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https://www.readbyqxmd.com/read/28231608/quantitative-analysis-of-malondialdehyde-guanine-adducts-in-genomic-dna-samples-by-liquid-chromatography-tandem-mass-spectrometry
#1
S A Yates, N M Dempster, M F Murphy, S A Moore
RATIONALE: The lipid peroxidation product malondialdehyde forms M1 dG adducts with guanine bases in genomic DNA. The analysis of these adducts is important as a biomarker of lipid peroxidation, oxidative stress and inflammation which may be linked to disease risk or exposure to a range of chemicals. METHODS: Genomic DNA samples were subjected to acid hydrolysis to release the adducts in the base form (M1 G) alongside the other purines. A liquid chromatography-mass spectrometry method was optimised for the quantitation of the M1 G adducts in genomic DNA samples using product ion and multiple reaction mode scans...
February 23, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28231394/adaptive-divergence-in-wine-yeasts-and-their-wild-relatives-suggests-a-prominent-role-for-introgressions-and-rapid-evolution-at-non-coding-sites
#2
Pedro Almeida, Raquel Barbosa, Douda Bensasson, Paula Gonçalves, José Paulo Sampaio
In Saccharomyces cerevisiae, the main yeast in wine fermentation, the opportunity to examine divergence at the molecular level between a domesticated lineage and its wild counterpart arose recently due to the identification of the closest relatives of wine strains, a wild population associated with Mediterranean oaks. Since genomic data is available for a considerable number of representatives belonging to both groups, we used population genomics to estimate the degree and distribution of nucleotide variation between wine yeasts and their closest wild relatives...
February 23, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28231338/genes-encoding-two-theileria-parva-antigens-recognized-by-cd8-t-cells-exhibit-sequence-diversity-in-south-sudanese-cattle-populations-but-the-majority-of-alleles-are-similar-to-the-muguga-component-of-the-live-vaccine-cocktail
#3
Diaeldin A Salih, Roger Pelle, Joram M Mwacharo, Moses N Njahira, Wani L Marcellino, Henry Kiara, Agol K Malak, Abdel Rahim M El Hussein, Richard Bishop, Robert A Skilton
East Coast fever (ECF), caused by Theileria parva infection, is a frequently fatal disease of cattle in eastern, central and southern Africa, and an emerging disease in South Sudan. Immunization using the infection and treatment method (ITM) is increasingly being used for control in countries affected by ECF, but not yet in South Sudan. It has been reported that CD8+ T-cell lymphocytes specific for parasitized cells play a central role in the immunity induced by ITM and a number of T. parva antigens recognized by parasite-specific CD8+ T-cells have been identified...
2017: PloS One
https://www.readbyqxmd.com/read/28231306/effects-of-adamts14-genetic-polymorphism-and-cigarette-smoking-on-the-clinicopathologic-development-of-hepatocellular-carcinoma
#4
Ming-Jen Sheu, Ming-Ju Hsieh, Ying-Erh Chou, Po-Hui Wang, Chao-Bin Yeh, Shun-Fa Yang, Hsiang-Lin Lee, Yu-Fan Liu
BACKGROUND: ADAMTS14 is a member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs), which are proteolytic enzymes with a variety of further ancillary domain in the C-terminal region for substrate specificity and enzyme localization via extracellular matrix association. However, whether ADAMTS14 genetic variants play a role in hepatocellular carcinoma (HCC) susceptibility remains unknown. METHODOLOGY/PRINCIPAL FINDINGS: Four non-synonymous single-nucleotide polymorphisms (nsSNPs) of the ADAMTS14 gene were examined from 680 controls and 340 patients with HCC...
2017: PloS One
https://www.readbyqxmd.com/read/28231288/characterization-and-expression-analysis-of-genes-encoding-ubiquitin-conjugating-domain-containing-enzymes-in-carica-papaya
#5
Dengwei Jue, Xuelian Sang, Bo Shu, Liqin Liu, Yicheng Wang, Zhiwei Jia, Yu Zou, Shengyou Shi
BACKGROUND: Ripening affects the quality and nutritional contents of fleshy fruits and is a crucial process of fruit development. Although several studies have suggested that ubiquitin-conjugating enzyme (E2s or UBC enzymes) are involved in the regulation of fruit ripening, little is known about the function of E2s in papaya (Carica papaya). METHODOLOGY/PRINCIPAL FINDINGS: In the present study, we searched the papaya genome and identified 34 putative UBC genes, which were clustered into 17 phylogenetic subgroups...
2017: PloS One
https://www.readbyqxmd.com/read/28231280/alkbh7-variant-related-to-prostate-cancer-exhibits-altered-substrate-binding
#6
Alice R Walker, Pavel Silvestrov, Tina A Müller, Robert H Podolsky, Gregory Dyson, Robert P Hausinger, Gerardo Andrés Cisneros
The search for prostate cancer biomarkers has received increased attention and several DNA repair related enzymes have been linked to this dysfunction. Here we report a targeted search for single nucleotide polymorphisms (SNPs) and functional impact characterization of human ALKBH family dioxygenases related to prostate cancer. Our results uncovered a SNP of ALKBH7, rs7540, which is associated with prostate cancer disease in a statistically significantly manner in two separate cohorts, and maintained in African American men...
February 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28231233/association-of-topoisomerase-ii-top2a-and-dual-specificity-phosphatase-6-dusp6-single-nucleotide-polymorphisms-with-radiation-treatment-response-and-prognosis-of-lung-cancer-in-han-chinese
#7
Tian-Lu Wang, Yang-Wu Ren, He-Tong Wang, Hong Yu, Yu-Xia Zhao
BACKGROUND Mutations of DNA topoisomerase II (TOP2A) are associated with chemotherapy resistance, whereas dual-specificity phosphatase 6 (DUSP6) negatively regulates members of the mitogen-activated protein (MAP) kinase superfamily to control cell proliferation. This study assessed TOP2A and DUSP6 single nucleotide polymorphisms (SNPs) in non-small cell lung cancer (NSCLC) patients for association with chemoradiotherapy responses and prognosis. MATERIAL AND METHODS A total of 140 Chinese patients with histologically confirmed NSCLC were enrolled and subjected to genotyping of TOP2A rs471692 and DUSP6 rs2279574 using Taqman PCR...
February 23, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28231077/association-of-genetic-variation-in-the-tachykinin-receptor-3-locus-with-hot-flashes-and-night-sweats-in-the-women-s-health-initiative-study
#8
Carolyn J Crandall, JoAnn E Manson, Chancellor Hohensee, Steve Horvath, Jean Wactawski-Wende, Erin S LeBlanc, Mara Z Vitolins, Rami Nassir, Janet S Sinsheimer
OBJECTIVE: Vasomotor symptoms (VMS, ie, hot flashes or night sweats) are reported by many, but not all, women. The extent to which VMS are genetically determined is unknown. We evaluated the relationship of genetic variation and VMS. METHODS: In this observational study, we accessed data from three genome-wide association studies (GWAS) (SNP Health Association Resource cohort [SHARe], WHI Memory Study cohort [WHIMS+], and Genome-Wide Association Studies of Treatment Response in Randomized Clinical Trials [GARNET] studies, total n = 17,695) of European American, African American, and Hispanic American postmenopausal women aged 50 to 79 years at baseline in the Women's Health Initiative Study...
March 2017: Menopause: the Journal of the North American Menopause Society
https://www.readbyqxmd.com/read/28231055/the-role-of-extracellular-vesicle-micrornas-in-cancer-biology
#9
Ryou-U Takahashi, Marta Prieto-Vila, Ai Hironaka, Takahiro Ochiya
MicroRNAs (miRNAs) constitute a large family of small, approximately 20-22 nucleotide non-coding RNAs that regulate the expression of target genes, mainly at the post-transcriptional level. Multiple studies report that miRNAs are involved in homeostatic maintenance and that aberrant expression of miRNAs is often observed in various types of diseases, including cancer. In cancer biology, miRNAs exert functional roles in tumor initiation, drug resistance, and metastasis. MiRNAs are also secreted through small vesicles called exosomes, which are endosome-derived vesicles derived from various cell types including immune and tumor cells...
February 23, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28230857/protein-phosphatase-4-coordinates-glial-membrane-recruitment-and-phagocytic-clearance-of-degenerating-axons-in-drosophila
#10
Lilly M Winfree, Sean D Speese, Mary A Logan
Neuronal damage induced by injury, stroke, or neurodegenerative disease elicits swift immune responses from glial cells, including altered gene expression, directed migration to injury sites, and glial clearance of damaged neurons through phagocytic engulfment. Collectively, these responses hinder further cellular damage, but the mechanisms that underlie these important protective glial reactions are still unclear. Here, we show that the evolutionarily conserved trimeric protein phosphatase 4 (PP4) serine/threonine phosphatase complex is a novel set of factors required for proper glial responses to nerve injury in the adult Drosophila brain...
February 23, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28230851/using-hiclip-to-identify-rna-duplexes-that-interact-with-a-specific-rna-binding-protein
#11
Yoichiro Sugimoto, Anob M Chakrabarti, Nicholas M Luscombe, Jernej Ule
The structure of RNA molecules has a critical role in regulating gene expression, largely through influencing their interactions with RNA-binding proteins (RBPs). RNA hybrid and individual-nucleotide resolution UV cross-linking and immunoprecipitation (hiCLIP) is a transcriptome-wide method of monitoring these interactions by identifying RNA duplexes bound by a specific RBP. The hiCLIP protocol consists of the following steps: in vivo cross-linking of RBPs to their bound RNAs; partial RNA digestion and purification of RNA duplexes interacting with the specific RBP using immunoprecipitation; ligation of the two arms of RNA duplexes via a linker; reverse transcription; cDNA library amplification; and finally high-throughput DNA sequencing...
March 2017: Nature Protocols
https://www.readbyqxmd.com/read/28230820/the-distribution-of-tp53-gene-polymorphisms-in-chronic-lymphocytic-leukemia-patients-sufferers-of-chornobyl-nuclear-power-plant-accident
#12
N I Bilous, I V Abramenko, A A Chumak, I S Dyagil, Z V Martina
: Previous analyses in a cohort of Chornobyl cleanup workers revealed significantly increased radiation-related risk for all leukemia types, including chronic lymphocytic leukemia (CLL). Numerous investigations emphasized the significance of genetic susceptibility to the radiation carcinogenesis. The aim of the work was to study the distribution of TP53 single nucleotide polymorphisms (SNPs) in CLL patients exposed to ionizing radiation (IR) due to Chornobyl nuclear power plant accident and estimate their impact on disease development...
December 2016: Experimental Oncology
https://www.readbyqxmd.com/read/28230814/m1a%C3%A2-post-transcriptional%C3%A2-modification%C3%A2-in%C3%A2-trnas
#13
REVIEW
Stephanie Oerum, Clément Dégut, Pierre Barraud, Carine Tisné
To date, about 90 post-transcriptional modifications have been reported in tRNA expanding their chemical and functional diversity. Methylation is the most frequent post-transcriptional tRNA modification that can occur on almost all nitrogen sites of the nucleobases, on the C5 atom of pyrimidines, on the C2 and C8 atoms of adenosine and, additionally, on the oxygen of the ribose 2'-OH. The methylation on the N1 atom of adenosine to form 1-methyladenosine (m1A) has been identified at nucleotide position 9, 14, 22, 57, and 58 in different tRNAs...
February 21, 2017: Biomolecules
https://www.readbyqxmd.com/read/28230734/deep%C3%A2-transcriptome%C3%A2-sequencing%C3%A2-of%C3%A2-two%C3%A2-green%C3%A2-algae-chara%C3%A2-vulgaris%C3%A2-and%C3%A2-chlamydomonas%C3%A2-reinhardtii-%C3%A2-provides%C3%A2-no%C3%A2-evidence%C3%A2-of%C3%A2-organellar%C3%A2-rna%C3%A2-editing
#14
A Bruce Cahoon, John A Nauss, Conner D Stanley, Ali Qureshi
Nearly all land plants post-transcriptionally modify specific nucleotides within RNAs, a process known as RNA editing. This adaptation allows the correction of deleterious mutations within the asexually reproducing and presumably non-recombinant chloroplast and mitochondrial genomes. There are no reports of RNA editing in any of the green algae so this phenomenon is presumed to have originated in embryophytes either after the invasion of land or in the now extinct algal ancestor of all land plants. This was challenged when a recent in silico screen for RNA edit sites based on genomic sequence homology predicted edit sites in the green alga Chara vulgaris, a multicellular alga found within the Streptophyta clade and one of the closest extant algal relatives of land plants...
February 20, 2017: Genes
https://www.readbyqxmd.com/read/28230641/peritransplant-energy-changes-and-their-correlation-to-outcome-after-human-liver-transplantation
#15
Bote G Bruinsma, James H Avruch, Gautham V Sridharan, Pepijn D Weeder, Marie Louise Jacobs, Kerry Crisalli, Beth Amundsen, Robert J Porte, James F Markmann, Korkut Uygun, Heidi Yeh
BACKGROUND: The ongoing shortage of donor livers for transplantation and the increased use of marginal livers necessitate the development of accurate pretransplant tests of viability. Considering the importance energy status during transplantation, we aimed to correlate peritransplant energy cofactors to posttransplant outcome and subsequently model this in an ex vivo setting. METHODS: Sequential biopsies were taken from 19 donor livers postpreservation, as well as 30 min after portal venous (PVR) and hepatic arterial reperfusion (HAR) and analyzed by LC-MS for energetic cofactors (ATP/ADP/AMP, NADH/NAD, NADPH/NADP, FAD, GSSG/GSH)...
February 23, 2017: Transplantation
https://www.readbyqxmd.com/read/28230599/a-targeted-next-generation-genetic-sequencing-study-on-tetralogy-of-fallot-combined-with-cleft-lip-and-palate
#16
Lin Liu, Haisong Bu, Yifeng Yang, Zhiping Tan, Fei Zhang, Shijun Hu, Tianli Zhao
BACKGROUND: Congenital heart disease (CHD), plus cleft lip and palate (CLP) are currently the most common types of structural malformation in infants. Many genes have been investigated for their involvement in CHD with CLP. Targeted next-generation sequencing can analyze large amounts of genetic information rapidly, and thus address this question. METHODS: The authors designed a targeted, next-generation sequencing gene panel for 455 genes previously implicated in CHD or CLP...
February 22, 2017: Journal of Craniofacial Surgery
https://www.readbyqxmd.com/read/28230168/phylogenetic-characterizations-of-highly-mutated-ev-b106-recombinants-showing-extensive-genetic-exchanges-with-other-ev-b-in-xinjiang-china
#17
Yang Song, Yong Zhang, Qin Fan, Hui Cui, Dongmei Yan, Shuangli Zhu, Haishu Tang, Qiang Sun, Dongyan Wang, Wenbo Xu
Human enterovirus B106 (EV-B106) is a new member of the enterovirus B species. To date, only three nucleotide sequences of EV-B106 have been published, and only one full-length genome sequence (the Yunnan strain 148/YN/CHN/12) is available in the GenBank database. In this study, we conducted phylogenetic characterisation of four EV-B106 strains isolated in Xinjiang, China. Pairwise comparisons of the nucleotide sequences and the deduced amino acid sequences revealed that the four Xinjiang EV-B106 strains had only 80...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28230082/tubz-filament-assembly-dynamics-requires-the-flexible-c-terminal-tail
#18
Maria E Fuentes-Pérez, Rafael Núñez-Ramírez, Alejandro Martín-González, David Juan-Rodríguez, Oscar Llorca, Fernando Moreno-Herrero, Maria A Oliva
Cytomotive filaments are essential for the spatial organization in cells, showing a dynamic behavior based on nucleotide hydrolysis. TubZ is a tubulin-like protein that functions in extrachromosomal DNA movement within bacteria. TubZ filaments grow in a helical fashion following treadmilling or dynamic instability, although the underlying mechanism is unclear. We have unraveled the molecular basis for filament assembly and dynamics combining electron and atomic force microscopy and biochemical analyses. Our findings suggest that GTP caps retain the filament helical structure and hydrolysis triggers filament stiffening upon disassembly...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28229982/circulating-free-dna-mutation-associated-with-response-of-targeted-therapy-in-human-epidermal-growth-factor-receptor-2-positive-metastatic-breast-cancer
#19
Qing Ye, Fan Qi, Li Bian, Shao-Hua Zhang, Tao Wang, Ze-Fei Jiang
BACKGROUND: The addition of anti-human epidermal growth factor receptor 2 (HER2)-targeted drugs, such as trastuzumab, lapatinib, and trastuzumab emtansine (T-DM1), to chemotherapy significantly improved prognosis of HER2-positive breast cancer patients. However, it was confused that metastatic patients vary in the response of targeted drug. Therefore, methods of accurately predicting drug response were really needed. To overcome the spatial and temporal limitations of biopsies, we aimed to develop a more sensitive and less invasive method of detecting mutations associated with anti-HER2 therapeutic response through circulating-free DNA (cfDNA)...
2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28229970/molecular-analysis-of-the-human-faecal-archaea-in-a-southern-indian-population
#20
Sandya B Rani, Ramadass Balamurugan, Balakrishnan S Ramakrishna
Archaea are an important constituent of the human gut microbiota, but there is no information on human gut archaea in an Indian population. In this study, faecal samples were obtained from different age groups (neonatal babies, preschool children, school-going children, adolescents, adults and elderly) of a southern Indian population, and from a tribal population also resident in southern India). 16S rRNA gene sequences specific to Archaea were amplified from pooled faecal DNA in each group, sequenced, and aligned against the NCBI database...
March 2017: Journal of Biosciences
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