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Search Results: 1 - 10 of 11290 matches for " dna analyses "
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Competitive amplification of differentially melting amplicons (CADMA) improves KRAS hotspot mutation testing in colorectal cancer
Kristensen Lasse,Kjeldsen Tina,Hager Henrik,Hansen Lise
BMC Cancer , 2012, DOI: 10.1186/1471-2407-12-548
Abstract: Background Cancer is an extremely heterogeneous group of diseases traditionally categorized according to tissue of origin. However, even among patients with the same cancer subtype the cellular alterations at the molecular level are often very different. Several new therapies targeting specific molecular changes found in individual patients have initiated the era of personalized therapy and significantly improved patient care. In metastatic colorectal cancer (mCRC) a selected group of patients with wild-type KRAS respond to antibodies against the epidermal growth factor receptor (EGFR). Testing for KRAS mutations is now required prior to anti-EGFR treatment, however, less sensitive methods based on conventional PCR regularly fail to detect KRAS mutations in clinical samples. Methods We have developed sensitive and specific assays for detection of the seven most common KRAS mutations based on a novel methodology named Competitive Amplification of Differentially Melting Amplicons (CADMA). The clinical applicability of these assays was assessed by analyzing 100 colorectal cancer samples, for which KRAS mutation status has been evaluated by the commercially available TheraScreen KRAS mutation kit. Results The CADMA assays were sensitive to at least 0.5% mutant alleles in a wild-type background when using 50 nanograms of DNA in the reactions. Consensus between CADMA and the TheraScreen kit was observed in 96% of the colorectal cancer samples. In cases where disagreement was observed the CADMA result could be confirmed by a previously published assay based on TaqMan probes and by fast COLD-PCR followed by Sanger sequencing. Conclusions The high analytical sensitivity and specificity of CADMA may increase diagnostic sensitivity and specificity of KRAS mutation testing in mCRC patients.
Next generation sequencing and comparative analyses of Xenopus mitogenomes
Lloyd Rhiannon E,Foster Peter G,Guille Matthew,Littlewood D Timothy J
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-496
Abstract: Background Mitochondrial genomes comprise a small but critical component of the total DNA in eukaryotic organisms. They encode several key proteins for the cell’s major energy producing apparatus, the mitochondrial respiratory chain. Additonally, their nucleotide and amino acid sequences are of great utility as markers for systematics, molecular ecology and forensics. Their characterization through nucleotide sequencing is a fundamental starting point in mitogenomics. Methods to amplify complete mitochondrial genomes rapidly and efficiently from microgram quantities of tissue of single individuals are, however, not always available. Here we validate two approaches, which combine long-PCR with Roche 454 pyrosequencing technology, to obtain two complete mitochondrial genomes from individual amphibian species. Results We obtained two new xenopus frogs (Xenopus borealis and X. victorianus) complete mitochondrial genome sequences by means of long-PCR followed by 454 of individual genomes (approach 1) or of multiple pooled genomes (approach 2), the mean depth of coverage per nucleotide was 9823 and 186, respectively. We also characterised and compared the new mitogenomes against their sister taxa; X. laevis and Silurana tropicalis, two of the most intensely studied amphibians. Our results demonstrate how our approaches can be used to obtain complete amphibian mitogenomes with depths of coverage that far surpass traditional primer-walking strategies, at either the same cost or less. Our results also demonstrate: that the size, gene content and order are the same among xenopus mitogenomes and that S. tropicalis form a separate clade to the other xenopus, among which X. laevis and X. victorianus were most closely related. Nucleotide and amino acid diversity was found to vary across the xenopus mitogenomes, with the greatest diversity observed in the Complex 1 gene nad4l and the least diversity observed in Complex 4 genes (cox1-3). All protein-coding genes were shown to be under strong negative (purifying selection), with genes under the strongest pressure (Complex 4) also being the most highly expressed, highlighting their potentially crucial functions in the mitochondrial respiratory chain. Conclusions Next generation sequencing of long-PCR amplicons using single taxon or multi-taxon approaches enabled two new species of Xenopus mtDNA to be fully characterized. We anticipate our complete mitochondrial genome amplification methods to be applicable to other amphibians, helpful for identifying the most appropriate markers for differentiating species, popu
Effect of Pressure on Thermal Stability of G-Quadruplex DNA and Double-Stranded DNA Structures
Shuntaro Takahashi,Naoki Sugimoto
Molecules , 2013, DOI: 10.3390/molecules181113297
Abstract: Pressure is a thermodynamic parameter that can induce structural changes in biomolecules due to a volumetric decrease. Although most proteins are denatured by pressure over 100 MPa because they have the large cavities inside their structures, the double-stranded structure of DNA is stabilized or destabilized only marginally depending on the sequence and salt conditions. The thermal stability of the G-quadruplex DNA structure, an important non-canonical structure that likely impacts gene expression in cells, remarkably decreases with increasing pressure. Volumetric analysis revealed that human telomeric DNA changed by more than 50 cm 3 mol ?1 during the transition from a random coil to a quadruplex form. This value is approximately ten times larger than that for duplex DNA under similar conditions. The volumetric analysis also suggested that the formation of G-quadruplex DNA involves significant hydration changes. The presence of a cosolute such as poly(ethylene glycol) largely repressed the pressure effect on the stability of G-quadruplex due to alteration in stabilities of the interactions with hydrating water. This review discusses the importance of local perturbations of pressure on DNA structures involved in regulation of gene expression and highlights the potential for application of high-pressure chemistry in nucleic acid-based nanotechnology.
Analyses of Dermatoglyphic Patterns in Ntamante, Boki Local Government Area (LGA) of Cross River State, Nigeria  [PDF]
Andrew Donatus Abue, Christopher Rose, Nappier Courage
Advances in Anthropology (AA) , 2018, DOI: 10.4236/aa.2018.83005
Abstract: Analysis of the dermatoglyphics pattern in Ntamante Boki LGA of Cross River State, South-South, Nigeria is a research work carried out with the sole aim of analysing the dermatoglyphics pattern of the Ntamante people of Boki LGA in Cross river. Two hundred persons were randomly selected for the research comprising male and females. The collection of the finger prints was done using the ink procedure described by Cummins and Midlo analysis of data that was done using SPSS. The result obtained was thus: for females, the mean standard deviation was least in the radial loop (1 ± 1.6), followed by the Arches (4.9 ± 3.8), the Whorls (6.4 ± 4.4) and highest on the Ulnar loop (9.1 ± 9.7). Variables measured differed significantly (p = 0.05) with a Chi-square (X2) value of 17.41. Pr > Chisq = 0.053. For males, the mean standard deviation was highest in the Ulnar Loop pattern (12.6 ± 9.2), followed by the arch pattern (4.7 ± 2.8), then the whorls (3.3 ± 3) and then the radial loops (0.1 ± 0.4). This index study shows a higher frequency distribution of patterns of the Ulnar Loop, followed by the arches, then the whorls and finally the radial loop in the male samples which is different from the usual trend of Ulnar loop > Whorls > Arches > Radial loop obtained in other ethnic groups in Nigeria following the work of Jaja et al. among the Ijaws, Ekanem et al. amongst the Annangs, Ujaddughe et al. amongst the Esan of Edo state. Sexual dimorphism was evident in this research work with males showing a higher Ulnar loop distribution (12.6 ± 9.2), while the female percentage frequency distribution was (9.1 ± 9.7). In conclusion, this study shows the percentage frequencies of patterns among the Ntamante with the Ulnar Loop >Arch > Whorls> Radial loop amongst the males. Amongst the females, this was the distribution of pattern: Ulnar Loop > Whorls > Arches > Radial Loop. This is in line with what was obtained in different ethnic groups in Nigeria with regards to the percentage frequency distribution in the females, while amongst the males, the distribution shows the distribution pattern in Asia and Europe.
Characterization of Endotrypanum (Kinetoplastida: Trypanosomatidae), a Unique Parasite Infecting the Neotropical Tree Sloths (Edentata)
Franco, Antonia M Ramos;Grimaldi Jr, Gabriel;
Memórias do Instituto Oswaldo Cruz , 1999, DOI: 10.1590/S0074-02761999000200026
Abstract: this article reviews current concepts of the biology of endotrypanum spp. data summarized here on parasite classification and taxonomic divergence found among these haemoflagellates come from our studies of molecular characterization of endotrypanum stocks (representing an heterogenous population of reference strains and isolates from the brazilian amazon region) and from scientific literature. using numerical zymotaxonomy we have demonstrated genetic diversity among these parasites. the molecular trees obtained revealed that there are, at least, three groups (distinct species?) of endotrypanum, which are distributed in central and south america. in concordance with this classification of the parasites there are further newer molecular data obtained using distinct markers. moreover, comparative studies (based on the molecular genetics of the organisms) have shown the phylogenetic relationships between some endotrypanum and related kinetoplastid lineages.
Characterization of Endotrypanum (Kinetoplastida: Trypanosomatidae), a Unique Parasite Infecting the Neotropical Tree Sloths (Edentata)
Franco Antonia M Ramos,Grimaldi Jr Gabriel
Memórias do Instituto Oswaldo Cruz , 1999,
Abstract: This article reviews current concepts of the biology of Endotrypanum spp. Data summarized here on parasite classification and taxonomic divergence found among these haemoflagellates come from our studies of molecular characterization of Endotrypanum stocks (representing an heterogenous population of reference strains and isolates from the Brazilian Amazon region) and from scientific literature. Using numerical zymotaxonomy we have demonstrated genetic diversity among these parasites. The molecular trees obtained revealed that there are, at least, three groups (distinct species?) of Endotrypanum, which are distributed in Central and South America. In concordance with this classification of the parasites there are further newer molecular data obtained using distinct markers. Moreover, comparative studies (based on the molecular genetics of the organisms) have shown the phylogenetic relationships between some Endotrypanum and related kinetoplastid lineages.
A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analysis of 606 Sequences
Guido W. Grimm,Susanne S. Renner,Alexandros Stamatakis,Vera Hemleben
Evolutionary Bioinformatics , 2006,
Abstract: The multi-copy internal transcribed spacer (ITS) region of nuclear ribosomal DNA is widely used to infer phylogenetic relationships among closely related taxa. Here we use maximum likelihood (ML) and splits graph analyses to extract phylogenetic information from ~ 600 mostly cloned ITS sequences, representing 81 species and subspecies of Acer, and both species of its sister Dipteronia. Additional analyses compared sequence motifs in Acer and several hundred Anacardiaceae, Burseraceae, Meliaceae, Rutaceae, and Sapindaceae ITS sequences in GenBank. We also assessed the effects of using smaller data sets of consensus sequences with ambiguity coding (accounting for within-species variation) instead of the full (partly redundant) original sequences. Neighbor-nets and bipartition networks were used to visualize conflict among character state patterns. Species clusters observed in the trees and networks largely agree with morphology-based classifications; of de Jong’s (1994) 16 sections, nine are supported in neighbor-net and bipartition networks, and ten by sequence motifs and the ML tree; of his 19 series, 14 are supported in networks, motifs, and the ML tree. Most nodes had higher bootstrap support with matrices of 105 or 40 consensus sequences than with the original matrix. Within-taxon ITS divergence did not differ between diploid and polyploid Acer, and there was little evidence of differentiated parental ITS haplotypes, suggesting that concerted evolution in Acer acts rapidly.
Evidence of Fungicides Degradation by Rhizobia  [PDF]
Hassan Moawad, Wafaa M. Abd El-Rahim, Haitham Shawky, Aziz M. Higazy, Zakaria Y. Daw
Agricultural Sciences (AS) , 2014, DOI: 10.4236/as.2014.57065

Fungicides which are not easily degradable have the greatest adverse effects on soil microbes. These pesticides negatively affect the growth and multiplication of fungi and bacteria and consequently cause the disturbance of the natural soil microbial balance. In this study two fungicide tolerant isolates of rhizobia; clover isolate (TA1) and peanut isolate (8) were assessed in their capacity to degrade Vitavax and Rizolex. The performance of these isolates in fungicides degradation was tested using the colorimetric assay for Rizolex and the HPLC analysis for Vitavax to detect the degradation products. Using HPLC analyses, the control sample showed specific peak indicating the Vitavax presence in the medium. The specific peak did not change in the control samples throughout the experiment.With the strainTA1 the specific peak of the Vitavax fungicides started to reduce as the incubation time goes on. The Vitavax fungicide did not degrade completely after 240 hours of incubation with rhizobial isolate. The Rizolex used in this study contained blend of Thiram (active ingredient of Rizolex) and Tolcofs methyl fungicides in 1:1 ratio. The biodegradation of Rizolex in the liquid media showed the formation of two new intermediates which were released into the medium indicating the degradation of the tested fungicide by peanut rhizobial isolate No. 8 in 48 hrs of incubation 45% of this compound was degraded. This work shows that the selection of fungicides tolerant rhizobial strains is important to protect the rhizobial inoculants from the toxic effect of the pesticides.

Cloning of Distinguishing DNA Sequences of Gastrodia elata Blume and Application of Them in Identifying Gastrodia Tuber

TAO Jun,FU Tie-Xiang,LUO Zhi-Yong,WEN Li,WANG Zhi-Cheng,SHU Xiao-Shun,LIU Shui-Ping,TAO Yao,HU Wei-Xin,

生物工程学报 , 2006,
Abstract: Gastrodia elata Bl. is a famous and costful traditional Chinese medicine. Their genomic DNA fingerprints were investigated using a modified Randomly Amplified Polymorphic DNA method. DNA fragments common to all or to fine populations were identified and recovered. Five DNA fragments were proven not to be reported through DNA cloning, PCR identifying, nucleotide sequencing and bioinformatics analyses and were received in and recorded by NCBI GenBank. Gastrodine contents of the Gastrodia tuber samples were determined using high performance liquid chromatography technique. The distribution of the five DNA fragments in 9 Gastrodia elata Blume populations and the correlation with gastrodine content were studied. The results show the distribution of these DNA sequences varied greatly among the populations whereby DNA Sequence 1 was the common and distinguishing molecular marker for all the populations studied and DNA Sequence 2 may relate to higher gastrodine content. In conclusion, these DNA marker sequences can be employed to identify genuine gastrodia tubers, better varieties and optimize their selection and cultivating.
Indehiscent sporangia enable the accumulation of local fern diversity at the Qinghai-Tibetan Plateau
Wang Li,Schneider Harald,Wu Zhiqiang,He Lijuan
BMC Evolutionary Biology , 2012, DOI: 10.1186/1471-2148-12-158
Abstract: Background Indehiscent sporangia are reported for only a few of derived leptosporangiate ferns. Their evolution has been likely caused by conditions in which promotion of self-fertilization is an evolutionary advantageous strategy such as the colonization of isolated regions and responds to stressful habitat conditions. The Lepisorus clathratus complex provides the opportunity to test this hypothesis because these derived ferns include specimens with regular dehiscent and irregular indehiscent sporangia. The latter occurs preferably in well-defined regions in the Himalaya. Previous studies have shown evidence for multiple origins of indehiscent sporangia and the persistence of populations with indehiscent sporangia at extreme altitudinal ranges of the Qinghai-Tibetan Plateau (QTP). Results Independent phylogenetic relationships reconstructed using DNA sequences of the uniparentally inherited chloroplast genome and two low-copy nuclear genes confirmed the hypothesis of multiple origins of indehiscent sporangia and the restriction of particular haplotypes to indehiscent sporangia populations in the Lhasa and Nyingchi regions of the QTP. In contrast, the Hengduan Mountains were characterized by high haplotype diversity and the occurrence of accessions with and without indehiscent sporangia. Evidence was found for polyploidy and reticulate evolution in this complex. The putative case of chloroplast capture in the Nyingchi populations provided further evidence for the promotion of isolated but persistent populations by indehiscent sporangia. Conclusions The presented results confirmed the hypothesis that indehiscent sporangia promote the establishment of persistent population in different regions of the QTP. These results are consistent with the expectations of reproductive reassurance by promotion of self-fertilization that played a critical role in the assembly of populations in isolated locations and/or extreme habitats.
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