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Variable Positions (variable + position)
Selected AbstractsQuantification of SMN1 and SMN2 genes by capillary electrophoresis for diagnosis of spinal muscular atrophyELECTROPHORESIS, Issue 13 2008Chun-Chi Wang Abstract We present the first CE method for the separation and quantification of SMN1 and SMN2 genes. Spinal muscular atrophy (SMA) is an inherited neuromuscular disorder deleted or mutated in SMN1 gene and retained at least one copy of SMN2 gene. However, these two genes are highly homologous, differentiation and quantification of SMN1 and SMN2 are therefore required in diagnosis to identify SMA patients and carriers. We developed a fluorescence-labeled conformation-sensitive CE method to quantitatively analyze PCR products covering the variable position in the SMN1/SMN2 genes using a copolymer solution composed of hydroxyethylcellulose and hydroxypropylcellulose. The DNA samples included 24 SMA patients, 52 parents of SMA patients (obligatory carriers), and 255 controls. Those 331 samples were blind analyzed to evaluate the method, and the results compared with those obtained using denaturing HPLC (DHPLC). Validation of accuracy was performed by comparing the results with those of DHPLC. Nine of total samples showed different results. Diagnosis of one fetus DNA among them was related to abortion or not, which was further confirmed by gel electrophoresis and DNA sequencing. Our method showed good coincidence with them, and proved the misdiagnosis of DHPLC. This simple and reliable CE method is a powerful tool for clinical genotyping of large populations to detect carriers and SMA patients. [source] Study of the Cytochrome b Gene Sequence in Populations of TaiwanJOURNAL OF FORENSIC SCIENCES, Issue 1 2010Hsiao-Lin Hwa M.D., Ph.D. Abstract:, The cytochrome b gene (MTCYB) has been widely used in taxonomic research. In this study, the sequence polymorphism of the MTCYB gene was determined in 417 subjects of eight populations living in Taiwan (Taiwanese Han, indigenous Taiwanese, Tao, mainland Chinese, Filipino, Thai, Vietnamese, and Caucasian). Sequence variation from the revised Cambridge Reference Sequence and genetic distance between these populations were analyzed. There were 108 variable positions with a total of 99 haplotypes. Population-specific positions of MTCYB gene were noted in Tao and Caucasian populations. There were statistically significant differences of genetic distance between Taiwanese Han and Caucasian, between Taiwanese Han and Tao, and between Taiwanese Han and Filipino. A phylogenetic tree presents the genetic distances between these populations. In conclusion, there are sufficient sequence polymorphisms of the MTCYB gene in individuals of different populations, which may be used in the analyses of human ethnic groups in forensic casework. [source] MOLECULAR AND PHYLOGENETIC CHARACTERIZATION OF PHORMIDIUM SPECIES (CYANOPROKARYOTA) USING THE CPCB-IGS-CPCA LOCUS,JOURNAL OF PHYCOLOGY, Issue 1 2005Ivanka Teneva The accurate determination of species of Cyanoprokaryota/Cyanophyceae has many important applications. These include the assessment of risk with regard to blooms in water reservoirs as well as the identification of species capable of producing valuable bioactive compounds. Commonly, Cyanoprokaryota are classified based on their morphology. However, morphological criteria are not always reliable because they may change, for example, due to environmental factors. Thus, genetic and molecular analyses are a promising additional approach, but their application has so far been limited to relatively few genera. In light of this, we present here the first characterization of species and strains of the genus Phormidium Kütz. based on the cpcB-IGS-cpcA locus of the phycocyanin operon. In phylogenetic analyses using deduced amino acid sequences of the cpcB-cpcA regions, Phormidium was found to be polyphyletic. This analysis appeared to be dominated by the cpcB region, which is characterized by a relatively high percentage of informative substitutions. The percentage of variable positions within the cpcB-IGS-cpcA locus overall was 16.5%, thereby indicating a level of divergence remarkably higher than that reported for Nodularia and Arthrospira in previous studies relying on cpcB-IGS-cpcA. Further, alignment of informative nucleotide substitutions in the cpcB-IGS-cpcA sequences revealed a mosaic distribution, which may be indicative of genetic recombination events. Finally, the length and sequences of the IGS region alone proved useful as markers to differentiate the cyanobacterial genus Phormidium. However, whether the IGS region per se is sufficiently discriminatory to differentiate between Phormidium species or even strains requires further investigation using newly identified Phormidium sequence data. [source] Mitochondrial DNA HVRI variation in Balearic populationsAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 1 2005A. Picornell Abstract The Balearic archipelago (Majorca, Minorca, and Ibiza islands and the Chuetas, a small and inbred community of descendants of Sephardic Jews) and Valencia were studied by means of the sequencing of a 404-bp segment of hypervariable region I (HVRI) mtDNA in 231 individuals. In total, 127 different haplotypes defined by 92 variable positions were identified. The incidence of unique haplotypes was very low, especially in Ibiza and the Chuetas. A remarkable observation in the Chueta community was the high frequency (23%) of preHV-1, a Middle Eastern lineage that is closely related, though not identical, to many others found at high frequencies in different Jewish populations. The presence of this haplogroup convincingly supported the Jewish origin of the Chueta community. The studied populations showed a reduced African contribution, and no individuals were detected with North African haplogroup U6, indicating a lack of maternal contribution from the Moslem settlement to these populations. Only Ibiza showed a lower diversity, indicating a possible genetic drift effect, also supported by the historical information known about this island. The variability in the sequence of mtDNA hypervariable region I correlated well with the existing information from the populations, with the exception of that of the Y-chromosome, which could indicate a differential contribution of the maternal and paternal lineages to the genetic pool of the Balearic Islands. The phylogenetic trees showed the intermediate position of the Chueta population between the Middle Eastern and Majorcan samples, confirming the Jewish origin of this population and their Spanish admixture. Am J Phys Anthropol 128:119-130, 2005. © 2005 Wiley-Liss, Inc. [source] Disentangling the bindweeds: hybridization and taxonomic diversity in British Calystegia (Convolvulaceae)BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2009JACQUELINE M. BROWN Calystegia is taxonomically complex. More than 65 taxa are currently recognized, but species circumscription is problematic, geographical intergradation between taxa is common and hybridization between species is known to occur. In this study, the nuclear ribosomal internal transcribed spacer 1 region (ITS1) was used to investigate the extent to which interspecific hybridization has contributed to the generation of taxonomic diversity in the C. sepium complex of the genus. Focusing principally on taxa that occur in Britain and their putative relatives, patterns of infra-individual ITS1 variation were examined by direct sequencing and cloning. Direct sequencing of the ITS region of 58 accessions representing 11 taxa and one hybrid revealed 22 variable positions that collectively defined 14 ribotypes. Diagnostic and invariant ribotypes lacking polymorphisms were found in C. sepium ssp. sepium, C. sepium ssp. limnophila, C. silvatica ssp. silvatica, C. pellita, C. pubescens and C. soldanella. Three ribotypes were recovered in C. sepium ssp. americana, two of which lacked polymorphisms, whereas the third exhibited two polymorphic sites. Calystegia sepium ssp. roseata, C. sepium ssp. spectabilis, C. silvatica ssp. disjuncta, C. pulchra and C. × howittiorum were each characterized by taxon-specific polymorphisms in the ITS1 region. In each case, the polymorphisms observed were consistent with the co-occurrence in the genome of nonpolymorphic ribotypes that were observed in other taxa. This observation is supported by cloning of the ITS region and is consistent with a hybrid origin for the taxa in which they occur. The hypotheses of hybridity proposed are further shown to be congruent with other data, notably morphology. This study suggests that taxonomic diversity within the C. sepium complex may have been promoted by hybridization. For at least some of the taxa investigated, it is at least possible that sympatry may have been achieved anthropogenically, through the introduction of taxa into cultivation. The processes revealed in this study may help to explain some of the taxonomic complexity observed in the genus more widely, although this remains to be tested. © 2009 The Natural History Museum, London, Botanical Journal of the Linnean Society, 2009, 160, 388,401. [source] | ||||||||||