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https://www.readbyqxmd.com/read/28735519/expression-of-the-hpv18-e6-oncoprotein-induces-dna-damage
#1
Elva I Cortés Gutiérrez, Catalina García-Vielma, Adriana Aguilar-Lemarroy, Veronica Vallejo-Ruíz, Patricia Piña-Sánchez, Pablo Zapata-Benavides, Jaime Gosalvez
This study investigated possible variations in DNA damage in HeLa cells with silenced expression of the HPV/E6 oncogene compared with HeLa cells with normal expression of the E6 oncogene using the DNA breakage detection-fluorescence in situ hybridization (DBD-FISH) technique and a whole human genome DNA probe. The variable levels of DNA breaks present were measured quantitatively using image analysis after whole-genome DNA hybridization. HeLa cells with silenced expression of the HPV18/E6 oncogene showed a significant decrease in DNA damage compared with parental cells with normal expression of the E6 oncogene...
June 15, 2017: European Journal of Histochemistry: EJH
https://www.readbyqxmd.com/read/28735485/genome-wide-analysis-of-dna-methylation-in-hematopoietic-cells-dna-methylation-analysis-by-wgbs
#2
Mira Jeong, Anna G Guzman, Margaret A Goodell
DNA methylation is a major epigenetic modification that regulates gene expression, genome imprinting, and development and has a role in diseases including cancer. There are various methods for whole-genome methylation profiling that differ in cost and resolution. Recent advances in high-throughput sequencing technologies coupled with bisulfite treatment enable absolute DNA methylation quantification and genome-wide single-nucleotide resolution analysis. In this chapter, we provide detailed protocols for whole-genome bisulfite sequencing (WGBS), which captures the complete methylome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735482/design-and-application-of-multiplex-pcr-seq-for-the-detection-of-somatic-mutations-associated-with-myeloid-malignancies
#3
Naomi Park, George Vassiliou
Targeted sequencing, in which only a selected set of genomic loci are sequenced, enables a much higher coverage of each target than what is obtained using whole genome or exome sequencing. Multiplex PCR offers a simple and affordable technique for specific capture of target regions and can be easily adapted to generate next-generation sequencing (NGS)-ready amplicons. Here we describe a multiplex PCR (MxPCR) approach for capturing 13 leukemia-associated mutation hotspots followed by MiSeq sequencing that enables robust detection of mutations with a variant allele fraction (VAF) as low as 0...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735394/detection-of-differential-dna-methylation-under-stress-conditions-using-bisulfite-sequence-analysis
#4
Ibtisam Al Harrasi, Rashid Al-Yahyai, Mahmoud W Yaish
DNA methylation is the most important epigenetic change affecting gene expression in plants grown under normal as well as under stress conditions. Therefore, researchers study differential DNA methylation under distinct environmental conditions and their relationship with transcriptome abundance. Up to date, more than 25 methods and techniques are available to detect DNA methylation based on different principles. Bisulfite sequencing method is considered as a gold standard since it is able to distinguish 5-methylcytosine from cytosine using the bisulfite treatment...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735012/fgwas-functional-genome-wide-association-analysis
#5
Chao Huang, Paul Thompson, Yalin Wang, Yang Yu, Jingwen Zhang, Dehan Kong, Rivka R Colen, Rebecca C Knickmeyer, Hongtu Zhu
Functional phenotypes (e.g., subcortical surface representation), which commonly arise in imaging genetic studies, have been used to detect putative genes for complexly inherited neuropsychiatric and neurodegenerative disorders. However, existing statistical methods largely ignore the functional features (e.g., functional smoothness and correlation). The aim of this paper is to develop a functional genome-wide association analysis (FGWAS) framework to efficiently carry out whole-genome analyses of functional phenotypes...
July 19, 2017: NeuroImage
https://www.readbyqxmd.com/read/28734942/calcium-calmodulin-dependent-protein-kinase-iv-gene-polymorphisms-in-korean-alcohol-dependent-patients
#6
Jung Woo-Young, Kim Sung-Gon, Kim Ji-Hoon, Lee Jin-Seong
INTRODUCTION: A relationship between alcohol dependence (AD) and calcium/calmodulin-dependent protein kinase IV (CAMKIV) has been reported in a whole genome study of Korean AD patients. The purpose of the present study is to compare the frequency of CAMKIV genotypes and alleles between AD and control subjects in Korea. METHODS: The present study includes 281 AD patients and 139 control subjects. Seven single nucleotide polymorphism of CAMKIV gene known to show significant separation ratio in Asians were searched in SNP database and previous studies related to CAMKIV gene...
July 19, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28734796/clonal-composition-of-human-ovarian-cancer-based-on-copy-number-analysis-reveals-a-reciprocal-relation-with-oncogenic-mutation-status
#7
Kazuko Sakai, Masayo Ukita, Jeanette Schmidt, Longyang Wu, Marco De Velasco, Alan Roter, Luis Jevons, Kazuto Nishio, Masaki Mandai
Intratumoral heterogeneity of cancer cells remains largely unexplored. Here we investigated the composition of ovarian cancer and its biological relevance. A whole-genome single nucleotide polymorphism array was applied to detect the clonal composition of 24 formalin-fixed, paraffin-embedded samples of human ovarian cancer. Genome-wide segmentation data consisting of the log2 ratio (log2R) and B allele frequency (BAF) were used to calculate an estimate of the clonal composition number (CC number) for each tumor...
July 19, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28734577/characterization-of-a-pvl-negative-community-acquired-methicillin-resistant-staphylococcus-aureus-strain-of-sequence-type-88-in-china
#8
Lu Sun, Dandan Wu, Yan Chen, Qian Wang, Haiping Wang, Yunsong Yu
Sequence type 88 community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) strain SR434, isolated from an outpatient with skin and soft tissue infection, was subjected to whole genome sequencing, antimicrobial susceptibility testing, mouse skin infection model and hemolysis analysis to identify its virulence and resistance determinants. MRSA strain SR434 is resistant to clindamycin, erythromycin and fosfomycin. Four plasmids with resistance genes were identified in this strain, including a 20,658bp blaZ-carrying plasmid, a 2473bp ermC-carrying plasmid, a 2622bp fosB7-carrying plasmid (86% identity with plasmid in a ST2590 MRSA strain) and a 4817bp lnuA-carrying plasmid (99% identity with pLNU4 from bovine coagulase-nagetive Staphylococci)...
July 13, 2017: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/28734070/genome-scans-on-experimentally-evolved-populations-reveal-candidate-regions-for-adaptation-to-plant-resistance-in-the-potato-cyst-nematode-globodera-pallida
#9
D Eoche-Bosy, M Gautier, M Esquibet, F Legeai, A Bretaudeau, O Bouchez, S Fournet, E Grenier, J Montarry
Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resistance QTL, GpaVvrn , has been identified in Solanum vernei. However, its durability is threatened as G. pallida populations are able to adapt to the resistance in few generations. The aim of the present study was to investigate the genomic regions involved in the resistance breakdown by coupling experimental evolution and high-density genome scan...
July 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28733861/an-infant-with-acute-gastroenteritis-caused-by-a-secondary-infection-with-a-rotarix-derived-strain
#10
Naomi Sakon, Ryohei Miyamoto, Jun Komano
Rotavirus vaccines have been successful in controlling severe diarrhea and have decreased deaths of young children globally. Rotarix and RotaTeq are the two currently available live-attenuated rotavirus vaccines. The vaccine virus can grow in a recipient's gut and spread from the vaccinee to naïve individuals. The potential for the emergence of revertant viruses is a concern with live-attenuated vaccines. We identified a previously healthy infant with severe acute gastroenteritis that was positive for rotavirus in a non-endemic season...
July 21, 2017: European Journal of Pediatrics
https://www.readbyqxmd.com/read/28733620/adaptive-evolution-of-a-hyperthermophilic-archaeon-pinpoints-a-formate-transporter-as-a-critical-factor-for-the-growth-enhancement-on-formate
#11
Hae-Chang Jung, Seong Hyuk Lee, Sung-Mok Lee, Young Jun An, Jung-Hyun Lee, Hyun Sook Lee, Sung Gyun Kang
Previously, we reported that the hyperthermophilic archaeon Thermococcus onnurineus NA1 could grow on formate and produce H2. Formate conversion to hydrogen was mediated by a formate-hydrogen lyase complex and was indeed a part of chemiosmotic coupling to ATP generation. In this study, we employed an adaptation approach to enhance the cell growth on formate and investigated molecular changes. As serial transfer continued on formate-containing medium at the serum vial, cell growth, H2 production and formate consumption increased remarkably...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733611/integrin-%C3%AE-6%C3%AE-4-upregulates-amphiregulin-and-epiregulin-through-base-excision-repair-mediated-dna-demethylation-and-promotes-genome-wide-dna-hypomethylation
#12
Brittany L Carpenter, Jinpeng Liu, Lei Qi, Chi Wang, Kathleen L O'Connor
Aberrant DNA methylation patterns are a common theme across all cancer types. Specific DNA demethylation of regulatory sequences can result in upregulation of genes that are critical for tumor development and progression. Integrin α6β4 is highly expressed in pancreatic carcinoma and contributes to cancer progression, in part, through the specific DNA demethylation and upregulation of epidermal growth factor receptor (EGFR) ligands amphiregulin (AREG) and epiregulin (EREG). Whole genome bisulfite sequencing (WGBS) revealed that integrin α6β4 signaling promotes an overall hypomethylated state and site specific DNA demethylation of enhancer elements within the proximal promoters of AREG and EREG...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733412/schizosaccharomyces-japonicus-a-distinct-dimorphic-yeast-among-the-fission-yeasts
#13
Keita Aoki, Kanji Furuya, Hironori Niki
Genomic sequencing data and morphological properties demonstrate evolutionary relationships among groups of the fission yeast, Schizosaccharomyces Phylogenetically, S. japonicus is the furthest removed from other species of fission yeast. The basic characteristics of cell proliferation are shared among all fission yeast, including the process of binary fission during vegetative growth, conjugation and karyogamy with horsetail movement, mating-type switching, and sporulation. However, S. japonicus also exhibits characteristics that are unique to filamentous fungi...
July 21, 2017: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/28733282/differentiating-botulinum-neurotoxin-producing-clostridia-with-a-simple-multiplex-pcr-assay
#14
Charles H D Williamson, Adam J Vazquez, Karen Hill, Theresa J Smith, Roxanne Nottingham, Nathan E Stone, Colin J Sobek, Jill H Cocking, Rafael A Fernández, Patricia A Caballero, Owen P Leiser, Paul Keim, Jason W Sahl
Diverse members of the genus clostridium produce botulinum neurotoxins (BoNTs), which cause a flaccid paralysis known as botulism. While multiple species of clostridia produce BoNTs, the majority of human botulism cases have been attributed to Clostridium botulinum Groups I and II. Recent comparative genomic studies have demonstrated the genomic diversity within these BoNT-producing species. This study introduces a multiplex polymerase chain reaction (PCR) assay for differentiating members of C. botulinum Group I, C...
July 21, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28732304/outbreak-of-salmonella-enteritidis-pt14b-gastroenteritis-at-a-restaurant-in-england-the-use-of-molecular-typing-to-achieve-a-successful-prosecution
#15
C Chatt, D Nicholds-Trainor, A Scrivener, S Suleman, M Harvey, T Dallman, J Hawker, B Sibal
OBJECTIVES: To describe an outbreak of Salmonella enteritidis phage type (PT) 14b in people who had eaten at a restaurant, and the investigation and subsequent prosecution of the food business operator (FBO). STUDY DESIGN: The local health protection team and environmental health department formed an outbreak control team to investigate the outbreak. METHODS: Epidemiological, microbiological, and environmental investigations were undertaken...
July 18, 2017: Public Health
https://www.readbyqxmd.com/read/28732184/high-throughput-identification-of-mir-596-inducing-p53-mediated-apoptosis-in-hela-and-hct116-cells-using-cell-microarray
#16
Ming Ma, Junyu Yang, Bolun Wang, Zhihua Zhao, Jianzhong Jeff Xi
miRNAs play a key role in the regulation of gene networks in mammalian cells. However, little is known about their roles and functions in the apoptosis pathway. Here, we conducted a whole-genome miRNA screening for apoptosis and identified more than 100 miRNAs as apoptosis inducers. To further explain the roles of these mRNAs in apoptosis, a second round of screening was conducted between p53 +/+ and -/- cells. Among the hits, miR-596 was identified as a regulator of p53. The overexpression of miR-596 significantly increased p53 at the protein level, thereby inducing apoptosis...
July 1, 2017: SLAS Technology
https://www.readbyqxmd.com/read/28732175/genome-wide-identification-functional-prediction-and-evolutionary-analysis-of-r2r3-myb-superfamily-in-brassica-napus
#17
Ali Hajiebrahimi, Hajar Owji, Shiva Hemmati
R2R3-MYBs are important transcription factors (TFs) in planta, involved in development and various stress conditions. Phylogenetic analysis showed the presence of 249 R2R3-MYB TFs in Brassica napus called BnaR2R3-MYBs, clustered into 38 clades. BnaR2R3-MYBs were distributed on 19 chromosomes of B. napus. Sixteen gene clusters were identified. BnaR2R3-MYBs were characterized by motif prediction, gene structure analysis and gene ontology. Evolutionary analysis revealed that BnaR2R3-MYBs are mainly formed as a result of whole genome duplication...
July 21, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28732043/investigation-of-horizontal-gene-transfer-of-pathogenicity-islands-in-escherichia-coli-using-next-generation-sequencing
#18
Maxim Messerer, Wolfgang Fischer, Sören Schubert
Horizontal gene transfer (HGT) contributes to the evolution of bacteria. All extraintestinal pathogenic Escherichia coli (ExPEC) harbour pathogenicity islands (PAIs), however relatively little is known about the acquisition of these PAIs. Due to these islands, ExPEC have properties to colonize and invade its hosts efficiently. Even though these PAIs are known to be acquired by HGT, only very few PAIs do carry mobilization and transfer genes required for the transmission by HGT. In this study, we apply for the first time next-generation sequencing (NGS) and in silico analyses in combination with in vitro experiments to decipher the mechanisms of PAI acquisition in ExPEC...
2017: PloS One
https://www.readbyqxmd.com/read/28731526/drug-discovery-and-development-for-rare-genetic-disorders
#19
REVIEW
Wei Sun, Wei Zheng, Anton Simeonov
Approximately 7,000 rare diseases affect millions of individuals in the United States. Although rare diseases taken together have an enormous impact, there is a significant gap between basic research and clinical interventions. Opportunities now exist to accelerate drug development for the treatment of rare diseases. Disease foundations and research centers worldwide focus on better understanding rare disorders. Here, the state-of-the-art drug discovery strategies for small molecules and biological approaches for orphan diseases are reviewed...
July 21, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28730524/genetic-characterization-of-novel-reassortant-h5n6-subtype-influenza-viruses-isolated-from-cats-in-eastern-china
#20
Xueliang Cao, Fan Yang, Haibo Wu, Lihua Xu
Cats are susceptible to influenza A viruses and therefore may act as transmission vectors within households, posing a potential public health concern. Two novel reassortant H5N6 influenza viruses were isolated from cats in Zhejiang Province, Eastern China, in 2016. Both viruses were characterized by whole-genome sequencing with subsequent phylogenetic analysis and genetic comparison. Phylogenetic analysis showed that these viruses received their genes from H5N6, H9N2, and H7N9 influenza viruses isolated from China...
July 21, 2017: Archives of Virology
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