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https://www.readbyqxmd.com/read/28640830/optimal-sequencing-strategies-for-identifying-disease-associated-singletons
#1
Sara Rashkin, Goo Jun, Sai Chen, Goncalo R Abecasis
With the increasing focus of genetic association on the identification of trait-associated rare variants through sequencing, it is important to identify the most cost-effective sequencing strategies for these studies. Deep sequencing will accurately detect and genotype the most rare variants per individual, but may limit sample size. Low pass sequencing will miss some variants in each individual but has been shown to provide a cost-effective alternative for studies of common variants. Here, we investigate the impact of sequencing depth on studies of rare variants, focusing on singletons-the variants that are sampled in a single individual and are hardest to detect at low sequencing depths...
June 22, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28636991/non-invasive-detection-of-somatic-mutations-using-next-generation-sequencing-in-primary-central-nervous-system-lymphoma
#2
Maxime Fontanilles, Florent Marguet, Élodie Bohers, Pierre-Julien Viailly, Sydney Dubois, Philippe Bertrand, Vincent Camus, Sylvain Mareschal, Philippe Ruminy, Catherine Maingonnat, Stéphane Lepretre, Elena-Liana Veresezan, Stéphane Derrey, Hervé Tilly, Jean-Michel Picquenot, Annie Laquerrière, Fabrice Jardin
PURPOSE: Primary central nervous system lymphomas (PCNSL) have recurrent genomic alterations. The main objective of our study was to demonstrate that targeted sequencing of circulating cell-free DNA (cfDNA) released by PCNSL at the time of diagnosis could identify somatic mutations by next-generation sequencing (NGS). PATIENTS AND METHODS: PlasmacfDNA and matched tumor DNA (tDNA) from 25 PCNSL patients were sequenced using an Ion Torrent Personal Genome Machine (Life Technologies®)...
June 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636653/the-ebola-virus-vp35-protein-binds-viral-immunostimulatory-and-host-rnas-identified-through-deep-sequencing
#3
Kari A Dilley, Alexander A Voorhies, Priya Luthra, Vinita Puri, Timothy B Stockwell, Hernan Lorenzi, Christopher F Basler, Reed S Shabman
Ebola virus and Marburg virus are members of the Filovirdae family and causative agents of hemorrhagic fever with high fatality rates in humans. Filovirus virulence is partially attributed to the VP35 protein, a well-characterized inhibitor of the RIG-I-like receptor pathway that triggers the antiviral interferon (IFN) response. Prior work demonstrates the ability of VP35 to block potent RIG-I activators, such as Sendai virus (SeV), and this IFN-antagonist activity is directly correlated with its ability to bind RNA...
2017: PloS One
https://www.readbyqxmd.com/read/28635951/new-insights-into-the-imprinted-meg8-dmr-in-14q32-and-clinical-and-molecular-description-of-novel-patients-with-temple-syndrome
#4
Jasmin Beygo, Alma Küchler, Gabriele Gillessen-Kaesbach, Beate Albrecht, Jonas Eckle, Thomas Eggermann, Alexandra Gellhaus, Deniz Kanber, Ulrike Kordaß, Hermann-Josef Lüdecke, Sabine Purmann, Eva Rossier, Johannes van de Nes, Ilse M van der Werf, Maren Wenzel, Dagmar Wieczorek, Bernhard Horsthemke, Karin Buiting
The chromosomal region 14q32 contains several imprinted genes, which are expressed either from the paternal (DLK1 and RTL1) or the maternal (MEG3, RTL1as and MEG8) allele only. Imprinted expression of these genes is regulated by two differentially methylated regions (DMRs), the germline DLK1/MEG3 intergenic (IG)-DMR (MEG3/DLK1:IG-DMR) and the somatic MEG3-DMR (MEG3:TSS-DMR), which are methylated on the paternal and unmethylated on the maternal allele. Disruption of imprinting in the 14q32 region results in two clinically distinct imprinting disorders, Temple syndrome (TS14) and Kagami-Ogata syndrome (KOS14)...
June 21, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28634789/detection-and-grading-of-prostate-cancer-using-temporal-enhanced-ultrasound-combining-deep-neural-networks-and-tissue-mimicking-simulations
#5
Shekoofeh Azizi, Sharareh Bayat, Pingkun Yan, Amir Tahmasebi, Guy Nir, Jin Tae Kwak, Sheng Xu, Storey Wilson, Kenneth A Iczkowski, M Scott Lucia, Larry Goldenberg, Septimiu E Salcudean, Peter A Pinto, Bradford Wood, Purang Abolmaesumi, Parvin Mousavi
PURPOSE  : Temporal Enhanced Ultrasound (TeUS) has been proposed as a new paradigm for tissue characterization based on a sequence of ultrasound radio frequency (RF) data. We previously used TeUS to successfully address the problem of prostate cancer detection in the fusion biopsies. METHODS  : In this paper, we use TeUS to address the problem of grading prostate cancer in a clinical study of 197 biopsy cores from 132 patients. Our method involves capturing high-level latent features of TeUS with a deep learning approach followed by distribution learning to cluster aggressive cancer in a biopsy core...
June 20, 2017: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/28630351/evolutionary-radiation-of-lanthipeptides-in-marine-cyanobacteria
#6
Andres Cubillos-Ruiz, Jessie W Berta-Thompson, Jamie W Becker, Wilfred A van der Donk, Sallie W Chisholm
Lanthipeptides are ribosomally derived peptide secondary metabolites that undergo extensive posttranslational modification. Prochlorosins are a group of lanthipeptides produced by certain strains of the ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus Unlike other lanthipeptide-producing bacteria, picocyanobacteria use an unprecedented mechanism of substrate promiscuity for the production of numerous and diverse lanthipeptides using a single lanthionine synthetase. Through a cross-scale analysis of prochlorosin biosynthesis genes-from genomes to oceanic populations-we show that marine picocyanobacteria have the collective capacity to encode thousands of different cyclic peptides, few of which would display similar ring topologies...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28630206/rapid-and-consistent-evolution-of-colistin-resistance-in-xdr-pseudomonas-aeruginosa-during-morbidostat-culture
#7
Bianca Regenbogen, Matthias Willmann, Matthias Steglich, Boyke Bunk, Ulrich Nübel, Silke Peter, Richard A Neher
Colistin is a last resort antibiotic commonly used against multidrug-resistant strains of Pseudomonas aeruginosa To investigate the potential for in-situ evolution of resistance against colistin and to map the molecular targets of colistin resistance, we exposed two P. aeruginosa isolates to colistin using a continuous culture device known as morbidostat. As a result, colistin resistance reproducibly increased 10-fold within ten days, and 100-fold within 20 days, along with highly stereotypic, yet strain specific mutation patterns...
June 19, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28630153/membrane-spanning-%C3%AE-helical-barrels-as-tractable-protein-design-targets
#8
REVIEW
Ai Niitsu, Jack W Heal, Kerstin Fauland, Andrew R Thomson, Derek N Woolfson
The rational (de novo) design of membrane-spanning proteins lags behind that for water-soluble globular proteins. This is due to gaps in our knowledge of membrane-protein structure, and experimental difficulties in studying such proteins compared to water-soluble counterparts. One limiting factor is the small number of experimentally determined three-dimensional structures for transmembrane proteins. By contrast, many tens of thousands of globular protein structures provide a rich source of 'scaffolds' for protein design, and the means to garner sequence-to-structure relationships to guide the design process...
August 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28630098/comparative-micrornaome-analysis-of-the-testis-and-ovary-of-the-chinese-giant-salamander
#9
Rui Chen, Jian Du, Lin Ma, Li-Qing Wang, Sheng-Song Xie, Chang-Ming Yang, Xian-Yong Lan, Chuan-Ying Pan, Wu-Zi Dong
MicroRNAs (miRNAs) are 18-24 nucleotides non-coding RNAs that regulate gene expression by post-transcriptional suppression of mRNA. The Chinese giant salamander (CGS, Andrias davidianus), which is an endangered species, has become one of important models of animal evolution; however, no miRNA studies on this species have been conducted. In this study, two small RNA libraries of CGS ovary and testis were constructed using deep sequencing technology. A bioinformatics pipeline was developed to distinguish miRNA sequences from other classes of small RNAs represented in the sequencing data...
June 19, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28629507/oceanisphaera-marina-sp-nov-isolated-from-a-deep-sea-seamount
#10
Jie Liu, Ya-Wen Sun, Dan-Dan Zhang, Sheng-Nan Li, De-Chao Zhang
A Gram-stain-negative, rod-shaped, strictly aerobic, motile bacterial strain, designated YM319T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain YM319T was related to the genus Oceanisphaera and had highest 16S rRNA gene sequence similarities with the type strains Oceanisphaera profunda SM1222T (97.4 %), Oceanisphaera sediminis TW92T (97.3 %) and Oceanisphaera ostreae T-w6T (97.1 %). The predominant cellular fatty acids were summed feature 3 (composed of iso-C15 : 0 2-OH and/or C16 : 1 ω7c), C16 : 0 and C18 : 1ω7c...
June 20, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28629190/biotechnological-potential-of-cold-adapted-pseudoalteromonas-spp-isolated-from-deep-sea-sponges
#11
Erik Borchert, Stephen Knobloch, Emilie Dwyer, Sinéad Flynn, Stephen A Jackson, Ragnar Jóhannsson, Viggó T Marteinsson, Fergal O'Gara, Alan D W Dobson
The marine genus Pseudoalteromonas is known for its versatile biotechnological potential with respect to the production of antimicrobials and enzymes of industrial interest. We have sequenced the genomes of three Pseudoalteromonas sp. strains isolated from different deep sea sponges on the Illumina MiSeq platform. The isolates have been screened for various industrially important enzymes and comparative genomics has been applied to investigate potential relationships between the isolates and their host organisms, while comparing them to free-living Pseudoalteromonas spp...
June 19, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28628615/flipping-chromosomes-in-deep-sea-archaea
#12
Matteo Cossu, Catherine Badel, Ryan Catchpole, Danièle Gadelle, Evelyne Marguet, Valérie Barbe, Patrick Forterre, Jacques Oberto
One of the major mechanisms driving the evolution of all organisms is genomic rearrangement. In hyperthermophilic Archaea of the order Thermococcales, large chromosomal inversions occur so frequently that even closely related genomes are difficult to align. Clearly not resulting from the native homologous recombination machinery, the causative agent of these inversions has remained elusive. We present a model in which genomic inversions are catalyzed by the integrase enzyme encoded by a family of mobile genetic elements...
June 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28628606/splicing-stimulates-sirna-formation-at-drosophila-dna-double-strand-breaks
#13
Karin Merk, Marco Breinig, Romy Böttcher, Stefan Krebs, Helmut Blum, Michael Boutros, Klaus Förstemann
DNA double-strand breaks trigger the production of locus-derived siRNAs in fruit flies, human cells and plants. At least in flies, their biogenesis depends on active transcription running towards the break. Since siRNAs derive from a double-stranded RNA precursor, a major question is how broken DNA ends can generate matching sense and antisense transcripts. We performed a genome-wide RNAi-screen in cultured Drosophila cells, which revealed that in addition to DNA repair factors, many spliceosome components are required for efficient siRNA generation...
June 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28627609/microrna-149-contributes-to-scarless-wound-healing-by-attenuating-inflammatory-response
#14
Hongxin Lang, Feng Zhao, Tao Zhang, Xiaoyu Liu, Zhe Wang, Rui Wang, Ping Shi, Xining Pang
A fibrotic or pathological scar is an undesired consequence of skin wound healing and may trigger a series of problems. An attenuated inflammatory response is a significant characteristic of fetal skin wound healing, which can contribute to the scarless healing of fetal skin. According to deep sequencing data, microRNA‑149 (miR‑149) expression was increased in mid-gestational compared with that in late‑gestational fetal skin keratinocytes. It was demonstrated that overexpression of miR‑149 in HaCaT cells can downregulate the expression of pro‑inflammatory cytokines interleukin (IL)‑1α, IL‑1β, and IL‑6 at basal levels and in inflammatory conditions...
June 15, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28626218/molecular-characterization-of-ezh2-mutant-patients-with-myelodysplastic-myeloproliferative-neoplasms
#15
J Rinke, J P Müller, M F Blaess, A Chase, M Meggendorfer, V Schäfer, N Winkelmann, C Haferlach, N C P Cross, A Hochhaus, T Ernst
Mutations in the epigenetic regulator gene EZH2 are frequently observed in patients with myelodysplastic/myeloproliferative neoplasms (MDS/MPN; 10-13%) and are associated with a poor outcome. To gain more insight into EZH2 pathology we sought to genetically characterize a cohort of 41 EZH2-mutated MDS/MPN patients using targeted deep next generation sequencing (NGS), colony forming progenitor assays and transcriptome analysis. Stable shRNA-mediated downregulation of EZH2 was performed in MDS derived F-36P, MOLM-13 and OCI-M2 cells to study EZH2 specific changes...
June 19, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28626163/lower-serum-levels-of-mir-29c-3p-and-mir-19b-3p-as-biomarkers-for-alzheimer-s-disease
#16
Yuquan Wu, Juan Xu, Jing Xu, Jun Cheng, Demin Jiao, Chun Zhou, Yi Dai, Qingyong Chen
MicroRNAs (miRNAs) are short noncoding RNA that participate in posttranscriptional gene regulation. However, little is understood about the roles of miRNAs in Alzheimer's disease (AD). In this study, we used next-generation sequencing on RNA extracted from the serum samples of 20 AD patients and 20 controls, yielding a total of 72 miRNAs with significantly changed expression levels. Among these candidates, we selected 9 miRNAs with most significant alteration in disease, and validated their expression levels using RT-qPCR analysis on serum samples from 45 AD patients and 40 control subjects...
2017: Tohoku Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28623886/epsilon-cp-using-deep-learning-to-combine-information-from-multiple-sources-for-protein-contact-prediction
#17
Kolja Stahl, Michael Schneider, Oliver Brock
BACKGROUND: Accurately predicted contacts allow to compute the 3D structure of a protein. Since the solution space of native residue-residue contact pairs is very large, it is necessary to leverage information to identify relevant regions of the solution space, i.e. correct contacts. Every additional source of information can contribute to narrowing down candidate regions. Therefore, recent methods combined evolutionary and sequence-based information as well as evolutionary and physicochemical information...
June 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28623734/ig-seq-deep-sequencing-of-the-variable-region-of-atlantic-salmon-igm-heavy-chain-transcripts
#18
Aleksei Krasnov, Sven Martin Jørgensen, Sergey Afanasyev
Immunoglobulin M plays a key role in systemic protection of Atlantic salmon against pathogens. Until recent, studies have focused on antigen-specific antibodies and little is known about the IgM repertoire: its size, developmental changes and responses to antigens. We report the development of deep sequencing protocol to characterize the repertoire of IgM heavy chain variable region. Its structure and changes were examined at the early stages of life and after infection with virus of cardiac myopathy. Clonotypes are identified by the V and J gene segments and amino acid sequences of CDR3, which determine the contribution of the heavy chain to the antigen binding properties...
June 14, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28623417/a-validated-clinical-mri-injury-scoring-system-in-neonatal-hypoxic-ischemic-encephalopathy
#19
Shamik B Trivedi, Zachary A Vesoulis, Rakesh Rao, Steve M Liao, Joshua S Shimony, Robert C McKinstry, Amit M Mathur
BACKGROUND: Deep nuclear gray matter injury in neonatal hypoxic-ischemic encephalopathy (HIE) is associated with worse neurodevelopmental outcomes. We previously published a qualitative MRI injury scoring system utilizing serial T1-weighted, T2-weighted and diffusion-weighted imaging (DWI), weighted for deep nuclear gray matter injury. OBJECTIVES: To establish the validity of the MRI scoring system with neurodevelopmental outcome at 18-24 months. MATERIALS AND METHODS: MRI scans from neonates with moderate to severe HIE treated with therapeutic hypothermia were evaluated...
June 16, 2017: Pediatric Radiology
https://www.readbyqxmd.com/read/28623315/avalanche-of-entanglement-and-correlations-at-quantum-phase-transitions
#20
Konstantin V Krutitsky, Andreas Osterloh, Ralf Schützhold
We study the ground-state entanglement in the quantum Ising model with nearest neighbor ferromagnetic coupling J and find a sequential increase of entanglement depth d with growing J. This entanglement avalanche starts with two-point entanglement, as measured by the concurrence, and continues via the three-tangle and four-tangle, until finally, deep in the ferromagnetic phase for J = ∞, arriving at a pure L-partite (GHZ type) entanglement of all L spins. Comparison with the two, three, and four-point correlations reveals a similar sequence and shows strong ties to the above entanglement measures for small J...
June 16, 2017: Scientific Reports
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