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Florence Koeppel, Alexandre Bobard, Céline Lefebvre, Marion Pedrero, Marc Deloger, Yannick Boursin, Catherine Richon, Romy Chen-Min-Tao, Guillaume Robert, Guillaume Meurice, Etienne Rouleau, Stefan Michiels, Christophe Massard, Jean-Yves Scoazec, Eric Solary, Jean-Charles Soria, Fabrice André, Ludovic Lacroix
Comprehensive genomic profiling using high-throughput sequencing brings a wealth of information, and its place in the clinical setting has been increasingly prominent. This review emphasizes the utility of whole-exome sequencing (WES) and transcriptome sequencing (RNAseq) in patient care and clinical research, based on published reports as well as our experience with the MOSCATO-01 (MOlecular Screening for CAncer Treatment Optimization) molecular triage trial at Gustave Roussy Cancer Center. In this trial, all contributive samples of patients with advanced solid tumors were analyzed prospectively with targeted gene sequencing (TGS) and comparative genomic hybridization...
July 2018: Cancer Journal
Anthony Moreira, Etelvina Figueira, Nélia C Mestre, Denise Schrama, Amadeu M V M Soares, Rosa Freitas, Maria João Bebianno
Proteomic analysis was performed to compare the effects of Arsenic (As), seawater acidification (Low pH) and the combination of both stressors (Low pH + As) on Crassostrea angulata and Crassostrea gigas juveniles in the context of global environmental change. This study aimed to elucidate if two closely related Crassostrea species respond similarly to these environmental stressors, considering both single and combined exposures, to infer if the simultaneous exposure to both stressors induced a differentiated response...
July 30, 2018: Aquatic Toxicology
Richard C Crist, Benjamin C Reiner, Wade H Berrettini
Opioid use disorder (OUD) affects millions of people worldwide and the risk of developing the disorder has a significant genetic component according to twin and family studies. Identification of the genetic variants underlying this inherited risk has focused on two different methods: candidate gene studies and genome-wide association studies (GWAS). The most studied candidate genes have included the mu-opioid receptor (OPRM1), the delta-opioid receptor (OPRD1), the dopamine D2 receptor (DRD2), and brain-derived neurotrophic factor (BDNF)...
August 9, 2018: Current Opinion in Psychology
Yasmine Ghantous, Zaher Bahouth, Imad Abu El-Naaj
PURPOSE: Recurrent and metastatic Oral Squamous Cell Carcinoma (OSCC) is often incurable. There are large gaps in the understanding of the clinical course, biology and genetic biomarkers of OSCC which could help us identify patients with high-risk of recurrence who may benefit from intensified therapy or novel targeted therapy trials. The purpose of this study was to identify significant clinical, pathological and genomic risk factors for local recurrence in OSCC. PATIENTS AND METHODS: Molecular data sets and clinicopathological characteristics of 159 head and neck carcinoma patients were obtained from The Cancer Genome Atlas (TCGA) data portal and analyzed using the Genome Data Analysis Center and cBioPortal to find significant risk factors for tumor recurrence...
August 6, 2018: Archives of Oral Biology
Sundus Naila Maqbool, Haleema Saadiya Nazeer, Mehak Rafiq, Aneela Javed, Rumeza Hanif
Breast Cancer is the most common cancer among women with several genes involved in disease susceptibility. As majority of genome-wide significant variants fall outside the coding region, it is likely that some of them alter specific gene functions. GWAS database was used to interpret the regulatory functions of these genetic variants. A total of 320 SNPs for breast cancer were selected via GWAS, which were entered into the SNAP web portal tool, to determine the one's found to be in Linkage Disequilibrium (r2  < 0...
August 14, 2018: Gene
Kennosuke Yorifuji, Yuko Uemura, Shinji Horibata, Goh Tsuji, Yoko Suzuki, Kazuya Miyagawa, Kazuhiko Nakayama, Ken-Ichi Hirata, Shunichi Kumagai, Noriaki Emoto
Bosentan, an endothelin receptor antagonist, has been widely used as a first-line drug for the treatment of pulmonary arterial hypertension (PAH). In addition, bosentan is approved for patients with digital ulcers related to systemic sclerosis. Liver dysfunction is a major adverse effect of bosentan and may lead to discontinuation of therapy. The purpose of this study was to identify genomic biomarkers to predict bosentan-induced liver injury. A total of 69 PAH patients were recruited into the study. An exploratory analysis of 1,936 single-nucleotide polymorphisms (SNPs) in 231 genes involved in absorption, distribution, metabolism, and elimination of multiple medications using Affimetrix DMET™ (Drug Metabolism Enzymes and Transporters) chips was performed...
August 14, 2018: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
Yu Liu, Pei-Dong Wu, Dai-Zhen Zhang, Hua-Bin Zhang, Bo-Ping Tang, Qiu-Ning Liu, Li-Shang Dai
The mitochondrial genome (mitogenome) can provide important information for understanding phylogenetic analysis and thus molecular evolution. Herein, we amplified the complete mitogenome sequence of Pelteobagrus fulvidraco. The mitogenome was 16,526 bp in length and included 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and a non-coding control region (D-loop). Both the organization and location of genes in the mitogenome were consistent with those from Siluriformes fishes previously published in GenBank...
August 14, 2018: Genomics
Didier Clenet, Tatiana Vinit, Damien Soulet, Claire Maillet, Françoise Guinet-Morlot, Aure Saulnier
Vaccine thermostability is key to successful global immunization programs as it may have a significant impact on the continuous cold-chain maintenance logistics, as well as affect vaccine potency. Modern biological and biophysical techniques were combined to in-depth characterize the thermostability of a formulated rabies virus (RABV) in terms of antigenic and genomic titer, virus particle count and aggregation state. Tunable resistive pulse sensing (TRPS) and nanoparticle tracking analysis (NTA) were used to count virus particles while simultaneously determining their size distribution...
August 14, 2018: European Journal of Pharmaceutics and Biopharmaceutics
Asako Murayama, Kei Fujiwara, Norie Yamada, Masaaki Shiina, Takahiro Masaki, Masamichi Muramatsu, Takaji Wakita, Takanobu Kato
Nonstructural protein 5A (NS5A) inhibitors of hepatitis C virus (HCV) are known to have potent anti-viral effects; however, these inhibitors have limited activities on strains with resistant-associated substitutions or non-genotype 1 strains. To overcome these shortcomings, novel NS5A inhibitors have been developed and approved for clinical application. The aim of this study was to evaluate the anti-viral effect of novel NS5A inhibitors (derivatives of odalasvir) on HCV genotype 2 strains in a cell culture system...
August 14, 2018: Antiviral Research
Julian C Kelman, Benjamin A Kamien, Natalia C Murray, Himanshu Goel, Clare L Fraser, John R Grigg
Inherited optic neuropathy is a rare cause of debilitating vision loss. It may occur in constellation with other syndromic features of neurological impairment, or present as an isolated finding. We describe a sibling pair, without a family history of vision loss, who developed visual impairment in early childhood consistent with optic neuropathy. Genetic testing identified novel compound heterozygous variants in the aconitase 2 (ACO2) gene. To date, seven families hosting ACO2 variants have been described in the literature...
August 17, 2018: Ophthalmic Genetics
Jana R Jenquin, Leslie A Coonrod, Quinn A Silverglate, Natalie A Pellitier, Melissa A Hale, Guangbin Xia, Masayuki Nakamori, J Andrew Berglund
Myotonic dystrophy type 1 (DM1) is an autosomal dominant, CTG•CAG microsatellite expansion disease. Expanded CUG repeat RNA sequester the muscleblind-like (MBNL) family of RNA-binding proteins, thereby disrupting their normal cellular function leading to global mis-regulation of RNA processing. Previously, the small molecule furamidine was shown to reduce CUG foci and rescue mis-splicing in a DM1 HeLa cell model and rescue mis-splicing in the HSALR DM1 mouse model, but furamidine's mechanism of action was not explored...
August 17, 2018: ACS Chemical Biology
Miriam Schalamun, Ramawatar Nagar, David Kainer, Eleanor Beavan, David Eccles, John P Rathjen, Robert Lanfear, Benjamin Schwessinger
Long-read sequencing technologies are transforming our ability to assemble highly complex genomes. Realising their full potential is critically reliant on extracting high quality, high molecular weight (HMW) DNA from the organisms of interest. This is especially the case for the portable MinION sequencer which enables all laboratories to undertake their own genome sequencing projects, due to its low entry cost and minimal spatial footprint. One challenge of the MinION is that each group has to independently establish effective protocols for using the instrument, which can be time consuming and costly...
August 17, 2018: Molecular Ecology Resources
Jinglan Jin, Hongqin Xu, Ruihong Wu, Junqi Niu, Shibo Li
PURPOSE: We aimed to study the aberrant DNA methylation profile associated with hepatitis B virus (HBV) infection and to identify key genes and pathways associated with the HBV infection stage. METHODS: A total of 54 antiviral treatment-naive HBV-infected patients and 6 healthy controls were included. Genome-wide methylated DNA immunoprecipitation analysis was performed, as previously described, after which the chip data were preprocessed. Subsequently, Cytoscape software was used for the construction of a protein-protein interaction network, and Database for Annotation, Visualization, and Integrated Discovery software was used to conduct functional enrichment analysis...
August 17, 2018: Journal of Medical Virology
Gerald A Tuskan, Ritesh Mewalal, Lee E Gunter, Kaitlin J Palla, Kelsey Carter, Daniel A Jacobson, Piet C Jones, Benjamin J Garcia, Deborah A Weighill, Philip D Hyatt, Yongil Yang, Jin Zhang, Nicholas Reis, Jin-Gui Chen, Wellington Muchero
A characteristic feature of plant cells is the ability to form callus from parenchyma cells in response to biotic and abiotic stimuli. Tissue culture propagation of recalcitrant plant species and genetic engineering for desired phenotypes typically depends on efficient in vitro callus generation. Callus formation is under genetic regulation, and consequently, a molecular understanding of this process underlies successful generation for propagation materials and/or introduction of genetic elements in experimental or industrial applications...
2018: PloS One
Han-Yuan Zhang, Zi-Xia Zhao, Jian Xu, Peng Xu, Qing-Li Bai, Shi-Yong Yang, Li-Kun Jiang, Bao-Hua Chen
Various salmonid species are cultivated in cold water aquaculture. However, due to limited genomic data resources, specific high-throughput genotyping tools are not available to many of the salmonid species. In this study, a 57K single nucleotide polymorphism (SNP) array for rainbow trout (Oncorhynchus mykiss) was utilized to detect polymorphisms in seven salmonid species, including Hucho taimen, Oncorhynchus masou, Salvelinus fontinalis, Brachymystax lenok, Salvelinus leucomaenis, O. kisutch, and O. mykiss...
2018: PloS One
Guojun Guo, Yutian Liu, Sen Ren, Yu Kang, Dominik Duscher, Hans-Günther Machens, Zhenbing Chen
Diabetic peripheral neuropathy is a common complication associated with diabetes mellitus with a pathogenesis that is incompletely understood. By regulating RNA silencing and post-transcriptional gene expression, microRNAs participate in various biological processes and human diseases. However, the relationship between microRNAs and the progress of diabetic peripheral neuropathy still lacks a thorough exploration. Here we used microarray microRNA and mRNA expression profiling to analyze the microRNAs and mRNAs which are aberrantly expressed in dorsal root ganglia from streptozotocin-induced diabetic rats...
2018: PloS One
Rebekah C Gullberg, J Jordan Steel, Venugopal Pujari, Joel Rovnak, Dean C Crick, Rushika Perera
Positive strand RNA viruses, such as dengue virus type 2 (DENV2) expand and structurally alter ER membranes to optimize cellular communication pathways that promote viral replicative needs. These complex rearrangements require significant protein scaffolding as well as changes to the ER chemical composition to support these structures. We have previously shown that the lipid abundance and repertoire of host cells are significantly altered during infection with these viruses. Specifically, enzymes in the lipid biosynthesis pathway such as fatty acid synthase (FAS) are recruited to viral replication sites by interaction with viral proteins and displayed enhanced activities during infection...
August 17, 2018: PLoS Pathogens
Mawuli Dzodzomenyo, Anita Ghansah, Nana Ensaw, Benjamin Dovie, Langbong Bimi, Reginald Quansah, Ben A Gyan, Mawuli Gyakobo, Benjamin Amoani
OBJECTIVE: We assessed the association of mutant allele frequencies of nitric oxide synthase 2 (NOS2) gene at two SNPs (-954 and -1173) with malaria disease severity in children from a malaria endemic area in Southern Ghana. METHOD: Using children recruited at the hospital, assigned into clinical subgroups of uncomplicated and severe malaria and matching with their "healthy control" counterparts, we designed a case control study. Genomic DNA was extracted and genotyping using Restriction Fragment Polymorphism was done...
2018: PloS One
John Soghigian, Theodore G Andreadis, Goudarz Molaei
BACKGROUND: Eastern Equine Encephalitis (EEE) (Togaviridae, Alphavirus) is a highly pathogenic mosquito-borne arbovirus that circulates in an enzootic cycle involving Culiseta melanura mosquitoes and wild Passeriformes birds in freshwater swamp habitats. Recently, the northeastern United States has experienced an intensification of virus activity with increased human involvement and northward expansion into new regions. In addition to its principal role in enzootic transmission of EEE virus among avian hosts, recent studies on the blood-feeding behavior of Cs...
August 17, 2018: PLoS Neglected Tropical Diseases
Lina M Valencia, Amely Martins, Edgardo M Ortiz, Anthony Di Fiore
Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods...
2018: PloS One
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