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https://www.readbyqxmd.com/read/29150517/multi-omics-reveal-the-lifestyle-of-the-acidophilic-mineral-oxidizing-model-species-leptospirillum-ferriphilum-t
#1
Stephan Christel, Malte Herold, Sören Bellenberg, Mohamed El Hajjami, Antoine Buetti-Dinh, Igor V Pivkin, Wolfgang Sand, Paul Wilmes, Ansgar Poetsch, Mark Dopson
Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of this model species' type strain is available, limiting the possibilities to investigate the strategies and adaptations Leptospirillum ferriphilum(T) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum(T) DSM 14647 obtained by PacBio SMRT long read sequencing for use as a high quality reference...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29136191/genome-sequence-of-the-small-brown-planthopper-laodelphax-striatellus
#2
Junjie Zhu, Feng Jiang, Xianhui Wang, Pengcheng Yang, Yanyuan Bao, Wan Zhao, Wei Wang, Hong Lu, Qianshuo Wang, Na Cui, Jing Li, Xiaofang Chen, Lan Luo, Jinting Yu, Le Kang, Feng Cui
Background: Laodelphax striatellus Fallén (Hemiptera: Delphacidae) is one of the most destructive rice pests. L. striatellus is different from two other rice planthoppers with a released genome sequence, Sogatella furcifera and Nilaparvata lugens, in many biological characteristics, such as host range, dispersal capacity, and vectoring plant viruses. Deciphering the genome of L. striatellus will help to understand the genetic basis of the biological differences among the three rice planthoppers...
November 10, 2017: GigaScience
https://www.readbyqxmd.com/read/29134592/identification-of-dna-base-modifications-by-means-of-pacific-biosciences-rs-sequencing-technology
#3
Philip Kelleher, James Murphy, Jennifer Mahony, Douwe van Sinderen
Whole phage genomes can be sequenced readily using one or a combination of next generation sequencing (NGS) technologies. One of the most recently developed NGS platforms, the so-called Single-Molecule Real-Time (SMRT) sequencing approach provided by the PacBio RS platform, is particularly useful in providing complete (i.e., un-gapped) genome sequences, but differs from other technologies in that the platform also allows for downstream analysis to identify nucleotides that have been modified by DNA methylation...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29126180/replong-de-novo-repeat-identification-using-long-read-sequencing-data
#4
Rui Guo, Yan-Ran Li, Shan He, Le Ou-Yang, Yiwen Sun, Zexuan Zhu
Motivation: The identification of repetitive elements is important in genome assembly and phylogenetic analyses. The existing de novo repeat identification methods exploiting the use of short reads are impotent in identifying long repeats. Since long reads are more likely to cover repeat regions completely, using long reads is more favorable for recognizing long repeats. Summary: In this study, we propose a novel de novo repeat elements identification method namely RepLong based on PacBio long reads...
November 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29116525/metasecretome-phage-display
#5
Milica Ciric, Filomena Ng, Jasna Rakonjac, Dragana Gagic
Metasecretome is a collection of cell-surface and secreted proteins that mediate interactions between microbial communities and their environment. These include adhesins, enzymes, surface structures such as pili or flagella, vaccine targets or proteins responsible for immune evasion. Traditional approaches to exploring matasecretome of complex microbial communities via cultivation of microorganisms and screening of individual strains fail to sample extraordinary diversity in these communities, since only a limited fraction of microorganisms are represented by cultures...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29114024/mechanisms-of-surface-antigenic-variation-in-the-human-pathogenic-fungus-pneumocystis-jirovecii
#6
Emanuel Schmid-Siegert, Sophie Richard, Amanda Luraschi, Konrad Mühlethaler, Marco Pagni, Philippe M Hauser
Microbial pathogens commonly escape the human immune system by varying surface proteins. We investigated the mechanisms used for that purpose by Pneumocystis jirovecii This uncultivable fungus is an obligate pulmonary pathogen that in immunocompromised individuals causes pneumonia, a major life-threatening infection. Long-read PacBio sequencing was used to assemble a core of subtelomeres of a single P. jirovecii strain from a bronchoalveolar lavage fluid specimen from a single patient. A total of 113 genes encoding surface proteins were identified, including 28 pseudogenes...
November 7, 2017: MBio
https://www.readbyqxmd.com/read/29112696/comprehensive-evaluation-of-non-hybrid-genome-assembly-tools-for-third-generation-pacbio-long-read-sequence-data
#7
Vasanthan Jayakumar, Yasubumi Sakakibara
Long reads obtained from third-generation sequencing platforms can help overcome the long-standing challenge of the de novo assembly of sequences for the genomic analysis of non-model eukaryotic organisms. Numerous long-read-aided de novo assemblies have been published recently, which exhibited superior quality of the assembled genomes in comparison with those achieved using earlier second-generation sequencing technologies. Evaluating assemblies is important in guiding the appropriate choice for specific research needs...
November 3, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29109705/complete-genome-sequence-of-vibrio-campbellii-lmb-29-isolated-from-red-drum-with-four-native-megaplasmids
#8
Jinxin Liu, Zhe Zhao, Yiqing Deng, Yan Shi, Yupeng Liu, Chao Wu, Peng Luo, Chaoqun Hu
Vibrio spp. are the most common pathogens for animals reared in aquaculture. Vibrio campbellii, which is often involved in shrimp, fish and mollusks diseases, is widely distributed in the marine environment worldwide, but our knowledge about its pathogenesis and antimicrobial resistance is very limited. The existence of this knowledge gap is at least partially because that V. campbellii was originally classified as Vibrio harveyi, and the detailed information of its comparative genome analysis to other Vibrio spp...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29105221/analysis-of-recombinational-switching-at-the-antigenic-variation-locus-of-the-lyme-spirochete-using-a-novel-pacbio-sequencing-pipeline
#9
Theodore B Verhey, Mildred Castellanos, George Chaconas
The Lyme disease spirochete evades the host immune system by combinatorial variation of VlsE, a surface antigen. Antigenic variation occurs via segmental gene conversion from contiguous silent cassettes into the vlsE locus. Because of the high degree of similarity between switch variants and the size of vlsE, short-read NGS technologies have been unsuitable for sequencing vlsE populations. Here we use PacBio sequencing technology coupled with the first fully-automated software pipeline (VAST) to accurately process NGS data by minimizing error frequency, eliminating heteroduplex errors and accurately aligning switch variants...
November 4, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/29103683/complete-genetic-analysis-of-a-salmonella-enterica-serovar-indiana-isolate-accompanying-four-plasmids-carrying-mcr-1-esbl-and-other-resistance-genes-in-china
#10
Juan Wang, Xianglei Li, Juan Li, Daniel Hurley, Xue Bai, Zhongyi Yu, Yu Cao, Ellen Wall, Séamus Fanning, Li Bai
One mcr-1-carrying Salmonella enterica serovar Indiana strain D90, was identified from 1320 Salmonella enterica isolates from poultry slaughterhouse in 2012 in China. The objective of this study was to verify the transferability of the mcr-1 gene and also completely characterize the sequence of the strain at the whole-genome level. Broth matting assays were carried out to detect the transferability and whole-genome sequencing (WGS) of S. enterica serovar Indiana D90 was performed using the PacBio RS II system...
October 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/29101320/dense-and-accurate-whole-chromosome-haplotyping-of-individual-genomes
#11
David Porubsky, Shilpa Garg, Ashley D Sanders, Jan O Korbel, Victor Guryev, Peter M Lansdorp, Tobias Marschall
The diploid nature of the human genome is neglected in many analyses done today, where a genome is perceived as a set of unphased variants with respect to a reference genome. This lack of haplotype-level analyses can be explained by a lack of methods that can produce dense and accurate chromosome-length haplotypes at reasonable costs. Here we introduce an integrative phasing strategy that combines global, but sparse haplotypes obtained from strand-specific single-cell sequencing (Strand-seq) with dense, yet local, haplotype information available through long-read or linked-read sequencing...
November 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/29092025/simulating-the-dynamics-of-targeted-capture-sequencing-with-capsim
#12
Minh Duc Cao, Devika Ganesamoorthy, Chenxi Zhou, Lachlan J M Coin
Motivation: Targeted sequencing using capture probes has become increasingly popular in clinical applications due to its scalability and cost-effectiveness. The approach also allows for higher sequencing coverage of the targeted regions resulting in better analysis statistical power. However, because of the dynamics of the hybridisation process, it is difficult to evaluate the efficiency of the probe design prior to the experiments which are time consuming and costly. Results: We developed CapSim, a software package for simulation of targeted sequencing...
October 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29091201/is26-mediated-formation-of-a-virulence-and-resistance-plasmid-in-salmonella-enteritidis
#13
Marcus Ho-Yin Wong, Edward Wai-Chi Chan, Sheng Chen
Objectives: To characterize a novel virulence-resistance plasmid pSE380T carried by a Salmonella enterica serotype Enteritidis clinical strain SE380. Methods: The plasmid pSE380T was conjugated to Escherichia coli strain J53 and sequenced by PacBio RSII, followed by subsequent annotation and genetic analysis. Results: Sequence analysis of this plasmid revealed that the entire Salmonella Enteritidis-specific virulence plasmid, pSEN, had been incorporated into an IncHI2 MDR plasmid, which comprises the cephalosporin and fosfomycin resistance determinants blaCTX-M-14 and fosA3...
October 1, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29091199/monitoring-microevolution-of-oxa-48-producing-klebsiella-pneumoniae-st147-in-a-hospital-setting-by-smrt-sequencing
#14
Andreas E Zautner, Boyke Bunk, Yvonne Pfeifer, Cathrin Spröer, Utz Reichard, Helmut Eiffert, Simone Scheithauer, Uwe Groß, Jörg Overmann, Wolfgang Bohne
Objectives: Carbapenemase-producing Klebsiella pneumoniae pose an increasing risk for healthcare facilities worldwide. A continuous monitoring of ST distribution and its association with resistance and virulence genes is required for early detection of successful K. pneumoniae lineages. In this study, we used WGS to characterize MDR blaOXA-48-positive K. pneumoniae isolated from inpatients at the University Medical Center Göttingen, Germany, between March 2013 and August 2014. Methods: Closed genomes for 16 isolates of carbapenemase-producing K...
October 1, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29078745/single-virion-sequencing-of-lamivudine-treated-hbv-populations-reveal-population-evolution-dynamics-and-demographic-history
#15
Yuan O Zhu, Pauline P K Aw, Paola Florez de Sessions, Shuzhen Hong, Lee Xian See, Lewis Z Hong, Andreas Wilm, Chen Hao Li, Stephane Hue, Seng Gee Lim, Niranjan Nagarajan, William F Burkholder, Martin Hibberd
BACKGROUND: Viral populations are complex, dynamic, and fast evolving. The evolution of groups of closely related viruses in a competitive environment is termed quasispecies. To fully understand the role that quasispecies play in viral evolution, characterizing the trajectories of viral genotypes in an evolving population is the key. In particular, long-range haplotype information for thousands of individual viruses is critical; yet generating this information is non-trivial. Popular deep sequencing methods generate relatively short reads that do not preserve linkage information, while third generation sequencing methods have higher error rates that make detection of low frequency mutations a bioinformatics challenge...
October 27, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29077841/filling-reference-gaps-via-assembling-dna-barcodes-using-high-throughput-sequencing-moving-toward-barcoding-the-world
#16
Shanlin Liu, Chentao Yang, Chengran Zhou, Xin Zhou
Over the past decade, biodiversity researchers have dedicated tremendous efforts in constructing DNA reference barcodes for rapid species registration and identification. Although analytical cost for standard DNA barcoding has been significantly reduced since early 2000, further dramatic reduction in barcoding costs is unlikely because the Sanger sequencing is approaching its limits in throughput and chemistry cost. Constraints in barcoding cost not only led to unbalanced barcoding efforts around the globe, but also refrained High-Throughput-Sequencing (HTS) based taxonomic identification from applying binomial species names, which provide crucial linkages to biological knowledge...
October 25, 2017: GigaScience
https://www.readbyqxmd.com/read/29074666/genome-sequence-of-the-lager-brewing-yeast-saccharomyces-sp-strain-m14-used-in-the-high-gravity-brewing-industry-in-china
#17
Chunfeng Liu, Qi Li, Chengtuo Niu, Feiyun Zheng, Yongxian Li, Yun Zhao, Xiangsheng Yin
Lager-brewing yeasts are mainly used for the production of lager beers. Illumina and PacBio-based sequence analyses revealed an approximate genome size of 22.8 Mb, with a GC content of 38.98%, for the Chinese lager-brewing yeast Saccharomyces sp. strain M14. Based on ab initio prediction, 9,970 coding genes were annotated.
October 26, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29069314/evaluation-of-tools-for-long-read-rna-seq-splice-aware-alignment
#18
Krešimir Križanovic, Amina Echchiki, Julien Roux, Mile Šikic
Motivation: High-throughput sequencing has transformed the study of gene expression levels through RNA-seq, a technique that is now routinely used by various fields, such as genetic research or diagnostics. The advent of third generation sequencing technologies providing significantly longer reads opens up new possibilities. However, the high error rates common to these technologies set new bioinformatics challenges for the gapped alignment of reads to their genomic origin. In this study, we have explored how currently available RNA-seq splice-aware alignment tools cope with increased read lengths and error rates...
October 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29068285/pectobacterium-polaris-sp-nov-isolated-from-potato-solanum-tuberosum
#19
Merete Wiken Dees, Erik Lysøe, Simeon Rossmann, Juliana Perminow, May Bente Brurberg
The genus Pectobacterium, which belongs to the bacterial family Enterobacteriaceae, contains numerous species that cause soft rot diseases in a wide range of plants. The species Pectobacterium carotovorum is highly heterogeneous, indicating a need for re-evaluation and a better classification of the species. PacBio was used for sequencing of two soft-rot-causing bacterial strains (NIBIO1006(T) and NIBIO1392), initially identified as P. carotovorumstrains by fatty acid analysis and sequencing of three housekeeping genes (dnaX, icdA and mdh)...
October 25, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29067005/characterization-of-four-multidrug-resistance-plasmids-captured-from-the-sediments-of-an-urban-coastal-wetland
#20
Ryan T Botts, Brooke A Apffel, C J Walters, Kelly E Davidson, Ryan S Echols, Michael R Geiger, Victoria L Guzman, Victoria S Haase, Michal A Montana, Chip A La Chat, Jenna A Mielke, Kelly L Mullen, Cierra C Virtue, Celeste J Brown, Eva M Top, David E Cummings
Self-transmissible and mobilizable plasmids contribute to the emergence and spread of multidrug-resistant bacteria by enabling the horizontal transfer of acquired antibiotic resistance. The objective of this study was to capture and characterize self-transmissible and mobilizable resistance plasmids from a coastal wetland impacted by urban stormwater runoff and human wastewater during the rainy season. Four plasmids were captured, two self-transmissible and two mobilizable, using both mating and enrichment approaches...
2017: Frontiers in Microbiology
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