin effects, typical phenotypic traits, including congenital malformations, auxological and endocrinological profiles, were compared. Results, The retained X chromosome was of maternal (Xm) origin in 60·6% patients and paternal (Xp) origin in 39·4% patients. No significant parent-of-origin effects on stature, body mass index, cardiac, renal, skeletal, lymphatic, hearing or ocular systems were evident. We observed no differences in height gain after GH treatment. In patients with the 45,X karyotype, patient height was positively correlated with maternal height in the Xm group (r = 0·60, P = 0·04). Moreover, patient height was more significantly correlated with maternal than paternal height, irrespective of the parental origin of the retained X chromosome. Conclusion, While we observed no significant impact of parental origin of the X chromosome on several phenotypic traits in patients with TS, a maternal imprinting effect on stature was suggested at least in patients with 45,X. Further studies on a larger number of patients with TS are essential to define the potential imprinting effects of undetermined genes on the X chromosome. [source] | |||||||||||||