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Restriction Digestion (restriction + digestion)
Selected AbstractsThe molecular diversity of the methanogenic community in a hypereutrophic freshwater lake determined by PCR-RFLPJOURNAL OF APPLIED MICROBIOLOGY, Issue 5 2004C. Whitby Abstract Aims:, To combine database-held sequence information with a programme of experimental molecular ecology to define the methanogenic community of a hypereutrophic lake by a PCR-restriction fragment length polymorphism (RFLP) analysis. Methods and Results:, Methanogen diversity in a hypereutrophic freshwater lake was analysed using 16S rDNA PCR-RFLP. Database-held 16S rRNA gene sequences for 76 diverse methanogens were analysed for specific restriction sites that permitted unequivocal differentiation of methanogens. Restriction digestion and agarose gel electrophoresis of the 16S rDNA from selected methanogen pure cultures generated observed restriction profiles that corroborated the expected patterns. This method was then tested by analysing methanogen diversity in samples obtained over 1 year from sediment and water samples taken from the same sampling site. Conclusions:, Restriction analysis of the 16S rRNA gene sequences from 157 methanogen clones generated from lakewater and sediment samples showed that over 50% were similar to Methanoculleus spp. Furthermore, a total of 16 RFLP types (1,16) were identified, eight of which contained no cultured representative archaeal 16S rRNA gene sequences. Significance and Impact of the Study:, This RFLP strategy provides a robust and reliable means to rapidly identify methanogens in the environment. [source] Restriction analysis of PCR amplified nrDNA regions revealed intraspecific variation within populations of Fusarium culmorumFEMS MICROBIOLOGY LETTERS, Issue 2 2002Prashant K Mishra Abstract Seventy-five isolates of Fusarium culmorum with diverse geographical origin and host were analyzed using restriction digestion of polymerase chain reaction amplified nuclear ribosomal DNA intergenic spacer (IGS) and 28S gene regions. The 28S gene was conserved and has produced identical restriction patterns, however, the IGS region was substantially variable. The isolates were divided into 29 unique IGS haplotypes. There was limited resolution between clustering of isolates and their origin and/or host. The variability was distributed largely equally at both macro- and micro-geographical scale. The phylogeographic distribution pattern suggests a seed-borne dispersal of F. culmorum. [source] DNA methylation and chromatin accessibility of the proximal Cyp19 promoter region 1.5/2 correlate with expression levels in sheep placentomesMOLECULAR REPRODUCTION & DEVELOPMENT, Issue 1 2008Rainer Fürbass Abstract Placental oestrogens play an important role as local regulators of placental growth and differentiation during gestation, and toward term they are also involved in the preparation of parturition. They are synthesized within the fetal cotyledons of placentomes by aromatase cytochrome P450 (P450arom; EC 1.14.14.1), the product of the Cyp19 gene. The first step of regulation of P450arom expression, and hence enzyme activity and oestrogen production, takes place at the level of Cyp19 transcription, which is driven by a proximal promoter region, P1.5/2, in the sheep placenta. The aim of the present study was to find out if different Cyp19 expression levels, which previously had been observed in ovine placentome tissues, correlate with the tissue-specific chromatin structure of the promoter. To this end, we investigated the chromatin structure across the P1.5/2 region in caruncles and cotyledons from 100 and 125 days pregnant ewes, and in term placentae, respectively, by analyzing the DNA methylation and the accessibility to restriction digestion. Our data show that: (1) cotyledonal DNA was significantly lower methylated than caruncular DNA; (2) methylation of cotyledonal DNA was low at 100 and 125 days of pregnancy, and increased to a significant higher level in term placentae; and (3) concurrently, cotyledonal chromatin became inaccessible to restriction digestion at term of gestation. The results imply that DNA methylation and chromatin accessibility of the P1.5/2 promoter region correlate with expression levels of the Cyp19 gene. Mol. Reprod. Dev. 75: 1,7, 2008. © 2007 Wiley-Liss, Inc. [source] Molecular characterization of sickle cell anemia in the Northern Brazilian state of ParáAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 5 2010Greice De Lemos Cardoso To assess ,+-thalassemia deletion alleles, ,-thalassemia mutations and haplotypes linked to the HBB*S cluster in a sample of 130 unrelated sickle cell anemia (SCA) patients (55% female) from Belém, Pará State, for their possible effects on the patients' survival. -,3.7, -,42, -,20.5, and ,MED ,+-thalassemia deletion alleles were investigated using multiplex gap-PCR method. Characterization of ,-thalassemia mutations was made by direct genomic sequencing of the ,-globin gene amplified through polymerase chain reaction (PCR). Haplotypes were determined by analysis of six polymorphic restriction sites [(1) XmnI-5,,G, (2) HindIII-,G, (3) HindIII-,A, (4) HincII-,,, (5) HincII-3,,,, and (6) HinfI-5,,] followed by restriction digestion and agarose gel electrophoresis. Twenty-one patients (16%) presented -,3.7 thalassemia. Sixteen of those (76%) were heterozygous (-,3.7/,,) and 5 (24%) were homozygous (-,3.7/-,3.7). -,4.2, -,20.5 and ,MED deletions were not found. Nine cases of sickle cell-, thalassemia were found and four different ,-thal mutations were identified: ,+ ,88 (C>T), 3.8%; ,+ codon 24 (T > A), 1.5%; ,+ IVSI-110 (G > A), 0.7% and , (IVSI-1 (G > A), 0.7%. No differences according to age were observed in -,3.7 deletion, ,-thalassemia and HHB*S haplotypes distribution. Our results suggest that although ,- and ,-thalassemia and ,S haplotypes may have modulating effect on clinical expression and hematological parameters of SCA, these genetic variables probably have little influence on the subjects' survival. Am. J. Hum. Biol. 22:573,577, 2010. © 2010 Wiley-Liss, Inc. [source] Rapid extraction of high-quality genomic DNA from Porphyra yezoensis (Bangiales, Rhodophyta)PHYCOLOGICAL RESEARCH, Issue 1 2000Maiko Nakajima SUMMARY We developed a simple, rapid and stable method for extraction of high molecular weight DNA from the marine red alga Porphyra yezoensis Ueda using both guanidium treatment and QIAGENÔ kit (Funakoshi, Tokyo, Japan). The method does not require expensive equipment and complex steps. The DNA yield averaged 1.5 ,g 100 mg,1 of Porphyra tissue and the A260/A280 and A230/A260 ratios of the DNA were approximately 1.8 and 0.4, respectively. It was of sufficient quality to be used for not only polymerase chain reactions but also other DNA manipulation techniques such as restriction digestion and construction of genomic libraries. [source] G Protein ,3 Subunit Gene Variants and Essential Hypertension in the Northern Chinese Han PopulationANNALS OF HUMAN GENETICS, Issue 4 2005Biao Li Summary Recently a novel C825T polymorphism in the G protein ,3 subunit gene was identified that showed an association with hypertension in a German population; the results of studies in other populations have been inconsistent. To examine the contribution of GNB3 polymorphisms to the development of hypertension in the northern Chinese Han population, we conducted a case-control study consisting of 501 hypertensive cases and 503 controls using the G(-350)A, C825T and C1429T polymorphisms. Genotypes of samples were determined by PCR and restriction digestion. Single locus analysis showed a significant association between G(-350)A and hypertension (P = 0.01) but no association for C825T or C1429T. The three polymorphisms were in tight linkage disequilibrium (D,=,1 for G(-350)A-C825T, D,= 0.92 for C825T-C1429T) and a total of 7 haplotypes were observed in the entire population. Haplotype A-C-C was found to be significantly related to hypertension (P = 0.032) and A-C-C carriers had a more than two-fold higher risk of hypertension than non-carriers, after adjustment for BMI and glucose. In conclusion, our study suggests that G(-350)A is a potential functional polymorphism that may be related to hypertension, whereas the C825T and C1429T polymorphisms are not associated with hypertension in the northern Chinese Han population. [source] | ||||||||||