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Yipeng Wang, Liping Guo, Lin Feng, Wen Zhang, Ting Xiao, Xuebing Di, Guoji Chen, Kaitai Zhang
Circulating tumour cell (CTC) behaviours are distinct from those of bulk tissues. Thus, treatments to eliminate CTCs differ from the regimens followed to reduce the primary tumour and its metastases. Accordingly, comprehensively deciphering the single nucleotide variant (SNV) profiles in CTCs, which partially determine CTC behaviours, is a priority. Using viable CTCs isolated with the oHSV1‑hTERT‑GFP virus coupled with fluorescence‑activated cell sorting (FACS), the whole genome was amplified using the multiple annealing and looping‑based amplification cycle (MALBAC) method...
May 2018: Oncology Reports
Yanwei Xing, Zhiwei Zhao, Yuekun Zhu, Liangliang Zhao, Anlong Zhu, Daxun Piao
The objective of this study was to identify potentially significant genes and long non-coding RNAs (lncRNAs) in colon cancer for a panel of lncRNA signatures that could be used as prognostic markers for colon adenocarcinoma (COAD) based on the data from The Cancer Genome Atlas (TCGA). RNA-seq V2 exon data of COAD were downloaded from the TCGA data portal for 285 tumor samples and 41 normal tissue samples adjacent to tumors. Differentially expressed mRNAs and lncRNAs were identified. A functional enrichment analysis of differentially expressed mRNAs was performed, followed by protein-protein interaction (PPI) network construction and significant module selection...
May 2018: Oncology Reports
Kurt D Christensen, Jason L Vassy, Kathryn A Phillips, Carrie L Blout, Danielle R Azzariti, Christine Y Lu, Jill O Robinson, Kaitlyn Lee, Michael P Douglas, Jennifer M Yeh, Kalotina Machini, Natasha K Stout, Heidi L Rehm, Amy L McGuire, Robert C Green, Dmitry Dukhovny
PurposeGreat uncertainty exists about the costs associated with whole-genome sequencing (WGS).MethodsOne hundred cardiology patients with cardiomyopathy diagnoses and 100 ostensibly healthy primary care patients were randomized to receive a family-history report alone or with a WGS report. Cardiology patients also reviewed prior genetic test results. WGS costs were estimated by tracking resource use and staff time. Downstream costs were estimated by identifying services in administrative data, medical records, and patient surveys for 6 months...
March 22, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Margaret P Adam
No abstract text is available yet for this article.
March 22, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Stephany Tandy-Connor, Jenna Guiltinan, Kate Krempely, Holly LaDuca, Patrick Reineke, Stephanie Gutierrez, Phillip Gray, Brigette Tippin Davis
PurposeThere is increasing demand from the public for direct-to-consumer (DTC) genetic tests, and the US Food and Drug Administration limits the type of health-related claims DTC tests can market. Some DTC companies provide raw genotyping data to customers if requested, and these raw data may include variants occurring in genes recommended by the American College of Medical Genetics and Genomics to be reported as incidental/secondary findings. The purpose of this study was to review the outcome of requests for clinical confirmation of DTC results that were received by our laboratory and to analyze variant classification concordance...
March 22, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Ahmed Alfares, Taghrid Aloraini, Lamia Al Subaie, Abdulelah Alissa, Ahmed Al Qudsi, Ahmed Alahmad, Fuad Al Mutairi, Abdulrahman Alswaid, Ali Alothaim, Wafaa Eyaid, Mohammed Albalwi, Saeed Alturki, Majid Alfadhel
PurposeWhole-exome sequencing (WES) and whole-genome sequencing (WGS) are used to diagnose genetic and inherited disorders. However, few studies comparing the detection rates of WES and WGS in clinical settings have been performed.MethodsVariant call format files were generated and raw data analysis was performed in cases in which the final molecular results showed discrepancies. We classified the possible explanations for the discrepancies into three categories: the time interval between the two tests, the technical limitations of WES, and the impact of the sequencing system type...
March 22, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Lynn W Bush, Louis E Bartoshesky, Karen L David, Benjamin Wilfond, Janet L Williams, Ingrid A Holm
Disclaimer: This article is designed primarily as an educational resource for medical geneticists and other health care providers to help them provide quality patient care. Adherence to the information contained in this article does not necessarily assure a successful medical outcome. This information and any associated recommendations should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, each provider should apply his or her own professional judgment to the specific clinical circumstances presented by the individual patient...
March 22, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Iñigo Olalde, Selina Brace, Morten E Allentoft, Ian Armit, Kristian Kristiansen, Thomas Booth, Nadin Rohland, Swapan Mallick, Anna Szécsényi-Nagy, Alissa Mittnik, Eveline Altena, Mark Lipson, Iosif Lazaridis, Thomas K Harper, Nick Patterson, Nasreen Broomandkhoshbacht, Yoan Diekmann, Zuzana Faltyskova, Daniel Fernandes, Matthew Ferry, Eadaoin Harney, Peter de Knijff, Megan Michel, Jonas Oppenheimer, Kristin Stewardson, Alistair Barclay, Kurt Werner Alt, Corina Liesau, Patricia Ríos, Concepción Blasco, Jorge Vega Miguel, Roberto Menduiña García, Azucena Avilés Fernández, Eszter Bánffy, Maria Bernabò-Brea, David Billoin, Clive Bonsall, Laura Bonsall, Tim Allen, Lindsey Büster, Sophie Carver, Laura Castells Navarro, Oliver E Craig, Gordon T Cook, Barry Cunliffe, Anthony Denaire, Kirsten Egging Dinwiddy, Natasha Dodwell, Michal Ernée, Christopher Evans, Milan Kuchařík, Joan Francès Farré, Chris Fowler, Michiel Gazenbeek, Rafael Garrido Pena, María Haber-Uriarte, Elżbieta Haduch, Gill Hey, Nick Jowett, Timothy Knowles, Ken Massy, Saskia Pfrengle, Philippe Lefranc, Olivier Lemercier, Arnaud Lefebvre, César Heras Martínez, Virginia Galera Olmo, Ana Bastida Ramírez, Joaquín Lomba Maurandi, Tona Majó, Jacqueline I McKinley, Kathleen McSweeney, Balázs Gusztáv Mende, Alessandra Modi, Gabriella Kulcsár, Viktória Kiss, András Czene, Róbert Patay, Anna Endrődi, Kitti Köhler, Tamás Hajdu, Tamás Szeniczey, János Dani, Zsolt Bernert, Maya Hoole, Olivia Cheronet, Denise Keating, Petr Velemínský, Miroslav Dobeš, Francesca Candilio, Fraser Brown, Raúl Flores Fernández, Ana-Mercedes Herrero-Corral, Sebastiano Tusa, Emiliano Carnieri, Luigi Lentini, Antonella Valenti, Alessandro Zanini, Clive Waddington, Germán Delibes, Elisa Guerra-Doce, Benjamin Neil, Marcus Brittain, Mike Luke, Richard Mortimer, Jocelyne Desideri, Marie Besse, Günter Brücken, Mirosław Furmanek, Agata Hałuszko, Maksym Mackiewicz, Artur Rapiński, Stephany Leach, Ignacio Soriano, Katina T Lillios, João Luís Cardoso, Michael Parker Pearson, Piotr Włodarczak, T Douglas Price, Pilar Prieto, Pierre-Jérôme Rey, Roberto Risch, Manuel A Rojo Guerra, Aurore Schmitt, Joël Serralongue, Ana Maria Silva, Václav Smrčka, Luc Vergnaud, João Zilhão, David Caramelli, Thomas Higham, Mark G Thomas, Douglas J Kennett, Harry Fokkens, Volker Heyd, Alison Sheridan, Karl-Göran Sjögren, Philipp W Stockhammer, Johannes Krause, Ron Pinhasi, Wolfgang Haak, Ian Barnes, Carles Lalueza-Fox, David Reich
This corrects the article DOI: 10.1038/nature25738.
March 21, 2018: Nature
Octavia Ramayanti, Mitch Brinkkemper, Sandra A W M Verkuijlen, Leni Ritmaleni, Mei Lin Go, Jaap M Middeldorp
Epstein-Barr virus (EBV) persists in nasopharyngeal (NPC) and gastric carcinomas (EBVaGC) in a tightly latent form. Cytolytic virus activation (CLVA) therapy employs gemcitabine and valproic acid (GCb+VPA) to reactivate latent EBV into the lytic phase and antiviral valganciclovir to enhance cell death and prevent virus production. CLVA treatment has proven safe in phase-I/II trials with promising clinical responses in patients with recurrent NPC. However, a major challenge is to maximize EBV lytic reactivation by CLVA...
March 22, 2018: Cancers
Delphine Adam, Marta Maciejewska, Aymeric Naômé, Loïc Martinet, Wouter Coppieters, Latifa Karim, Denis Baurain, Sébastien Rigali
Cave moonmilk deposits host an abundant and diverse actinobacterial population that has a great potential for producing novel natural bioactive compounds. In our previous attempt to isolate culturable moonmilk-dwelling Actinobacteria, only Streptomyces species were recovered, whereas a metagenetic study of the same deposits revealed a complex actinobacterial community including 46 actinobacterial genera in addition to streptomycetes. In this work, we applied the rehydration-centrifugation method to lessen the occurrence of filamentous species and tested a series of strategies to achieve the isolation of hard-to-culture and rare Actinobacteria from the moonmilk deposits of the cave "Grotte des Collemboles"...
March 22, 2018: Antibiotics
Takafumi Ito, Jun Kurita, Koh-Ichiro Mori, Helle Frank Skall, Niels Lorenzen, Niccolò Vendramin, Nikolaj Gedsted Andersen, Katja Einer-Jensen, Niels Jørgen Olesen
Four major genotypes of viral haemorrhagic septicaemia virus (VHSV), which have been isolated from many marine and freshwater fish species, are known to differ in virulence. While fast and low-cost genotyping systems based on monoclonal antibodies (MAbs) have been developed for typing of VHSV virulence, there is a need for supplementing the knowledge. In particular, 2 field isolates from viral haemorrhagic septicaemia (VHS) outbreaks in sea-reared rainbow trout Oncorhynchus mykiss in Sweden, SE-SVA-14 and SE-SVA-1033 (both genotype Ib), have yielded contradictory reactions...
March 22, 2018: Diseases of Aquatic Organisms
Covadonga Alonso, Manuel Borca, Linda Dixon, Yolanda Revilla, Fernando Rodriguez, Jose M Escribano, Ictv Report Consortium
The family Asfarviridae includes the single species African swine fever virus, isolates of which have linear dsDNA genomes of 170-194 kbp. Virions have an internal core, an internal lipid membrane, an icosahedral capsid and an outer lipid envelope. Infection of domestic pigs and wild boar results in an acute haemorrhagic fever with transmission by contact or ingestion, or by ticks of the genus Ornithodoros. Indigenous pigs act as reservoirs in Africa, where infection is endemic, and from where introductions occur periodically to Europe...
March 22, 2018: Journal of General Virology
Samiran Bandyopadhyay, Jaydeep Banerjee, Debaraj Bhattacharyya, Indranil Samanta, Achintya Mahanti, Tapan K Dutta, Sarbaswarup Ghosh, Pramod K Nanda, Premanshu Dandapat, Subhasish Bandyopadhyay
We investigated the occurrence of extended-spectrum β-lactamase (ESBL) and AmpC-type β-lactamase (ACBL) producing quinolone-resistant Klebsiella pneumoniae (KP) in milk samples of apparently healthy buffaloes (n = 348) and buffaloes (n = 19) with evidence of subclinical mastitis from seven districts of West Bengal, India. In total, 12 ESBL producing KP were isolated with blaCTX-M-15 gene and 7 of them were ACBL producers, as well. The blaCTX-M-15 genes were carried by transposable element ISEcp1. The plasmid-mediated quinolone resistance genes-qnrS, qnrA, qnrB, qepA, and aac(6')-Ib-cr were detected in five, one, three, four, and one isolate (s), respectively...
March 22, 2018: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
Xiaokun Xu, Haibo Zhou, Yang Liu, Xiaotong Liu, Jun Fu, Aiying Li, Yue-Zhong Li, Yuemao Shen, Xiaoying Bian, Youming Zhang
The indole alkaloid antibiotic chuangxinmycin, from Actinobacteria Actinoplanes tsinanensis, containing a unique thiopyrano[4,3,2- cd]indole scaffold, is a potent and selective inhibitor of bacterial tryptophanyl-tRNA synthetase. The chuangxinmycin biosynthetic gene cluster was identified by in silico analysis of the genome sequence, then verified by heterologous expression. Systemic gene inactivation and intermediate identification determined the minimum set of genes for unique thiopyrano[4,3,2- cd]indole formation and the concerted action of a radical S-adenosylmethionine protein plus an unknown protein for addition of the 3-methyl group...
March 22, 2018: Journal of Natural Products
Ahmed S Bayoumi, Tatsuya Aonuma, Jian-Peng Teoh, Yao-Liang Tang, Il-Man Kim
Recent advancements in genome-wide analyses and RNA-sequencing technologies led to the discovery of small noncoding RNAs, such as microRNAs (miRs), as well as both linear long noncoding RNAs (lncRNAs) and circular long noncoding RNAs (circRNAs). The importance of miRs and lncRNAs in the treatment, prognosis and diagnosis of cardiovascular diseases (CVDs) has been extensively reported. We also previously reviewed their implications in therapies and as biomarkers for CVDs. More recently, circRNAs have also emerged as important regulators in CVDs...
March 22, 2018: Acta Pharmacologica Sinica
Nigel W Beebe
Mosquitoes' importance as vectors of pathogens that drive disease underscores the importance of precise and comparable methods of taxa identification among their species. While several molecular targets have been used to study mosquitoes since the initiation of PCR in the 1980s, its application to mosquito identification took off in the early 1990s. This review follows the research's recent journey into the use of mitochondrial DNA (mtDNA) cytochrome oxidase 1 (COI or COX1) as a DNA barcode target for mosquito species identification - a target whose utility for discriminating mosquitoes is now escalating...
March 22, 2018: Parasitology
Tomoyasu Marui, Youta Torii, Shuji Iritani, Hirotaka Sekiguchi, Chikako Habuchi, Hiroshige Fujishiro, Kenichi Oshima, Kazuhiro Niizato, Shotaro Hayashida, Katsuhisa Masaki, Junichi Kira, Norio Ozaki
OBJECTIVE: Recent studies based on the neuroimaging analysis, genomic analysis and transcriptome analysis of the postmortem brain suggest that the pathogenesis of schizophrenia is related to myelin-oligodendrocyte abnormalities. However, no serious neuropathological investigation of this protein in the schizophrenic brain has yet been performed. In this study, to confirm the change in neuropathological findings due to the pathogenesis of this disease, we observed the expression of myelin-oligodendrocyte directly in the brain tissue of schizophrenia patients...
March 22, 2018: Acta Neuropsychiatrica
Yunyun Jiang, Jian Zhang, Xiao Zhao, Wen Zhao, Zhijian Yu, Chao Chen, Zhennai Yang
Lactobacillus plantarum (L. plantarum) K25 is a probiotic strain isolated from Tibetan kefir. Previous studies showed that this exopolysaccharide (EPS)-producing strain was antimicrobial active and cold tolerant. These functional traits were evidenced by complete genome sequencing of strain K25 with a circular 3,175,846-bp chromosome and six circular plasmids, encoding 3365 CDSs, 16 rRNA genes and 70 tRNA genes. Genomic analysis of L. plantarum K25 illustrates that this strain contains the previous reported mechanisms of probiotic functionality and cold tolerance, involving plantaricins, lysozyme, bile salt hydrolase, chaperone proteins, osmoprotectant, oxidoreductase, EPSs and terpenes...
March 22, 2018: Bioscience, Biotechnology, and Biochemistry
Kevin Yauy, Vincent Gatinois, Thomas Guignard, Satish Sati, Jacques Puechberty, Jean Baptiste Gaillard, Anouck Schneider, Franck Pellestor
Apparition of next-generation sequencing (NGS) was a breakthrough on knowledge of genome structure. Bioinformatic tools are a key point to analyze this huge amount of data from NGS and characterize the three-dimensional organization of chromosomes. This chapter describes usage of different browsers to explore publicly available online data and to search for possible 3D chromatin changes involved during complex chromosomal rearrangements as chromothripsis. Their pathogenic impact on clinical phenotype and gene misexpression can also be evaluated with annotated databases...
2018: Methods in Molecular Biology
Christine J Ye, Guo Liu, Henry H Heng
Genome chaos, or karyotype chaos, represents a powerful survival strategy for somatic cells under high levels of stress/selection. Since the genome context, not the gene content, encodes the genomic blueprint of the cell, stress-induced rapid and massive reorganization of genome topology functions as a very important mechanism for genome (karyotype) evolution. In recent years, the phenomenon of genome chaos has been confirmed by various sequencing efforts, and many different terms have been coined to describe different subtypes of the chaotic genome including "chromothripsis," "chromoplexy," and "structural mutations...
2018: Methods in Molecular Biology
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