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SMRT sequencing

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https://www.readbyqxmd.com/read/29046457/hiv-1-infection-of-primary-cd4-t-cells-regulates-the-expression-of-specific-herv-k-hml-2-elements
#1
George R Young, Sandra N Terry, Lara Manganaro, Alvaro Cuesta-Dominguez, Gintaras Deikus, Dabeiba Bernal-Rubio, Laura Campisi, Ana Fernandez-Sesma, Robert Sebra, Viviana Simon, Lubbertus C F Mulder
Endogenous retroviruses (ERVs) occupy extensive regions of the human genome. Although many of these retroviral elements have lost their ability to replicate, those whose insertion took place more recently, such as the HML-2 group of HERV-K elements, still retain intact open reading frames and the capacity to produce certain viral RNA and/or proteins. Transcription of these ERVs is, however, tightly regulated by dedicated epigenetic control mechanisms. Nonetheless, it has been reported that some pathologic states, such as viral infections and certain cancers, coincide with ERV expression suggesting transcriptional reawakening is possible...
October 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29036602/n6-adenine-dna-methylation-is-associated-with-the-linker-dna-of-h2a-z-containing-well-positioned-nucleosomes-in-pol-ii-transcribed-genes-in-tetrahymena
#2
Yuanyuan Wang, Xiao Chen, Yalan Sheng, Yifan Liu, Shan Gao
DNA N6-methyladenine (6mA) is newly rediscovered as a potential epigenetic mark across a more diverse range of eukaryotes than previously realized. As a unicellular model organism, Tetrahymena thermophila is among the first eukaryotes reported to contain 6mA modification. However, lack of comprehensive information about 6mA distribution hinders further investigations into its function and regulatory mechanism. In this study, we provide the first genome-wide, base pair-resolution map of 6mA in Tetrahymena by applying single-molecule real-time (SMRT) sequencing...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036429/genome-re-annotation-of-the-wild-strawberry-fragaria-vesca-using-extensive-illumina-and-smrt-based-rna-seq-datasets
#3
Yongping Li, Wei Wei, Jia Feng, Huifeng Luo, Mengting Pi, Zhongchi Liu, Chunying Kang
The genome of the wild diploid strawberry species Fragaria vesca, an ideal model system of cultivated strawberry (Fragaria × ananassa, octoploid) and other Rosaceae family crops, was first published in 2011 and followed by a new assembly (Fvb). However, the annotation for Fvb mainly relied on ab initio predictions and included only predicted coding sequences, therefore an improved annotation is highly desirable. Here, a new annotation version named v2.0.a2 was created for the Fvb genome by a pipeline utilizing one PacBio library, 90 Illumina RNA-seq libraries, and 9 small RNA-seq libraries...
September 23, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29019980/radically-truncated-mecp2-rescues-rett-syndrome-like-neurological-defects
#4
Rebekah Tillotson, Jim Selfridge, Martha V Koerner, Kamal K E Gadalla, Jacky Guy, Dina De Sousa, Ralph D Hector, Stuart R Cobb, Adrian Bird
Heterozygous mutations in the X-linked MECP2 gene cause the neurological disorder Rett syndrome. The methyl-CpG-binding protein 2 (MeCP2) protein is an epigenetic reader whose binding to chromatin primarily depends on 5-methylcytosine. Functionally, MeCP2 has been implicated in several cellular processes on the basis of its reported interaction with more than 40 binding partners, including transcriptional co-repressors (for example, the NCoR/SMRT complex), transcriptional activators, RNA, chromatin remodellers, microRNA-processing proteins and splicing factors...
October 11, 2017: Nature
https://www.readbyqxmd.com/read/29018412/a-novel-lactobacilli-based-teat-disinfectant-for-improving-bacterial-communities-in-the-milks-of-cow-teats-with-subclinical-mastitis
#5
Jie Yu, Yan Ren, XiaoXia Xi, Weiqiang Huang, Heping Zhang
Teat disinfection pre- and post-milking is important for the overall health and hygiene of dairy cows. The objective of this study was to evaluate the efficacy of a novel probiotic lactobacilli-based teat disinfectant based on changes in somatic cell count (SCC) and profiling of the bacterial community. A total of 69 raw milk samples were obtained from eleven Holstein-Friesian dairy cows over 12 days of teat dipping in China. Single molecule, real-time sequencing technology (SMRT) was employed to profile changes in the bacterial community during the cleaning protocol and to compare the efficacy of probiotic lactic acid bacteria (LAB) and commercial teat disinfectants...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29017889/complete-genome-sequence-of-acinetobacter-baumannii-a1296-st1469-with-a-small-plasmid-harboring-the-tet39-tetracycline-resistance-gene
#6
Xiaoting Hua, Chao Pan, Li Zhu, Zhicheng Liu, Qingye Xu, Hengliang Wang, Yunsong Yu
OBJECTIVES: Acinetobacter baumannii is considered an important nosocomial pathogen worldwide due to its increasing antibiotic resistance. This study aimed to determine the complete genome sequence of A. baumannii strain A1296 and comparative analysis among A. baumannii. METHODS: The complete genome sequence of A. baumannii A1296 was sequenced on two SMRT cells using P6C4 chemistry on a Pacific Biosciences Single Molecule, Real-Time RS II instrument. The A1296 genome sequence was annotated via NCBI, and its MLST and resistance genes were analyzed...
October 7, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28986786/dna-methylation-profiling-using-long-read-single-molecule-real-time-bisulfite-sequencing-smrt-bs
#7
Yao Yang, Stuart A Scott
For the past two decades, bisulfite sequencing has been a widely used method for quantitative CpG methylation detection of genomic DNA. Coupled with PCR amplicon cloning, bisulfite Sanger sequencing allows for allele-specific CpG methylation assessment; however, its time-consuming protocol and inability to multiplex has recently been overcome by next-generation bisulfite sequencing techniques. Although high-throughput sequencing platforms have enabled greater accuracy in CpG methylation quantitation as a result of increased bisulfite sequencing depth, most common sequencing platforms generate reads that are similar in length to the typical bisulfite PCR size range (~300-500 bp)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28982984/draft-genome-sequences-of-two-uncultured-armatimonadetes-associated-with-a-microcystis-sp-cyanobacteria-isolate
#8
Jason N Woodhouse, A Katharina Makower, Hans-Peter Grossart, Elke Dittmann
Two genome sequences of the phylum Armatimonadetes, derived from terrestrial environments, have been previously described. Here, two additional Armatimonadetes genome sequences were obtained via single-molecule real-time (SMRT) sequencing of an enrichment culture of the bloom-forming cyanobacterium Microcystis sp. isolated from a eutrophic lake (Brandenburg, Germany). The genomes are most closely affiliated with the class Fimbriimonadales, although they are smaller than the 5.6-Mbp type strain genome.
October 5, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28981454/hybrid-sequencing-of-full-length-cdna-transcripts-of-stems-and-leaves-in-dendrobium-officinale
#9
Liu He, Shuhua Fu, Zhichao Xu, Jun Yan, Jiang Xu, Hong Zhou, Jianguo Zhou, Xinlian Chen, Ying Li, Kin Fai Au, Hui Yao
Dendrobium officinale is an extremely valuable orchid used in traditional Chinese medicine, so sought after that it has a higher market value than gold. Although the expression profiles of some genes involved in the polysaccharide synthesis have previously been investigated, little research has been carried out on their alternatively spliced isoforms in D. officinale. In addition, information regarding the translocation of sugars from leaves to stems in D. officinale also remains limited. We analyzed the polysaccharide content of D...
October 5, 2017: Genes
https://www.readbyqxmd.com/read/28961789/remilo-reference-assisted-misassembly-detection-algorithm-using-short-and-long-reads
#10
Ergude Bao, Changjin Song, Lingxiao Lan
Motivation: Contigs assembled from the second generation sequencing short reads may contain misassemblies, and thus complicate downstream analysis or even lead to incorrect analysis results. Fortunately, with more and more sequenced species available, it becomes possible to use the reference genome of a closely related species to detect misassemblies. In addition, long reads of the third generation sequencing technology have been more and more widely used, and can also help detect misassemblies...
August 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28935727/complete-genome-sequences-of-lactobacillus-curvatus-kg6-l-curvatus-mrs6-and-lactobacillus-sakei-fam18311-isolated-from-fermented-meat-products
#11
Christoph Jans, Sandra Lagler, Christophe Lacroix, Leo Meile, Marc J A Stevens
The genomes of Lactobacillus curvatus KG6, L. curvatus MRS6, and Lactobacillus sakei FAM18311 were sequenced and assembled using PacBio single-molecule real-time (SMRT) technology. The strains were isolated from Swiss fermented meat products. Circular chromosomes were of 1.98 Mbp (KG6), 2.11 Mbp (MRS6), and 1.95 Mbp (FAM18311), with a G+C content of 41.3 to 42.0%.
September 21, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28934361/restriction-modification-mediated-barriers-to-exogenous-dna-uptake-and-incorporation-employed-by-prevotella-intermedia
#12
Christopher D Johnston, Chelsey A Skeete, Alexey Fomenkov, Richard J Roberts, Susan R Rittling
Prevotella intermedia, a major periodontal pathogen, is increasingly implicated in human respiratory tract and cystic fibrosis lung infections. Nevertheless, the specific mechanisms employed by this pathogen remain only partially characterized and poorly understood, largely due to its total lack of genetic accessibility. Here, using Single Molecule, Real-Time (SMRT) genome and methylome sequencing, bisulfite sequencing, in addition to cloning and restriction analysis, we define the specific genetic barriers to exogenous DNA present in two of the most widespread laboratory strains, P...
2017: PloS One
https://www.readbyqxmd.com/read/28929458/backbone-resonance-assignment-of-the-bcl6-btb-poz-domain
#13
Li-Ying Lin, S E Evans, L Fairall, John W R Schwabe, Simon D Wagner, Frederick W Muskett
BCL6 is a transcriptional repressor. Two domains of the protein, the N-terminal BTB-POZ domain and the RD2 domain are responsible for recruitment of co-repressor molecules and histone deacetylases. The BTB-POZ domain is found in a large and diverse range of proteins that play important roles in development, homeostasis and neoplasia. Crystal structures of several BTB-POZ domains, including BCL6 have been determined. The BTB-POZ domain of BCL6 not only mediates dimerisation but is also responsible for recruitment of co-repressors such as SMRT, NCOR and BCOR...
September 19, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28922869/genome-organization-of-sphingobium-indicum-b90a-an-archetypal-hexachlorocyclohexane-hch-degrading-genotype
#14
Helianthous Verma, Abhay Bajaj, Roshan Kumar, Jasvinder Kaur, Shailly Anand, Namita Nayyar, Akshita Puri, Yogendra Singh, Jitendra P Khurana, Rup Lal
Among sphingomonads, Sphingobium indicum B90A is widely investigated for its ability to degrade a manmade pesticide, γ-hexachlorocyclohexane (γ-HCH) and its isomers (α-, β-, δ-, and ε-HCH). In this study, complete genome of strain B90A was constructed using Single Molecule Real Time Sequencing (SMRT) and Illumina platform. The complete genome revealed that strain B90A harbors four replicons: one chromosome (3,654,322 bp) and three plasmids designated as pSRL1 (139,218 bp), pSRL2 (108,430 bp) and pSRL3 (43,761 bp)...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28921562/a-novel-approach-using-long-read-sequencing-and-ddpcr-to-investigate-gonadal-mosaicism-and-estimate-recurrence-risk-in-two-families-with-developmental-disorders
#15
Maria Wilbe, Sanna Gudmundsson, Josefin Johansson, Adam Ameur, Eva-Lena Stattin, Göran Annerén, Helena Malmgren, Carina Frykholm, Marie-Louise Bondeson
OBJECTIVE: De novo mutations contribute significantly to severe early-onset genetic disorders. Even if the mutation is apparently de novo there is a recurrence risk due to parental germ line mosaicism, depending on the gonadal generation the mutation occurred. METHODS: We demonstrate the power of using SMRT sequencing and ddPCR to determine parental origin and allele frequencies of de novo mutations in germ cells in two families whom had undergone assisted reproduction...
September 16, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/28910288/genomics-enabled-analysis-of-the-emergent-disease-cotton-bacterial-blight
#16
Anne Z Phillips, Jeffrey C Berry, Mark C Wilson, Anupama Vijayaraghavan, Jillian Burke, J Imani Bunn, Tom W Allen, Terry Wheeler, Rebecca S Bart
Cotton bacterial blight (CBB), an important disease of (Gossypium hirsutum) in the early 20th century, had been controlled by resistant germplasm for over half a century. Recently, CBB re-emerged as an agronomic problem in the United States. Here, we report analysis of cotton variety planting statistics that indicate a steady increase in the percentage of susceptible cotton varieties grown each year since 2009. Phylogenetic analysis revealed that strains from the current outbreak cluster with race 18 Xanthomonas citri pv...
September 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28899344/bacteriophages-are-the-major-drivers-of-shigella-flexneri-serotype-1c-genome-plasticity-a-complete-genome-analysis
#17
Pawan Parajuli, Marcin Adamski, Naresh K Verma
BACKGROUND: Shigella flexneri is the primary cause of bacillary dysentery in the developing countries. S. flexneri serotype 1c is a novel serotype, which is found to be endemic in many developing countries, but little is known about its genomic architecture and virulence signatures. We have sequenced for the first time, the complete genome of S. flexneri serotype 1c strain Y394, to provide insights into its diversity and evolution. RESULTS: We generated a high-quality reference genome of S...
September 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28893775/a-nosocomial-outbreak-of-extensively-drug-resistant-xdr-acinetobacter-baumannii-isolates-containing-blaoxa-237-encoded-on-a-plasmid
#18
Andrea M Hujer, Paul G Higgins, Susan D Rudin, Genevieve L Buser, Steven H Marshall, Kyriaki Xanthopoulou, Harald Seifert, Laura J Rojas, T Nicholas Domitrovic, P Maureen Cassidy, Margaret C Cunningham, Robert Vega, Jon P Furuno, Christopher D Pfeiffer, Zintars G Beldavs, Meredith S Wright, Michael R Jacobs, Mark D Adams, Robert A Bonomo
Carbapenem antibiotics are among the mainstay for treating infections caused by Acinetobacter baumannii, especially in the Northwest United States where carbapenem resistant A. baumannii remain relatively rare. However, between June 2012 and October 2014, an outbreak of carbapenem-resistant A. baumannii occurred in 16 patients from 5 healthcare facilities in the state of Oregon. All isolates were defined as extensively-drug resistant (XDR). MLST revealed that the isolates belonged to sequence type 2 (international clone 2, IC2), and were greater than 95% similar by rep-PCR analysis...
September 11, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28892102/length-independent-dna-packing-into-nanopore-zero-mode-waveguides-for-low-input-dna-sequencing
#19
Joseph Larkin, Robert Y Henley, Vivek Jadhav, Jonas Korlach, Meni Wanunu
Compared with conventional methods, single-molecule real-time (SMRT) DNA sequencing exhibits longer read lengths than conventional methods, less GC bias, and the ability to read DNA base modifications. However, reading DNA sequence from sub-nanogram quantities is impractical owing to inefficient delivery of DNA molecules into the confines of zero-mode waveguides-zeptolitre optical cavities in which DNA sequencing proceeds. Here, we show that the efficiency of voltage-induced DNA loading into waveguides equipped with nanopores at their floors is five orders of magnitude greater than existing methods...
September 11, 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/28890930/parkinson-s-disease-associated-with-pure-atxn10-repeat-expansion
#20
Birgitt Schüle, Karen N McFarland, Kelsey Lee, Yu-Chih Tsai, Khanh-Dung Nguyen, Chao Sun, Mei Liu, Christie Byrne, Ramesh Gopi, Neng Huang, J William Langston, Tyson Clark, Francisco Javier Jiménez Gil, Tetsudo Ashizawa
Large, non-coding pentanucleotide repeat expansions of ATTCT in intron 9 of the ATXN10 gene typically cause progressive spinocerebellar ataxia with or without seizures and present neuropathologically with Purkinje cell loss resulting in symmetrical cerebellar atrophy. These ATXN10 repeat expansions can be interrupted by sequence motifs which have been attributed to seizures and are likely to act as genetic modifiers. We identified a Mexican kindred with multiple affected family members with ATXN10 expansions...
2017: NPJ Parkinson's Disease
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