Isolation of a human thiopurine S-methyltransferase (TPMT) complementary DNA with a single nucleotide transition A719G (TPMT*3C) and its association with loss of TPMT protein and catalytic activity in humans*

1998 ◽  
Vol 64 (1) ◽  
pp. 46-51 ◽  
Author(s):  
Thrina Loennechen ◽  
Charles R. Yates ◽  
Michael Y. Fessing ◽  
Mary V. Relling ◽  
Eugene Y. Krynetski ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Single Nucleotide ◽  
Complementary Dna ◽  
Nucleotide Transition

scholarly journals Genetic Polymorphism Analysis of Mitochondrial DNA from Chinese Guangdong Liannan Yao ethnic group

2020 ◽  
Author(s):  
Shiyu Sun ◽  
Jinpeng Chen ◽  
Mingqi Zhang ◽  
Huang Huang ◽  
Xihong Lin ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Polymorphism ◽  
Ethnic Group ◽  
Southern China ◽  
Forensic Identification ◽  
Polymorphism Analysis ◽  
Single Nucleotide ◽  
Ethnic Populations ◽  
Characteristics Analysis ◽  
Nucleotide Transition

Abstract Background Genetic polymorphism and haplotype distribution characteristics analysis of mitochondrial DNA in Chinese Guangdong Liannan Yao group was conducted in this study, to provide genetic basis for tracing the origin and historical migration of Liannan Yao people.Results 46 mutation sites were found, and among which single nucleotide transition was the most commonly observed variant (86.17%). Multiple (sub)haplogroups were detected in Liannan Yao ethnic group, among which haplogroup D was the most common haplogroup (29.80%), and the least were C and Y(0.48% respectively). Conclusions The Liannan Yao population had the commonalities of the ethnic groups in southern China, but it was significantly different from other Chinese ethnic populations. The present results revealed that Liannan Yao ethnic group was genetically closer related to Fujian She ethnic population, Yunnan Yao population, and Hunnan Miao population. The data enriched the Chinese mtDNA database and provided a reference for forensic identification and screening for potential pathogenic mutations.

A Single Nucleotide Polymorphism of CYP2B6 Found in Japanese Enhances Catalytic Activity by Autoactivation

2001 ◽  
Vol 281 (5) ◽  
pp. 1256-1260 ◽  
Author(s):  
Noritaka Ariyoshi ◽  
Masafumi Miyazaki ◽  
Kenji Toide ◽  
Yu-ichi Sawamura ◽  
Tetsuya Kamataki
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Catalytic Activity ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Sensitive and Selective Detection of DNA Fragments Associated with Ganoderma Boninense by DNA-Nanoparticle Conjugate Hybridisation

2020 ◽  
Author(s):  
Ekta Rani ◽  
Siti Akhtar Mohshim ◽  
Nor Hidayat Yusof ◽  
Muhammad Zamharir Ahmad ◽  
Royston Goodacre ◽  
...  
Keyword(s):  
Colorimetric Assay ◽  
Colour Change ◽  
Dna Fragments ◽  
Label Free ◽  
Ganoderma Boninense ◽  
Large Excess ◽  
Single Nucleotide ◽  
Free System ◽  
Complementary Dna ◽  
Double Stranded Dna

<u><strong> </strong></u><p>A colorimetric assay for the detection of DNA fragments associated with the oil palm pathogen Ganoderma boninense is reported, which is based on the aggregation of DNA-nanoparticle conjugated in the presence of complementary DNA from the pathogen. Here, various designs of DNA-nanoparticle conjugates were evaluated, and it was found that the best design gave a visually observable colour change with as little as 2 pmol of double-stranded DNA analyte even in the presence of a large excess of a mixture of non-complementary DNA. The assay was also able to differentiate analyte sequences with three or more single nucleotide mismatches. Overall, this label-free system is rapid, sensitive, selective, simple in design and easy to carry out. It does not require specialist equipment or specialist training for the interpretation of the results and therefore has the potential to be deployed of agricultural diagnostics in the field.</p><u><strong></strong></u>

HIGH-TILLERING AND DWARF 12 regulates photosynthesis and plant architecture by affecting carotenoid biosynthesis in rice

2020 ◽  
Author(s):  
Hui Zhou ◽  
Mai Yang ◽  
Lei Zhao ◽  
Zuofeng Zhu ◽  
Fengxia Liu ◽  
...  
Keyword(s):  
Plant Architecture ◽  
Oryza Sativa L ◽  
Carotenoid Biosynthesis ◽  
Acceptor Site ◽  
Wild Type ◽  
Amino Acid Deletion ◽  
Single Nucleotide ◽  
Positional Mapping ◽  
Nucleotide Transition ◽  
High Tillering

Abstract Photosynthesis and plant architecture are important factors influencing grain yield in rice (Oryza sativa L.). Here, we identified a high-tillering and dwarf 12 (htd12) mutant and analyzed the effects of the HTD12 mutation on these important factors. HTD12 encodes a 15-cis-ζ-carotene isomerase (Z-ISO) belonging to the nitrite and nitric oxide reductase U (NnrU) protein family, as revealed by positional mapping and transformation experiments. Sequence analysis showed that a single nucleotide transition from guanine (G) to adenine (A) in the 3’ acceptor site between the first intron and second exon of HTD12 alters its mRNA splicing in htd12 plants, resulting in a 49-amino acid deletion that affects carotenoid biosynthesis and photosynthesis. In addition, compared with the wild type, htd12 had significantly lower concentrations of ent-2’-epi-5-deoxystrigol (epi-5DS), a native strigolactone, in both roots and root exudates, resulting in an obvious increase in tiller number and decrease in plant height. These findings indicate that HTD12, the rice homolog of Z-ISO, regulates chloroplast development and photosynthesis by functioning in carotenoid biosynthesis, and modulates plant architecture by affecting strigolactone concentrations.

scholarly journals Highly specific enrichment of rare nucleic acids using Thermus thermophilus Argonaute

2018 ◽  
Author(s):  
Jinzhao Song ◽  
Jorrit W. Hegge ◽  
Michael G. Mauk ◽  
Neha Bhagwat ◽  
Jacob E. Till ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Thermus Thermophilus ◽  
Wild Type ◽  
Single Nucleotide ◽  
Blood Samples ◽  
Complementary Dna ◽  
Enzymatic Amplification ◽  
Dna And Rna ◽  
Rare Alleles

ABSTRACTCharacterization of disease-associated, cell-free nucleic acids (liquid biopsy) provides a powerful, minimally-invasive means for early detection, genotyping, and personalized therapy; but is challenged by alleles of interest differing by single nucleotide from and residing among large abundance of wild-type alleles. We describe a new multiplexed enrichment assay, dubbed NAVIGATER, that utilizes short nucleic acid-guided endonucleases Argonaute (Ago), derived from the bacterium Thermus thermophilus (TtAgo), to specifically cleave complementary DNA and RNA while sparing alleles having single nucleotide mismatches with the guides. NAVIGATER greatly increases the fractions of rare alleles of interest in samples and enhances sensitivity of downstream procedures such ddPCR, sequencing, and clamped enzymatic amplification. We demonstrate 60-fold enrichment of KRAS G12D in blood samples from pancreatic cancer patients and detection of KRAS, EGFR, and BRAF mutants with XNA-PCR at 0.01% fraction.

Highly sensitive detection of rare mutant alleles by combining argonaute-based enrichment and XNA-PCR.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e14605-e14605
Author(s):  
Jinzhao Song ◽  
Michael Joseph Powell ◽  
Wei Liu ◽  
Junman Chen ◽  
Haim Bau
Keyword(s):  
Nucleic Acids ◽  
High Efficiency ◽  
Elevated Temperatures ◽  
Thermus Thermophilus ◽  
Thermophilic Bacterium ◽  
Detection Methods ◽  
Single Nucleotide ◽  
Complementary Dna ◽  
Dna And Rna ◽  
Rna Targets

e14605 Background: Characterization of disease-associated, cell-free nucleic acids (liquid biopsy) provides a powerful, minimally-invasive means for early disease detection, genotyping, and personalized therapy. Detection of alleles of clinical interest is often challenged by their low concentration and sequence homology with the much more abundant wildtype nucleic acids. Methods: Argonuate (Ago) from the thermophilic bacterium Thermus thermophilus ( TtAgo) utilizes short DNA guides to specifically cleave complementary DNA and RNA targets. We found that under optimized conditions, TtAgo cleaves DNA and RNA complementary to the guide DNA with high efficiency, but spares nucleic acids with a single nucleotide mismatch at and around its catalytic site with high sensitivity. Based on these findings, we designed a new multiplexed enrichment assay, dubbed NAVIGATER (Nucleic Acid enrichment Via DNA Guided Argonaute from Thermus thermophilus), that utilizes TtAgo, to specifically cleave perfectly complementary DNA and RNA while sparing alleles of interest. Results: NAVIGATER greatly increases the fractions of rare mutant alleles with single nucleotide precision enhancing the sensitivity of downstream detection methods such as XNA-PCR. We demonstrate 60-fold enrichment of KRAS G12D in blood samples from pancreatic cancer patients and over ten-fold improved sensitivity of XNA-PCR, enabling multiplex detection of KRAS and EGFR mutants at 0.01% fractions. Conclusions: NAVIGATER has important advantages over other mutant allele enrichment assays such as the ones based on CRISPR-Cas. It does not require the target to contain a protospacer-adjacent motif; is a true (turnover) catalyst; can cleave both DNA and associated exosomal RNA targets, improving sensitivity; and can operate at elevated temperatures for higher selectivity and compatibility with detection schemes.

scholarly journals Functional impact of cytochrome P450 3A (CYP3A) missense variants in cattle

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mery Giantin ◽  
Minna Rahnasto-Rilla ◽  
Roberta Tolosi ◽  
Lorena Lucatello ◽  
Marianna Pauletto ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Catalytic Activity ◽  
Ex Vivo ◽  
Liver Microsomes ◽  
Individual Variability ◽  
Cytochrome P450 3A ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Functional Impact ◽  
Genotype Variation

AbstractCytochrome P450 3A is the most important CYP subfamily in humans, and CYP3A4/CYP3A5 genetic variants contribute to inter-individual variability in drug metabolism. However, no information is available for bovine CYP3A (bCYP3A). Here we described bCYP3A missense single nucleotide variants (SNVs) and evaluated their functional effects. CYP3A28, CYP3A38 and CYP3A48 missense SNVs were identified in 300 bulls of Piedmontese breed through targeted sequencing. Wild-type and mutant bCYP3A cDNAs were cloned and expressed in V79 cells. CYP3A-dependent oxidative metabolism of testosterone (TST) and nifedipine (NIF) was assessed by LC-MS/MS. Finally, SNVs functional impact on TST hydroxylation was measured ex vivo in liver microsomes from individually genotyped animals. Thirteen missense SNVs were identified and validated. Five variants showed differences in CYP3A catalytic activity: three CYP3A28 SNVs reduced TST 6β-hydroxylation; one CYP3A38 variant increased TST 16β-hydroxylation, while a CYP3A48 SNV showed enhanced NIF oxidation. Individuals homozygous for rs384467435 SNV showed a reduced TST 6β-hydroxylation. Molecular modelling showed that most of SNVs were distal to CYP3A active site, suggesting indirect effects on the catalytic activity. Collectively, these findings demonstrate the importance of pharmacogenetics studies in veterinary species and suggest bCYP3A genotype variation might affect the fate of xenobiotics in food-producing species such as cattle.

Two non-amplified alleles at the canine microsatelliteAHTh171locus due to a single nucleotide transition in the primer-binding region

2005 ◽  
Vol 36 (3) ◽  
pp. 281-282 ◽  
Author(s):  
M. Nurimoto ◽  
K. Yoneda ◽  
A. Onogi ◽  
Y. Kozono ◽  
H. Kimura ◽  
...  
Keyword(s):  
Binding Region ◽  
Single Nucleotide ◽  
Primer Binding Region ◽  
Nucleotide Transition

scholarly journals Sensitive and Selective Detection of DNA Fragments Associated with Ganoderma Boninense by DNA-Nanoparticle Conjugate Hybridisation

2020 ◽  
Author(s):  
Ekta Rani ◽  
Siti Akhtar Mohshim ◽  
Nor Hidayat Yusof ◽  
Muhammad Zamharir Ahmad ◽  
Royston Goodacre ◽  
...  
Keyword(s):  
Colorimetric Assay ◽  
Colour Change ◽  
Dna Fragments ◽  
Label Free ◽  
Ganoderma Boninense ◽  
Large Excess ◽  
Single Nucleotide ◽  
Free System ◽  
Complementary Dna ◽  
Double Stranded Dna

<u><strong> </strong></u><p>A colorimetric assay for the detection of DNA fragments associated with the oil palm pathogen Ganoderma boninense is reported, which is based on the aggregation of DNA-nanoparticle conjugated in the presence of complementary DNA from the pathogen. Here, various designs of DNA-nanoparticle conjugates were evaluated, and it was found that the best design gave a visually observable colour change with as little as 2 pmol of double-stranded DNA analyte even in the presence of a large excess of a mixture of non-complementary DNA. The assay was also able to differentiate analyte sequences with three or more single nucleotide mismatches. Overall, this label-free system is rapid, sensitive, selective, simple in design and easy to carry out. It does not require specialist equipment or specialist training for the interpretation of the results and therefore has the potential to be deployed of agricultural diagnostics in the field.</p><u><strong></strong></u>

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