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Daniel P Depledge, Werner J D Ouwendijk, Tomohiko Sadaoka, Shirley E Braspenning, Yasuko Mori, Randall J Cohrs, Georges M G M Verjans, Judith Breuer
Varicella-zoster virus (VZV), an alphaherpesvirus, establishes lifelong latent infection in the neurons of >90% humans worldwide, reactivating in one-third to cause shingles, debilitating pain and stroke. How VZV maintains latency remains unclear. Here, using ultra-deep virus-enriched RNA sequencing of latently infected human trigeminal ganglia (TG), we demonstrate the consistent expression of a spliced VZV mRNA, antisense to VZV open reading frame 61 (ORF61). The spliced VZV latency-associated transcript (VLT) is expressed in human TG neurons and encodes a protein with late kinetics in productively infected cells in vitro and in shingles skin lesions...
March 21, 2018: Nature Communications
Brian S White, Irena Lanc, Julie O'Neal, Harshath Gupta, Robert S Fulton, Heather Schmidt, Catrina Fronick, Edward A Belter, Mark Fiala, Justin King, Greg J Ahmann, Mary DeRome, Elaine R Mardis, Ravi Vij, John F DiPersio, Joan Levy, Daniel Auclair, Michael H Tomasson
Multiple myeloma (MM) is a disease of copy number variants (CNVs), chromosomal translocations, and single-nucleotide variants (SNVs). To enable integrative studies across these diverse mutation types, we developed a capture-based sequencing platform to detect their occurrence in 465 genes altered in MM and used it to sequence 95 primary tumor-normal pairs to a mean depth of 104×. We detected cases of hyperdiploidy (23%), deletions of 1p (8%), 6q (21%), 8p (17%), 14q (16%), 16q (22%), and 17p (4%), and amplification of 1q (19%)...
March 21, 2018: Blood Cancer Journal
Almudena Cascajero, Alberto Rastrojo, Francisco Díez-Fuertes, Beatriz Hernández-Novoa, Begoña Aguado, Santiago Moreno, José Alcami, Mayte Pérez-Olmeda
In this study we have characterized quasispecies dynamics and the evolution of viral tropism in naive HIV-1-infected patients treated with a short-course of maraviroc monotherapy (NCT01060618) independently of their tropism. We randomly selected 20 patients displaying different basal tropism -10 R5 and 10 DMX4- at recruitment as determined by phenotypic tests (Trofile® ). Evolution of viral quasiespecies at the end of treatment was determined by ultra-deep sequencing of the V3 region using a 454 Life Sciences Platform and geno2pheno (g2p) algorithm for viral tropism prediction...
March 21, 2018: Journal of Virology
BingNan Liao, YouJin Hao, JunXing Lu, HuiYang Bai, Li Guan, Tao Zhang
BACKGROUND: Perilla frutescens is well known for its high α-linolenic acid (ALA) accumulation in seeds and medicinal values as well as a source of edible and general-purpose oils. However, the regulatory mechanisms of the biosynthesis of fatty acid in its seeds remain poorly understood due to the lacking of sequenced genome. For better understanding the regulation of lipid metabolism and further increase its oil content or modify oil composition, time-course transcriptome and lipid composition analyses were performed...
March 21, 2018: BMC Genomics
Anna Lange-Consiglio, Barbara Lazzari, Claudia Perrini, Flavia Pizzi, Alessandra Stella, Fausto Cremonesi, Emanuele Capra
Cell-derived microvesicles (MVs) are a recently discovered mechanism of cell-to-cell communication. Our previous data show that MVs secreted by equine amniotic mesenchymal-derived cells (AMCs) are involved in downregulation of proinflammatory genes in lipopolysaccharide-stressed equine tendon and endometrial cells. The aim of the present study was to evaluate whether AMC-MVs contain selected microRNAs (miRNAs) involved in inflammation. Two pools of cells, derived from 3 amniotic membranes each, and their respective MVs were collected...
January 2018: Cell Transplantation
Woosuk Kim, Myunggyu Kim
In sports motion analysis, observation is a prerequisite for understanding the quality of motions. This paper introduces a novel approach to detect and segment sports motions using a wearable sensor for supporting systematic observation. The main goal is, for convenient analysis, to automatically provide motion data, which are temporally classified according to the phase definition. For explicit segmentation, a motion model is defined as a sequence of sub-motions with boundary states. A sequence classifier based on deep neural networks is designed to detect sports motions from continuous sensor inputs...
March 19, 2018: Sensors
Raúl Cruz-Barbosa, Erik-German Ramos-Pérez, Jesús Giraldo
G protein-coupled receptors (GPCRs) are integral cell membrane proteins of relevance for pharmacology. The complete tertiary structure including both extracellular and transmembrane domains has not been determined for any member of class C GPCRs. An alternative way to work on GPCR structural models is the investigation of their functionality through the analysis of their primary structure. For this, sequence representation is a key factor for the GPCRs' classification context, where usually, feature engineering is carried out...
March 19, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Gábor Zsurka, Viktoriya Peeva, Alexander Kotlyar, Wolfram S Kunz
Recent deep sequencing data has provided compelling evidence that the spectrum of somatic point mutations in mitochondrial DNA (mtDNA) in aging tissues lacks G > T transversion mutations. This fact cannot, however, be used as an argument for the missing contribution of reactive oxygen species (ROS) to mitochondria-related aging because it is probably caused by the nucleotide selectivity of mitochondrial DNA polymerase γ (POLG). In contrast to point mutations, the age-dependent accumulation of mitochondrial DNA deletions is, in light of recent experimental data, still explainable by the segregation of mutant molecules generated by the direct mutagenic effects of ROS (in particular, of HO· radicals formed from H₂O₂ by a Fenton reaction)...
March 21, 2018: Genes
Justine R Smith, Larry L David, Binoy Appukuttan, Phillip A Wilmarth
Diseases that involve retinal or choroidal vascular endothelial cells are leading causes of vision loss: age-related macular degeneration, retinal ischemic vasculopathies and non-infectious posterior uveitis. Proteins differentially expressed by these endothelial cell populations are potential drug targets. We used deep proteomic profiling to define the molecular phenotype of human retinal and choroidal endothelial cells at the protein level. MethodsRetinal and choroidal vascular endothelial cells were separately isolated from five human eye pairs by selection on CD31...
March 17, 2018: American Journal of Ophthalmology
Deyu Zhou, Lei Miao, Yulan He
OBJECTIVE: A drug-drug interaction (DDI) is a situation in which a drug affects the activity of another drug synergistically or antagonistically when being administered together. The information of DDIs is crucial for healthcare professionals to prevent adverse drug events. Although some known DDIs can be found in purposely-built databases such as DrugBank, most information is still buried in scientific publications. Therefore, automatically extracting DDIs from biomedical texts is sorely needed...
March 17, 2018: Artificial Intelligence in Medicine
Nikolaos P Daskalakis, Allison C Provost, Richard G Hunter, Guia Guffanti
Posttraumatic stress disorder (PTSD) is a pathologic response to trauma that impacts ∼8% of the population and is highly comorbid with other disorders, such as traumatic brain injury. PTSD affects multiple biological systems throughout the body, including the hypothalamic-pituitary-adrenal axis, cortical function, and the immune system, and while the study of the biological underpinnings of PTSD and related disorders are numerous, the roles of noncoding RNAs (ncRNAs) are just emerging. Moreover, deep sequencing has revealed that ncRNAs represent most of the transcribed mammalian genome...
January 31, 2018: Biological Psychiatry
Timothy Becker, Wan-Ping Lee, Joseph Leone, Qihui Zhu, Chengsheng Zhang, Silvia Liu, Jack Sargent, Kritika Shanker, Adam Mil-Homens, Eliza Cerveira, Mallory Ryan, Jane Cha, Fabio C P Navarro, Timur Galeev, Mark Gerstein, Ryan E Mills, Dong-Guk Shin, Charles Lee, Ankit Malhotra
Comprehensive and accurate identification of structural variations (SVs) from next generation sequencing data remains a major challenge. We develop FusorSV, which uses a data mining approach to assess performance and merge callsets from an ensemble of SV-calling algorithms. It includes a fusion model built using analysis of 27 deep-coverage human genomes from the 1000 Genomes Project. We identify 843 novel SV calls that were not reported by the 1000 Genomes Project for these 27 samples. Experimental validation of a subset of these calls yields a validation rate of 86...
March 20, 2018: Genome Biology
Yuanyuan Zhou, Xia Zheng, Jiaojiao Lu, Wei Chen, Xu Li, Le Zhao
BACKGROUND/AIMS: The Warburg effect is one of the main energy metabolism features supporting cancer cell growth. 20(S)-Rg3 exerts anti-tumor effect on ovarian cancer partly by inhibiting the Warburg effect. microRNAs are important regulators of the Warburg effect. However, the microRNA regulatory network mediating the anti-Warburg effect of 20(S)-Rg3 was largely unknown. METHODS: microRNA deep sequencing was performed to identify the 20(S)-Rg3-influenced microRNAs in SKOV3 ovarian cancer cells...
March 16, 2018: Cellular Physiology and Biochemistry
Wilson Huanca-Mamani, Raúl Arias-Carrasco, Steffany Cárdenas-Ninasivincha, Marcelo Rojas-Herrera, Gonzalo Sepúlveda-Hermosilla, José Carlos Caris-Maldonado, Elizabeth Bastías, Vinicius Maracaja-Coutinho
Long non-coding RNAs (lncRNAs) have been defined as transcripts longer than 200 nucleotides, which lack significant protein coding potential and possess critical roles in diverse cellular processes. Long non-coding RNAs have recently been functionally characterized in plant stress-response mechanisms. In the present study, we perform a comprehensive identification of lncRNAs in response to combined stress induced by salinity and excess of boron in the Lluteño maize, a tolerant maize landrace from Atacama Desert, Chile...
March 20, 2018: Genes
Fangying Song, Ning Liu, Minghao Liu, Yihua Chen, Ying Huang
Mycemycins A-E are new members of the dibenzoxazepinone (DBP) family, derived from the gntR gene-disrupted deep sea strain Streptomyces olivaceus FXJ8.012Δ1741 and the soil strain Streptomyces sp. FXJ1.235. In this paper, we report the identification of the gene clusters and pathways' inference for mycemycin biosynthesis in the two strains. Bioinformatics analyses of the genome sequences of S. olivaceus FXJ8.012Δ1741 and S . sp. FXJ1.235 predicted two divergent mycemycin gene clusters, mym and mye , respectively...
March 20, 2018: Marine Drugs
Li Bao, Zhaoyang Qian, Maria B Lyng, Ling Wang, Yuan Yu, Ting Wang, Xiuqing Zhang, Huanming Yang, Nils Brünner, Jun Wang, Henrik J Ditzel
Single cancer cell sequencing studies currently use randomly-selected cells, limiting correlations between genomic aberrations, morphology and spatial localization. We laser-captured microdissected single cells from morphologically-distinct areas of primary breast cancer and corresponding lymph node metastasis and performed whole-exome or deep-target sequencing of greater than 100 such cells. Two major subclones co-existed in different areas of the primary tumor, and the lymph node metastasis originated from a minor subclone in the invasive front of the primary tumor with additional copy number changes including 8q gain, but no additional point mutations in driver genes...
March 15, 2018: Journal of Clinical Investigation
Yuli Wei, Jiasong Fang, Yunping Xu, Weiqiang Zhao, Junwei Cao
A novel heterotrophic, Gram-stain-positive, facultatively anaerobic and rod-shaped bacterium, designated strain NBT06-6T , was isolated from the deep seawater in the New Britain Trench and characterized phylogenetically and phenotypically. Optimal bacterial growth occurred at 35 °C (range 22-41 °C), at pH 6 (4-8) and with 4 % (w/v) NaCl (0-10 %). The strain grew at hydrostatic pressures of 0.1-100 MPa (optimum, 0.1 MPa) at 35 °C. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain NBT06-6T belonged to the genus Corynebacterium, with the highest sequence similarity (97...
March 20, 2018: International Journal of Systematic and Evolutionary Microbiology
Utako Okata-Karigane, Yasuki Hata, Emiko Watanabe-Okada, Shunichi Miyakawa, Michi Ota, Yutaka Uzawa, Shigekazu Iguchi, Atsushi Yoshida, Ken Kikuchi
A 60-year-old Japanese man presented with multiple subcutaneous nodules in his left groin. Histologically, the nodules consisted of suppurative granulomas and abscesses not involving the hair follicles. Trichophyton rubrum TWCC57922 was detected by fungal culture and polymerase chain reaction (PCR) sequencing of the rDNA genes. We diagnosed these nodules as deeper dermal dermatophytosis, a rare form of invasive dermatophytosis. He was treated with terbinafine. We compared these findings with previous reports of deep dermal dermatophytosis...
September 2018: Medical Mycology Case Reports
Ying Liu, Brent Logan, Ning Liu, Zhiyuan Xu, Jian Tang, Yanzhi Wang
In this paper, we propose the first deep reinforcement learning framework to estimate the optimal Dynamic Treatment Regimes from observational medical data. This framework is more flexible and adaptive for high dimensional action and state spaces than existing reinforcement learning methods to model real life complexity in heterogeneous disease progression and treatment choices, with the goal to provide doctor and patients the data-driven personalized decision recommendations. The proposed deep reinforcement learning framework contains a supervised learning step to predict the most possible expert actions; and a deep reinforcement learning step to estimate the long term value function of Dynamic Treatment Regimes...
August 2017: Healthcare Informatics: the Business Magazine for Information and Communication Systems
Jorge Ruiz-Orera, Pol Verdaguer-Grau, José Luis Villanueva-Cañas, Xavier Messeguer, M Mar Albà
Accumulating evidence indicates that some protein-coding genes have originated de novo from previously non-coding genomic sequences. However, the processes underlying de novo gene birth are still enigmatic. In particular, the appearance of a new functional protein seems highly improbable unless there is already a pool of neutrally evolving peptides that are translated at significant levels and that can at some point acquire new functions. Here, we use deep ribosome-profiling sequencing data, together with proteomics and single nucleotide polymorphism information, to search for these peptides...
March 19, 2018: Nature Ecology & Evolution
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