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Microsatellite Regions (microsatellite + regions)
Selected AbstractsDevelopment of microsatellite markers for Pythium helicoidesFEMS MICROBIOLOGY LETTERS, Issue 1 2009Yin-Ling Abstract A strategy combining dual-suppression PCR and thermal asymmetric interlaced PCR was used to determine sequences flanking microsatellite regions in Pythium helicoides. The primer pairs were designed to amplify loci containing (AC)n, (GA)n, (AGC)n, (CAC)n(CAA)n, (TCA)n and (CTTT)n repeats from the P. helicoides nuclear genome. The PCR products of each primer pair, amplified from three representative isolates collected from different hosts and locations, were cloned and sequenced. Different degrees of polymorphism were detected among these microsatellite markers. The numbers of alleles were 6, 2, 4, 11, 4 and 4 in YL-AC, YL-AGC, YL-CAA, YL-CTTT, YL-GA and YL-TCA, respectively. Allele analysis of 30 P. helicoides isolates showed length polymorphisms in all loci, except for YL-AC, using capillary electrophoresis. Thus, we have developed a simple method for designing PCR primers to amplify microsatellite markers from P. helicoides. [source] Cross-species amplification of Lolium microsatellites in Poa sspGRASSLAND SCIENCE, Issue 3 2006Bryan Kindiger Abstract Cross-species amplification of 47 Lolium ssp. microsatellite primers were evaluated across eight Poa species or subspecies. Of the 47 evaluated Lolium simple sequence repeat (SSR) primer pairs examined, 18 generated one or more amplification products. Of these, only two resulted in the identification of Poa ssp. microsatellite motifs, of which only one was complementary to the microsatellite motif identified in Lolium. Though few Poa ssp. microsatellite regions were identified, several of the amplification products were polymorphic within and across the Poa ssp. and could be utilized as markers in Poa ssp. intergeneric hybrid studies. Results of the research suggest the use of Lolium microsatellite derived primers to identify complementary SSR regions in Poa is not an effective approach for the development of microsatellite markers in Poa. [source] Development and characterization of polymorphic markers for the sap-stain fungus Ophiostoma quercusMOLECULAR ECOLOGY RESOURCES, Issue 1 2009J. W. GROBBELAAR Abstract Eight polymorphic markers were developed from South African isolates of Ophiostoma quercus. The genome was screened for repeat regions using the fast isolation by amplified fragment length polymorphism of sequences containing repeats protocol and 20 de novo primer pairs flanking putative microsatellite regions were designed. Eight loci were optimized and their polymorphisms evaluated by sequencing. The repeat and flanking regions were highly polymorphic containing both indels and base-pair substitutions revealing a total of 46 alleles in 14 isolates and an average heterozygosity of 0.68. Substantial sequence variability makes these markers useful for genotyping populations in order to calculate diversity and monitor global movement of O. quercus. [source] Microsatellite markers for the red band needle blight pathogen, Dothistroma septosporumMOLECULAR ECOLOGY RESOURCES, Issue 5 2008I BARNES Abstract Twelve microsatellite markers were developed for population analyses of the fungal pathogen, Dothistroma septosporum. Intersimple sequence repeat polymerase chain reaction (ISSR-PCR) and an enrichment protocol (fast isolation by amplified fragment length polymorphism of sequences containing repeats [FIASCO]) were both used to identify 28 unique microsatellite regions in the genome. From 22 primer pairs designed, 12 were polymorphic. These markers, screened on two populations representing 42 isolates, produced 40 alleles across all loci with an allelic diversity of 0.09,0.76 per locus. Cross-species amplification showed variable success with Dothistroma rhabdoclinis and Mycosphaerella dearnessi and some sequence variation within isolates of Dothistroma pini. These markers will be used to further study the population structure and diversity of D. septosporum. [source] Isolation and characterization of microsatellite loci in Coccoloba cereifera (Polygonaceae), an endangered species endemic to the Serra do Cipó, BrazilMOLECULAR ECOLOGY RESOURCES, Issue 4 2008RENNAN G. MOREIRA Abstract Microsatellite primers were isolated from the microendemic and threatened species Coccoloba cereifera, a shrub known only from a small region in the Serra do Cipó, Brazil. Thirteen primer pairs amplifying perfect and imperfect microsatellite regions were tested in 40 individuals from the one known occurrence of the species. Number of alleles ranged from two to six and levels of observed heterozygosities ranged from 0.21 to 0.95. These markers will be useful for the analysis of questions concerning population genetic structure and will assist in providing information for future conservation management programmes. [source] Isolation and characterization of polymorphic microsatellite DNA markers in the brown sole, Pleuronectes herzensteiniMOLECULAR ECOLOGY RESOURCES, Issue 1 2007S. G. KIM Abstract New microsatellite DNA markers from brown sole were developed and characterized. Fourteen primer sets were designed from 40 microsatellite regions. Eight of 14 loci exhibited variations comprising 8,31 alleles. Observed and expected heterozygosities ranged from 0.611 to 0.833 and from 0.647 to 0.968 among 36 individuals, respectively. Phz3, Phz8 and Phz12 significantly deviated from Hardy,Weinberg equilibrium, and there was a significant linkage disequilibrium between Phz2 and Phz12. Seven of eight loci conformed to the Mendelian manner of inheritance in a full-sib family. Seven to four loci of three related species were cross-amplified by primers for brown sole. [source] Isolation and characterization of microsatellites in Pacific white shrimp Penaeus (Litopenaeus) vannameiMOLECULAR ECOLOGY RESOURCES, Issue 3 2002P. Cruz Abstract Five polymorphic microsatellite loci were characterized for Penaeus (Litopenaeus) vannamei. Loci were isolated using a partial Sau3A1 genomic library by the sequencing of randomly selected clones and by a biotinylated (CT)10 and (GT)10 probes screening procedure. The last strategy resulted in the most useful data. About 40% of the clones showed a previously reported satellite/microsatellite (PVS1), reducing the chance of finding new microsatellite regions. Whereas two of the microsatellite loci with more than 10 alleles will be useful for mating analysis in a breeding program, the others might prove useful for population genetic studies. [source] Biomarker Assays in Nipple Aspirate FluidTHE BREAST JOURNAL, Issue 6 2001Pamela Klein MD The noninvasive technique of nipple aspiration as a potential source of biomarkers of breast cancer risk was evaluated. The feasibility of performing mutagenesis assays, amplifying DNA, and performing protein electrophoresis on nipple aspirate fluid was explored. A tool was developed to measure the level of discomfort, if any, from this procedure. Twenty-five healthy women (20 premenopausal and 5 postmenopausal) were enrolled. Fluid was obtained using a modified breast pump. Premenopausal women were scheduled for four to six weekly aspirations, and postmenopausal women were scheduled for one to two weekly aspirations. Mutagenesis assays were performed using the Salmonella (Ames) assay. DNA amplification of several microsatellite regions was carried out using polymerase chain reaction. Protein was quantified, and two-dimensional protein electrophoresis was performed. Overall, fluid was obtained from 80% of the women, and the level of discomfort was minimal. Acid hydrolysis of one sample resulted in mutagenicity; all six nonhydrolyzed samples were not mutagenic. The ability to amplify DNA ranged from 34% to 96%, depending on length of the microsatellite region examined. The average protein concentration was 71 ,g/mL. Two-dimensional protein electrophoresis was successfully performed on samples from two subjects. Nipple aspiration is a simple technique and is easily learned and well tolerated, which yields a reagent useful for a variety of investigations. This technique may facilitate the identification and application of biomarkers for future breast cancer risk assessment and chemopreventive protocols. [source] Characteristics of PCR fragments amplified using five microsatellite markers for identifying the Nagoya breedANIMAL SCIENCE JOURNAL, Issue 4 2010Akihiro NAKAMURA ABSTRACT The Nagoya breed is a native chicken of Aichi Prefecture, Japan, a dual-purpose breed for eggs and meat. A method for distinguishing the Nagoya breed from Aichi Prefecture from other chickens using five microsatellite markers (ABR0015, ABR0257, ABR0417, ABR0495 and ADL0262) has already been utilized in order to check the authenticity of Nagoya breed-labeled chicken on the market. The present study was conducted to investigate nucleotide sequences and sizes of PCR fragments containing the five microsatellite regions for the Nagoya breed and to confirm that the genomic identification could continue to be applied in the future. The DNA sequencing of fragments containing the five markers showed that ABR0015, ABR0417 and ABR0495 had a single haplotype, ABR0257 had three haplotypes, and ADL0262 had two haplotypes, although all the markers exhibited one fixed fragment size each upon sequencing of the fragments and fragment analysis. The results of the fragment analysis of each marker using DNA samples of 28 Nagoya breed males (G0 generation) reared in 2000,2001 and 20 of their offspring males (G8) reared in 2008,2009 showed one fixed fragment size in both populations. Therefore, we confirmed that the five microsatellite markers are useful tools for accurately distinguishing the Nagoya breed from other chickens. [source] Microsatellite Instability And Allelic Imbalance In Primary And Secondary Colorectal CancerANZ JOURNAL OF SURGERY, Issue 8 2000Anne Schneider Background: Several studies of colorectal cancer have shown an association between the number and type of genomic defects and the stage of disease. A subset of colorectal tumours are due to inactivation of DNA mismatch repair genes and these tumours exhibit microsatellite instability. The aim of the present study was to compare and contrast the genomic defects present in both the primary and metastatic stages of the disease using microsatellite probes. Methods: Modifications of the allelic profiles of 25 microsatellite regions were studied in a total of 85 colorectal tumours using fluorescent polymerase chain reaction (PCR) technology and subsequent direct analysis on an automatic sequencer. This approach was used because it allows the study of microsatellite instability and allelic imbalance. Stepwise logistic regression analysis was used to develop a model to predict whether the tumour was primary or secondary from the percentage of allelic imbalance. Subsequently, a group of 17 patients with primary colorectal tumours was analysed prospectively to test the proposed model. Results: Six of 39 primary tumours showed microsatellite instability compared to 0 of 29 liver metastases (P = 0.03). Primary tumours showed significantly less allelic imbalance than liver metastases (P < 0.001). Three probes (d18s53, d9s158 and d10s191) were selected for use in a model to classify a tumour as primary or secondary on the basis of the degree of allelic imbalance. When tested prospectively this model had a specificity of 82%. Conclusions: The present study demonstrates the potential importance of using microsatellite probes both as a diagnostic tool and as a research technique to investigate the mechanisms of tumour progression. An important clinical finding is that none of the colorectal liver metastases showed microsatellite instability (0 of 29). This analysis also confirmed other work that has shown a direct relationship between the degree of allelic imbalance and the stage of disease. [source] Anthocyanin profile of Spanish Vitis vinifera L. red grape varieties in danger of extinctionAUSTRALIAN JOURNAL OF GRAPE AND WINE RESEARCH, Issue 3 2007S. GÓMEZ-ALONSO Abstract This paper reports on a study of the anthocyanin fraction in berry skins of ten minority red and pink grapevine varieties from Castilla-La Mancha (Spain) and two traditional varieties from this growing region, Tempranillo and Garnacha Tinta, as references. These varieties were correctly identified beforehand by analysing six microsatellite regions recommended by the GENRES 081 project; five varieties were identified with genotypes identical to those described previously, and five new genotypes not described for any variety according to the literature consulted. Grape skin extracts of each variety were analysed by HPLC-UV-Vis, and four perfectly differentiated anthocyanin profiles were obtained. In six out of ten varieties (Churriago, Unknown 1, Unknown 2, Ariño, Brujidera and Moravia Agria) the major anthocyanin was malvidin-3-glucoside (39%). Tinto Velasco contained more than 29% delphinidin-3-glucoside, Gordera Roja and Teta de Vaca Tinta more than 40% peonidin-3-glucoside, and Rojal more than 29% cyanidin-3-glucoside. Results of this work point out the existence of unusual anthocyanic profiles in several of these indigenous varieties, and highlight the necessity of studying the effects of variety on other flavonoids and their impact on wine colour. [source] | |||||||||||||