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https://www.readbyqxmd.com/read/28334874/efficient-cnv-breakpoint-analysis-reveals-unexpected-structural-complexity-and-correlation-of-dosage-sensitive-genes-with-clinical-severity-in-genomic-disorders
#1
Ling Zhang, Jingmin Wang, Cheng Zhang, Dongxiao Li, Claudia M B Carvalho, Haoran Ji, Jianqiu Xiao, Ye Wu, Weichen Zhou, Hongyan Wang, Li Jin, Yang Luo, Xiru Wu, James R Lupski, Feng Zhang, Yuwu Jiang
Genomic disorders are the clinical conditions manifested by submicroscopic genomic rearrangements including copy number variants (CNVs). The CNVs can be identified by array-based comparative genomic hybridization (aCGH), the most commonly used technology for molecular diagnostics of genomic disorders. However, clinical aCGH only informs CNVs in the probe interrogated regions. Neither orientational information nor the resulting genomic rearrangement structure is provided, which is a key to uncovering mutational and pathogenic mechanisms underlying genomic disorders...
March 14, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28272530/hybrid-sequencing-and-map-finding-hysemafi-optional-strategies-for-extensively-deciphering-gene-splicing-and-expression-in-organisms-without-reference-genome
#2
Guogui Ning, Xu Cheng, Ping Luo, Fan Liang, Zhen Wang, Guoliang Yu, Xin Li, Depeng Wang, Manzhu Bao
Using second-generation sequencing (SGS) RNA-Seq strategies, extensive alterative splicing prediction is impractical and high variability of isoforms expression quantification is inevitable in organisms without true reference dataset. we report the development of a novel analysis method, termed hybrid sequencing and map finding (HySeMaFi) which combines the specific strengths of third-generation sequencing (TGS) (PacBio SMRT sequencing) and SGS (Illumina Hi-Seq/MiSeq sequencing) to effectively decipher gene splicing and to reliably estimate the isoforms abundance...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28265515/genomic-analysis-of-st88-community-acquired-methicillin-resistant-staphylococcus-aureus-in-ghana
#3
Grace Kpeli, Andrew H Buultjens, Stefano Giulieri, Evelyn Owusu-Mireku, Samuel Y Aboagye, Sarah L Baines, Torsten Seemann, Dieter Bulach, Anders Gonçalves da Silva, Ian R Monk, Benjamin P Howden, Gerd Pluschke, Dorothy Yeboah-Manu, Timothy Stinear
BACKGROUND: The emergence and evolution of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strains in Africa is poorly understood. However, one particular MRSA lineage called ST88, appears to be rapidly establishing itself as an "African" CA-MRSA clone. In this study, we employed whole genome sequencing to provide more information on the genetic background of ST88 CA-MRSA isolates from Ghana and to describe in detail ST88 CA-MRSA isolates in comparison with other MRSA lineages worldwide...
2017: PeerJ
https://www.readbyqxmd.com/read/28256586/characterization-of-the-dynamic-transcriptome-of-a-herpesvirus-with-long-read-single-molecule-real-time-sequencing
#4
Dóra Tombácz, Zsolt Balázs, Zsolt Csabai, Norbert Moldován, Attila Szűcs, Donald Sharon, Michael Snyder, Zsolt Boldogkői
Herpesvirus gene expression is co-ordinately regulated and sequentially ordered during productive infection. The viral genes can be classified into three distinct kinetic groups: immediate-early, early, and late classes. In this study, a massively parallel sequencing technique that is based on PacBio Single Molecule Real-time sequencing platform, was used for quantifying the poly(A) fraction of the lytic transcriptome of pseudorabies virus (PRV) throughout a 12-hour interval of productive infection on PK-15 cells...
March 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28223461/identification-of-a-pseudomonas-aeruginosa-pao1-dna-methyltransferase-its-targets-and-physiological-roles
#5
Sebastian Doberenz, Denitsa Eckweiler, Olga Reichert, Vanessa Jensen, Boyke Bunk, Cathrin Spröer, Adrian Kordes, Emanuela Frangipani, Khai Luong, Jonas Korlach, Stephan Heeb, Jörg Overmann, Volkhard Kaever, Susanne Häussler
DNA methylation is widespread among prokaryotes, and most DNA methylation reactions are catalyzed by adenine DNA methyltransferases, which are part of restriction-modification (R-M) systems. R-M systems are known for their role in the defense against foreign DNA; however, DNA methyltransferases also play functional roles in gene regulation. In this study, we used single-molecule real-time (SMRT) sequencing to uncover the genome-wide DNA methylation pattern in the opportunistic pathogen Pseudomonas aeruginosa PAO1...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28216103/a-clostridioides-difficile-bacteriophage-genome-encodes-functional-binary-toxin-associated-genes
#6
Thomas Riedel, Johannes Wittmann, Boyke Bunk, Isabel Schober, Cathrin Spröer, Sabine Gronow, Jörg Overmann
Pathogenic clostridia typically produce toxins as virulence factors which cause severe diseases in both humans and animals. Whereas many clostridia like e.g., Clostridium perfringens, Clostridium botulinum or Clostridium tetani were shown to contain toxin-encoding plasmids, only toxin genes located on the chromosome were detected in Clostridioides difficile so far. In this study, we determined, annotated, and analyzed the complete genome of the bacteriophage phiSemix9P1 using single-molecule real-time sequencing technology (SMRT)...
February 17, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28181326/single-molecule-rna-sequencing-uncovers-trans-splicing-and-improves-annotations-in-anopheles-stephensi
#7
X Jiang, A B Hall, J K Biedler, Z Tu
Single molecule real-time (SMRT) sequencing has recently been used to obtain full-length cDNA sequences that improve genome annotation and reveal RNA isoforms. Here, we used one such method called isoform sequencing from Pacific Biosciences (PacBio) to sequence a cDNA library from the Asian malaria mosquito Anopheles stephensi. More than 600 000 full-length cDNAs, referred to as reads of insert, were identified. Owing to the inherently high error rate of PacBio sequencing, we tested different approaches for error correction...
February 9, 2017: Insect Molecular Biology
https://www.readbyqxmd.com/read/28159629/a-quantitative-smrt-cell-sequencing-method-for-ribosomal-amplicons
#8
Bethan M Jones, Adam B Kustka
Advances in sequencing technologies continue to provide unprecedented opportunities to characterize microbial communities. For example, the Pacific Biosciences Single Molecule Real-Time (SMRT) platform has emerged as a unique approach harnessing DNA polymerase activity to sequence template molecules, enabling long reads at low costs. With the aim to simultaneously classify and enumerate in situ microbial populations, we developed a quantitative SMRT (qSMRT) approach that involves the addition of exogenous standards to quantify ribosomal amplicons derived from environmental samples...
February 1, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28152050/draft-genome-sequence-of-karnal-bunt-pathogen-tilletia-indica-of-wheat-provides-insights-into-the-pathogenic-mechanisms-of-quarantined-fungus
#9
Anil Kumar, Vishakha Pandey, Manoj Singh, Dinesh Pandey, M S Saharan, Soma S Marla
Karnal bunt disease in wheat is caused by hemibiotrophic fungus, Tilletia indica that has been placed as quarantine pest in more than 70 countries. Despite its economic importance, little knowledge about the molecular components of fungal pathogenesis is known. In this study, first time the genome sequence of T. indica has been deciphered for unraveling the effectors' functions of molecular pathogenesis of Karnal bunt disease. The T. indica genome was sequenced employing hybrid approach of PacBio Single Molecule Real Time (SMRT) and Illumina HiSEQ 2000 sequencing platforms...
2017: PloS One
https://www.readbyqxmd.com/read/28143951/single-molecule-sequencing-of-the-drosophila-serrata-genome
#10
Scott L Allen, Emily K Delaney, Artyom Kopp, Stephen F Chenoweth
Long-read sequencing technology promises to greatly enhance de novo assembly of genomes for nonmodel species. Although the error rates of long reads have been a stumbling block, sequencing at high coverage permits the self-correction of many errors. Here, we sequence and de novo assemble the genome of Drosophila serrata, a species from the montium subgroup that has been well-studied for latitudinal clines, sexual selection, and gene expression, but which lacks a reference genome. Using 11 PacBio single-molecule real-time (SMRT cells), we generated 12 Gbp of raw sequence data comprising ∼65 × whole-genome coverage...
March 10, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28138840/pacbio-for-haplotyping-in-gene-families
#11
Wei Zhang, Joachim Messing
The throughput and read length provided by Pacific Bioscience (PacBio) Single Molecule Real Time (SMRT) sequencing platform makes it feasible to construct contiguous, non-chimeric sequences. This is especially useful for genes with repetitive sequences in their gene bodies in gene families. We illustrate the use of PacBio to sequence and assemble hundreds of transcripts of gluten gene families from different cultivars of wheat using sequence from a single SMRT cell. To this end, we barcoded amplicons from different cultivars, then pooled these into one library for sequencing...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28125102/use-of-the-supported-membrane-tube-assay-system-for-real-time-analysis-of-membrane-fission-reactions
#12
Srishti Dar, Sukrut C Kamerkar, Thomas J Pucadyil
The process of membrane fission is fundamental to diverse cellular processes such as nutrient uptake, synaptic transmission and organelle biogenesis, and it involves the localized application of curvature stress to a tubular membrane intermediate, forcing it to undergo scission. Alternative techniques for creating such substrates necessitate the use of micromanipulators or sophisticated optical traps and require a high level of technical expertise. We present a facile method to generate an array of membrane tubes supported on a passivated glass coverslip, which we refer to as supported membrane tubes (SMrTs)...
February 2017: Nature Protocols
https://www.readbyqxmd.com/read/28124151/the-helicobacter-pylori-methylome-roles-in-gene-regulation-and-virulence
#13
Rebecca Gorrell, Terry Kwok
The methylome is defined as a map of DNA methylation patterns at single-base resolution. DNA methylation in bacteria was first discovered as a function of restriction-modification (R-M) systems. R-M systems in Helicobacter pylori, like those in other bacteria, are important host-specificity determinants that provide protection against foreign DNA. Moreover, the gene regulatory role of the methyltransferase (Mtase) unit of various Helicobacter pylori R-M systems is being increasingly recognized. Recent advances in the application of single-molecule real-time (SMRT) DNA sequencing to analyse DNA methylation have revealed for the first time comprehensive pictures of the genome-wide distribution of methylation sites in various strains of H...
2017: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/28078358/major-histocompatibility-complex-haplotyping-and-long-amplicon-allele-discovery-in-cynomolgus-macaques-from-chinese-breeding-facilities
#14
Julie A Karl, Michael E Graham, Roger W Wiseman, Katelyn E Heimbruch, Samantha M Gieger, Gaby G M Doxiadis, Ronald E Bontrop, David H O'Connor
Very little is currently known about the major histocompatibility complex (MHC) region of cynomolgus macaques (Macaca fascicularis; Mafa) from Chinese breeding centers. We performed comprehensive MHC class I haplotype analysis of 100 cynomolgus macaques from two different centers, with animals from different reported original geographic origins (Vietnamese, Cambodian, and Cambodian/Indonesian mixed-origin). Many of the samples were of known relation to each other (sire, dam, and progeny sets), making it possible to characterize lineage-level haplotypes in these animals...
April 2017: Immunogenetics
https://www.readbyqxmd.com/read/28077634/characterization-of-hepatitis-c-virus-hcv-envelope-diversification-from-acute-to-chronic-infection-within-a-sexually-transmitted-hcv-cluster-by-using-single-molecule-real-time-sequencing
#15
Cynthia K Y Ho, Jayna Raghwani, Sylvie Koekkoek, Richard H Liang, Jan T M Van der Meer, Marc Van Der Valk, Menno De Jong, Oliver G Pybus, Janke Schinkel, Richard Molenkamp
In contrast to other available next-generation sequencing platforms, PacBio single-molecule, real-time (SMRT) sequencing has the advantage of generating long reads albeit with a relatively higher error rate in unprocessed data. Using this platform, we longitudinally sampled and sequenced the hepatitis C virus (HCV) envelope genome region (1,680 nucleotides [nt]) from individuals belonging to a cluster of sexually transmitted cases. All five subjects were coinfected with HIV-1 and a closely related strain of HCV genotype 4d...
March 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28068902/bacterial-microbiota-of-kazakhstan-cheese-revealed-by-single-molecule-real-time-smrt-sequencing-and-its-comparison-with-belgian-kalmykian-and-italian-artisanal-cheeses
#16
Jing Li, Yi Zheng, Haiyan Xu, Xiaoxia Xi, Qiangchuan Hou, Shuzhen Feng, Laga Wuri, Yanfei Bian, Zhongjie Yu, Lai-Yu Kwok, Zhihong Sun, Tiansong Sun
BACKGROUND: In Kazakhstan, traditional artisanal cheeses have a long history and are widely consumed. The unique characteristics of local artisanal cheeses are almost completely preserved. However, their microbial communities have rarely been reported. The current study firstly generated the Single Molecule, Real-Time (SMRT) sequencing bacterial diversity profiles of 6 traditional artisanal cheese samples of Kazakhstan origin, followed by comparatively analyzed the microbiota composition between the current dataset and those from cheeses originated from Belgium, Russian Republic of Kalmykia (Kalmykia) and Italy...
January 9, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28068217/manual-curation-and-reannotation-of-the-genomes-of-clostridium-difficile-630%C3%AE-erm-and-clostridium-difficile-630
#17
Henning Dannheim, Thomas Riedel, Meina Neumann-Schaal, Boyke Bunk, Isabel Schober, Cathrin Spröer, Cynthia Maria Chibani, Sabine Gronow, Heiko Liesegang, Jörg Overmann, Dietmar Schomburg
We resequenced the genome of Clostridium difficile 630Δerm (DSM 28645), a model strain commonly used for the generation of insertion mutants. The genome sequence was obtained by a combination of single-molecule real-time (SMRT) and Illumina sequencing technology. Detailed manual curation and comparison to the previously published genomic sequence revealed sequence differences including inverted regions and the presence of plasmid pCD630. Manual curation of our previously deposited genome sequence of the parental strain 630 (DSM 27543) led to an improved genome sequence...
January 9, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28062671/targeting-hdac3-in-crebbp-mutant-lymphomas-counterstrikes-unopposed-enhancer-deacetylation-of-b-cell-signaling-and-immune-response-genes
#18
Uta E Höpken
The cellular phenotype of B-cell lymphomas arising from B cells undergoing germinal center reactions, such as follicular lymphoma and diffuse large B-cell lymphoma, is strongly shaped by mutations in chromatin-modifying genes. The work presented by Jiang and colleagues addresses how somatic mutations in CREBBP disable acetylation and cause unopposed deacetylation by BCL6/SMRT/HDAC3 complexes on enhancers of B-cell signaling and immune response genes. This opens a therapeutic avenue toward targeted inhibition of CREBBP-mutant lymphomas by HDAC inhibitors...
January 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28061749/organelle_pba-a-pipeline-for-assembling-chloroplast-and-mitochondrial-genomes-from-pacbio-dna-sequencing-data
#19
Aboozar Soorni, David Haak, David Zaitlin, Aureliano Bombarely
BACKGROUND: The development of long-read sequencing technologies, such as single-molecule real-time (SMRT) sequencing by PacBio, has produced a revolution in the sequencing of small genomes. Sequencing organelle genomes using PacBio long-read data is a cost effective, straightforward approach. Nevertheless, the availability of simple-to-use software to perform the assembly from raw reads is limited at present. RESULTS: We present Organelle-PBA, a Perl program designed specifically for the assembly of chloroplast and mitochondrial genomes...
January 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28056367/bacterial-community-structure-in-simultaneous-nitrification-denitrification-and-organic-matter-removal-process-treating-saline-mustard-tuber-wastewater-as-revealed-by-16s-rrna-sequencing
#20
Jiale Wang, Benzhou Gong, Wei Huang, Yingmu Wang, Jian Zhou
A simultaneous nitrification, denitrification and organic matter removal (SNDOR) process in sequencing batch biofilm reactor (SBBR) was established to treat saline mustard tuber wastewater (MTWW) in this study. An average COD removal efficiency of 86.48% and total nitrogen removal efficiency of 86.48% were achieved at 30gNaClL(-1) during 100days' operation. The underlying mechanisms were investigated by PacBio SMRT DNA sequencing (V1-V9) to analyze the microbial community structures and its variation from low salinity at 10gNaClL(-1) to high salinity at 30gNaClL(-1)...
March 2017: Bioresource Technology
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