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deep sequencing

Yi Zhou, Megan Othus, Roland B Walter, Elihu H Estey, David Wu, Brent L Wood
Relapse is the major cause of death in patients with acute myeloid leukemia (AML) after allogeneic hematopoietic cell transplant (HCT). Measurable residual disease (MRD) detected by multiparameter flow cytometry (MFC) before and after HCT is a strong, independent risk factor for relapse. As next generation sequencing (NGS) is increasingly applied in AML MRD detection, it remains to be determined if NGS can improve prediction of post-HCT relapse. Herein, we investigated pre-HCT MRD detected by MFC and NGS in 59 adult patients with NPM1-mutated AML in morphologic remission; 45 of the 59 had post-HCT MRD determined by MFC and NGS around day 28...
April 20, 2018: Biology of Blood and Marrow Transplantation
Pengpeng Zhang, Haixia Xu, Rui Li, Wei Wu, Zhe Chao, Cencen Li, Wei Xia, Lei Wang, Jinzeng Yang, Yongjie Xu
Myoblast differentiation is a highly complex process that is regulated by proteins as well as by non-coding RNAs. Circular RNAs have been identified as an emerging new class of non-coding RNA in the modulation of skeletal muscle development, whereas their expression profiles and functional regulation in myoblast differentiation remain unknown. In the present study, we performed deep RNA-sequencing of C2C12 myoblasts during cell differentiation and uncovered 37,751 unique circular RNAs derived from 6,943 hosting genes...
April 20, 2018: International Journal of Biochemistry & Cell Biology
Ana Rachel Leda, James Hunter, Ursula Castro Oliveira, Inacio Junqueira Azevedo, Maria Cecilia Araripe Sucupira, Ricardo Sobhie Diaz
Objectives: The presence of minority transmitted drug resistance mutations was assessed using ultra-deep sequencing and correlated with disease progression among recently HIV-1-infected individuals from Brazil. Methods: Samples at baseline during recent infection and 1 year after the establishment of the infection were analysed. Viral RNA and proviral DNA from 25 individuals were subjected to ultra-deep sequencing of the reverse transcriptase and protease regions of HIV-1...
April 19, 2018: Journal of Antimicrobial Chemotherapy
Chen Peng, Ying Ding, Xin Yi, Zhiqiang Dong, Limei Cao, Qiang Li, Haiyan Ren, Lin He, Daizhan Zhou, Xu Chen
Aims Ischemic stroke (IS) is one of the most common diseases of neurology and the main cause of death and disability in Chinese population. CACNA1C was considered to be involved in the process of atherosclerosis, but there was little information about the association between genotypic polymorphisms of CACNA1C and ischemic stroke. Our study was designed to elucidate the relationship between four single-nucleotide polymorphisms (SNPs) variants in CACNA1C gene and the risk of large-artery atherosclerotic (LAA) stroke patients...
April 23, 2018: Neurological Research
Charissa Kim, Ruli Gao, Emi Sei, Rachel Brandt, Johan Hartman, Thomas Hatschek, Nicola Crosetto, Theodoros Foukakis, Nicholas E Navin
Triple-negative breast cancer (TNBC) is an aggressive subtype that frequently develops resistance to chemotherapy. An unresolved question is whether resistance is caused by the selection of rare pre-existing clones or alternatively through the acquisition of new genomic aberrations. To investigate this question, we applied single-cell DNA and RNA sequencing in addition to bulk exome sequencing to profile longitudinal samples from 20 TNBC patients during neoadjuvant chemotherapy (NAC). Deep-exome sequencing identified 10 patients in which NAC led to clonal extinction and 10 patients in which clones persisted after treatment...
April 13, 2018: Cell
Masaya Kibe, Satoshi Ibara, Hidehito Inagaki, Takema Kato, Hiroki Kurahashi, Toshiro Ikeda
Bohring-Opitz syndrome (BOS) is a rare disease with a number of characteristic features, including hypertelorism, prominent metopic suture, exophthalmos, cleft palate, abnormal posture, and developmental retardation. Here, we report a BOS patient presenting with lethal persistent pulmonary hypertension of the newborn (PPHN) and inspiratory respiratory failure. The female infant was treated with nitric oxide and vasodilator, which did not improve her condition. The inspiratory respiratory failure required management with deep sedation...
May 2018: American Journal of Medical Genetics. Part A
Abramowicz Anna, Gos Monika
Precise pre-mRNA splicing, essential for appropriate protein translation, depends on the presence of consensus "cis" sequences that define exon-intron boundaries and regulatory sequences recognized by splicing machinery. Point mutations at these consensus sequences can cause improper exon and intron recognition and may result in the formation of an aberrant transcript of the mutated gene. The splicing mutation may occur in both introns and exons and disrupt existing splice sites or splicing regulatory sequences (intronic and exonic splicing silencers and enhancers), create new ones, or activate the cryptic ones...
April 21, 2018: Journal of Applied Genetics
Carolina Torres, Melina Elizabeth Barrios, Robertina Viviana Cammarata, Matías Victoria, Xavier Fernandez-Cassi, Silvia Bofill-Mas, Rodney Colina, María Dolores Blanco Fernández, Viviana Andrea Mbayed
New human polyomaviruses have been described in the last years, including the Merkel-cell polyomavirus (MCPyV; Human polyomavirus 5) and the Human polyomavirus 6 (HPyV6). Although their infection is usually asymptomatic, in immunocompromised host can cause life-threatening pathologies, such as the Merkel cell carcinoma, an aggressive skin neoplasia associated to the MCPyV. Despite being prevalent viruses in population, epidemiological data from South America are scarce, as well as the characterization of the viral types circulating and their origin...
April 19, 2018: Molecular Phylogenetics and Evolution
Jian Wu, Thomas R Mazur, Su Ruan, Chunfeng Lian, Nalini Daniel, Hilary Lashmett, Laura Ochoa, Imran Zoberi, Mark A Anastasio, H Michael Gach, Sasa Mutic, Maria Thomas, Hua Li
Heart motion tracking for radiation therapy treatment planning can result in effective motion management strategies to minimize radiation-induced cardiotoxicity. However, automatic heart motion tracking is challenging due to factors that include the complex spatial relationship between the heart and its neighboring structures, dynamic changes in heart shape, and limited image contrast, resolution, and volume coverage. In this study, we developed and evaluated a deep generative shape model-driven level set method to address these challenges...
April 6, 2018: Medical Image Analysis
Noemi M Fernandes, Vinicius F Vizzoni, Bárbara do N Borges, Carlos A G Soares, Inácio D da Silva-Neto, Thiago da S Paiva
The odontostomatids are among the least studied ciliates, possibly due to their small sizes, restriction to anaerobic environments and difficulty in culturing. Consequently, their phylogenetic affinities to other ciliate taxa are still poorly understood. In the present study, we analyzed newly obtained ribosomal gene sequences of the odontostomatids Discomorphella pedroeneasi and Saprodinium dentatum, together with sequences from the literature, including Epalxella antiquorum and a large assemblage of ciliate sequences representing the major recognized classes...
April 18, 2018: Molecular Phylogenetics and Evolution
Wen Zhong, Zonghong Li, Maoge Zhou, Tao Xu, You Wang
DEAD-box helicase 1 (DDX1) is a multifunction protein involved in diverse cellular processes including transcription, viral replication, mRNA/miRNA processing, and tRNA splicing. Here, we report a novel function of DDX1 in mRNA alternative splicing in pancreatic β cells. By performing integrated data analysis of high-throughput RNA sequencing (RNA-Seq), and cross-linking and immunoprecipitation coupled with deep sequencing (CLIP-Seq), we identify hundreds of alternative splicing genes that are targeted by DDX1...
April 18, 2018: Biochemical and Biophysical Research Communications
Jingxue Wang, Huali Cao, John Z H Zhang, Yifei Qi
Computational protein design has a wide variety of applications. Despite its remarkable success, designing a protein for a given structure and function is still a challenging task. On the other hand, the number of solved protein structures is rapidly increasing while the number of unique protein folds has reached a steady number, suggesting more structural information is being accumulated on each fold. Deep learning neural network is a powerful method to learn such big data set and has shown superior performance in many machine learning fields...
April 20, 2018: Scientific Reports
Jeremiah D Heredia, Jihye Park, Riley J Brubaker, Steven K Szymanski, Kevin S Gill, Erik Procko
Chemokine receptors CXCR4 and CCR5 regulate WBC trafficking and are engaged by the HIV-1 envelope glycoprotein gp120 during infection. We combine a selection of human CXCR4 and CCR5 libraries comprising nearly all of ∼7000 single amino acid substitutions with deep sequencing to define sequence-activity landscapes for surface expression and ligand interactions. After consideration of sequence constraints for surface expression, known interaction sites with HIV-1-blocking Abs were appropriately identified as conserved residues following library sorting for Ab binding, validating the use of deep mutational scanning to map functional interaction sites in G protein-coupled receptors...
April 20, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
Aouda Khalfa, Senia Mellouk, Kheira Marouf-Khelifa, Amine Khelifa
Dolomite was treated at 800 °C (D800), characterized, and used in the adsorptive removal of catechol (1,2-dihydroxybenzene) from aqueous solutions. The performances of the D800 sample, named dolomitic solid, were compared with those of the raw material. A bibliographic review shows that the data on the adsorption of phenolic compounds by dolomites are non-existent. Kinetic data, equilibrium isotherms, thermodynamic parameters, and pH influence were reported. Special attention was paid to the spectroscopic study, before and after adsorption...
April 2018: Water Science and Technology: a Journal of the International Association on Water Pollution Research
Evgeniya N Solovyeva, Evgeniy N Dunayev, Roman A Nazarov, Mehdi Radjabizadeh, Nikolay A Poyarkov, Jr
The morphological and genetic variation of a wide-ranging Secret Toad-headed agama, Phrynocephalus mystaceus that inhabits sand deserts of south-eastern Europe, Middle East, Middle Asia, and western China is reviewed. Based on the morphological differences and high divergence in COI (mtDNA) gene sequences a new subspecies of Ph. mystaceus is described from Khorasan Razavi Province in Iran. Partial sequences of COI mtDNA gene of 31 specimens of Ph. mystaceus from 17 localities from all major parts of species range were analyzed...
2018: ZooKeys
Bastiaan W Haak, Eric R Littmann, Jean-Luc Chaubard, Amanda J Pickard, Emily Fontana, Fatima Adhi, Yangtsho Gyaltshen, Lilan Ling, Sejal M Morjaria, Jonathan U Peled, Marcel R van den Brink, Alexander I Geyer, Justin R Cross, Eric G Pamer, Ying Taur
Respiratory viral infections are frequent in patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HCT), and can potentially progress to lower respiratory tract infection (LRTI). The intestinal microbiota contributes to resistance against viral and bacterial pathogens in the lung. However, whether intestinal microbiota composition and associated changes in microbe-derived metabolites contribute to the risk of LRTI following upper respiratory tract viral infection remains unexplored in the setting of allo-HCT...
April 19, 2018: Blood
Shiomi Yoshida, Tsubasa Araki, Tomohito Asai, Kazunari Tsuyuguchi, Kentaro Arikawa, Tomotada Iwamoto, Chie Nakajima, Yasuhiko Suzuki, Kenji Ohya, Tokuma Yanai, Takayuki Wada, Taro Yamamoto
Mycobacterium avium subspecies hominissuis (MAH) is an important cause of infection in human pulmonary and swine intestinal cases. Although MAH is isolated from environmental sources frequently, infections of other animals have rarely been analysed. Recently, we detected granulomatous inflammation in bovine lung as an abnormal postmortem inspection case. To ascertain its genetic profile, we conducted a variable numbers of tandem repeats (VNTR) analysis and genomic characterization using deep sequencing. The VNTR type was a unique profile that differed from reported genotypes, but it was assigned within a broad genotypic complex of isolates from human patients and bathrooms...
April 16, 2018: Infection, Genetics and Evolution
Alexander J Probst, Jillian F Banfield
DPANN archaea are primarily known based on genomes from metagenomes and single cells. We reconstructed a complete population genome for Candidatus "Forterrea," a Diapherotrite with a predicted symbiotic lifestyle probably centered around nucleotide metabolism and RuBisCO. Genome-wide analysis of sequence variation provided insights into the processes that shape its population structure in the deep subsurface. The genome contains many transposons, yet reconstruction of a complete genome from a short-read insert data set was possible because most occurred only in some individuals...
April 1, 2018: Genome Biology and Evolution
Edgar Liberis, Petar Velickovic, Pietro Sormanni, Michele Vendruscolo, Pietro Liò
Motivation: Antibodies play essential roles in the immune system of vertebrates and are powerful tools in research and diagnostics. While hypervariable regions of antibodies, which are responsible for binding, can be readily identified from their amino acid sequence, it remains challenging to accurately pinpoint which amino acids will be in contact with the antigen (the paratope). Results: In this work, we present a sequence-based probabilistic machine learning algorithm for paratope prediction, named Parapred...
April 16, 2018: Bioinformatics
He Zhao, Li-Jun Duan, Qing-Ling Sun, Yu-Shan Gao, Yong-Dong Yang, Xiang-Sheng Tang, Ding-Yan Zhao, Yang Xiong, Zhen-Guo Hu, Chuan-Hong Li, Si-Xue Chen, Tao Liu, Xing Yu
BACKGROUND: Peripheral nerve injury (PNI) has devastating consequences. Dorsal root ganglion as a pivotal locus participates in the process of neuropathic pain and nerve regeneration. In recent years, gene sequencing technology has seen rapid rise in the biomedicine field. So, we attempt to gain insight into in the mechanism of neuropathic pain and nerve regeneration in the transcriptional level and to explore novel genes through bioinformatics analysis. METHODS: The gene expression profiles of GSE96051 were downloaded from GEO database...
April 19, 2018: Journal of Investigative Surgery: the Official Journal of the Academy of Surgical Research
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