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https://www.readbyqxmd.com/read/28701704/concatseq-a-method-for-increasing-throughput-of-single-molecule-sequencing-by-concatenating-short-dna-fragments
#1
Ulrich Schlecht, Janine Mok, Carolina Dallett, Jan Berka
Single molecule sequencing (SMS) platforms enable base sequences to be read directly from individual strands of DNA in real-time. Though capable of long read lengths, SMS platforms currently suffer from low throughput compared to competing short-read sequencing technologies. Here, we present a novel strategy for sequencing library preparation, dubbed ConcatSeq, which increases the throughput of SMS platforms by generating long concatenated templates from pools of short DNA molecules. We demonstrate adaptation of this technique to two target enrichment workflows, commonly used for oncology applications, and feasibility using PacBio single molecule real-time (SMRT) technology...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28701143/smrt-gate-a-method-for-validation-of-synthetic-constructs-on-pacific-biosciences-sequencing-platforms
#2
Rosalinda D'Amore, James Johnson, Sam Haldenby, Neil Hall, Margaret Hughes, Ryan Joynson, John G Kenny, Nicola Patron, Christiane Hertz-Fowler, Anthony Hall
Current DNA assembly methods are prone to sequence errors, requiring rigorous quality control (QC) to identify incorrect assemblies or synthesized constructs. Such errors can lead to misinterpretation of phenotypes. Because of this intrinsic problem, routine QC analysis is generally performed on three or more clones using a combination of restriction endonuclease assays, colony PCR, and Sanger sequencing. However, as new automation methods emerge that enable high-throughput assembly, QC using these techniques has become a major bottleneck...
July 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28687524/pierpont-syndrome-associated-with-the-p-tyr446cys-missense-mutation-in-tbl1xr1
#3
Anne Slavotinek, Heather Pua, Ugur Hodoglugil, Jude Abadie, Joseph Shieh, Jessica Van Ziffle, Mark Kvale, Hane Lee, Pui-Yan Kwok, Neil Risch, Marta Sabbadini
We present a 7-year old male with severe delays, hypotonia and dysmorphic features who had striking, deep palmar and plantar creases and pillowing of the soft tissues of the palms and soles. His facial features included a high anterior hairline, small eyes with narrowed palpebral fissures, a bulbous nasal tip with a short columella, and a large mouth with a thin upper vermilion, and small chin. He had a submucous cleft palate, bilateral cryptorchidism and hydronephrosis. Cranial imaging demonstrated an Arnold Chiari malformation that was also present in his maternal uncle by report...
July 4, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28679546/untangling-heteroplasmy-structure-and-evolution-of-an-atypical-mitochondrial-genome-by-pacbio-sequencing
#4
Jean Peccoud, Mohamed Amine Chebbi, Alexandre Cormier, Bouziane Moumen, Clément Gilbert, Isabelle Marcadé, Christopher Chandler, Richard Cordaux
The highly compact mitochondrial genome of terrestrial isopods (Oniscidae) presents two unusual features. First, several loci can individually encode two tRNAs, thanks to single-nucleotide polymorphisms at anticodon sites. Within-individual variation (heteroplasmy) at these loci is thought to have been maintained for millions of years because individuals that do not carry all tRNA genes die, resulting in strong balancing selection. Second, the oniscid mtDNA genome comes in two conformations: a ~14kb linear monomer and a ~28kb circular dimer comprising two monomer units fused in palindrome...
July 5, 2017: Genetics
https://www.readbyqxmd.com/read/28633514/metagenomic-smrt-sequencing-based-exploration-of-novel-lignocellulose-degrading-capability-in-wood-detritus-from-torreya-nucifera-in-bija-forest-on-jeju-island
#5
Han Na Oh, Tae Kwon Lee, Jae Wan Park, Jee Hyun No, Dockyu Kim, Woo Jun Sul
Lignocellulose, mostly composed of cellulose, hemicellulose and lignin generated through secondary growth of woody plant, is considered as promising resources for bio-fuel. In order to use lignocellulose as a biofuel, the biodegradation besides high-cost chemical treatments were applied, but its knowledge on decomposition of lignocellulose occurring in a natural environment were insufficient. We analyzed 16S rRNA gene and metagenome to understand how the lignocellulose are decomposed naturally in decayed Torreya nucifera (L) of Bija forest (Bijarim) in Gotjawal, an ecologically distinct environment...
June 21, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28620408/quality-control-of-the-traditional-patent-medicine-yimu-wan-based-on-smrt-sequencing-and-dna-barcoding
#6
Jing Jia, Zhichao Xu, Tianyi Xin, Linchun Shi, Jingyuan Song
Substandard traditional patent medicines may lead to global safety-related issues. Protecting consumers from the health risks associated with the integrity and authenticity of herbal preparations is of great concern. Of particular concern is quality control for traditional patent medicines. Here, we establish an effective approach for verifying the biological composition of traditional patent medicines based on single-molecule real-time (SMRT) sequencing and DNA barcoding. Yimu Wan (YMW), a classical herbal prescription recorded in the Chinese Pharmacopoeia, was chosen to test the method...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28611492/genome-mining-and-predictive-functional-profiling-of-acidophilic-rhizobacterium-pseudomonas-fluorescens-pt14
#7
Pooja Rani, Nitish Kumar Mahato, Anukriti Sharma, Desiraju Lakshmi Narsimha Rao, Komal Kamra, Rup Lal
Pseudomonas fluorescens Pt14 is a non-pathogenic and acidophilic bacterium isolated from acidic soil (pH 4.65). Genome sequencing of strain Pt14 was performed using Single Molecule Real Time (SMRT) sequencing to get insights into unique existence of this strain in acidic environment. Complete genome sequence of this strain revealed a chromosome of 5,841,722 bp having 5354 CDSs and 88 RNAs. Phylogenomic reconstruction based on 16S rRNA gene, Average Nucleotide Identity (ANI) values and marker proteins revealed that strain Pt14 shared a common clade with P...
June 2017: Indian Journal of Microbiology
https://www.readbyqxmd.com/read/28606056/comparative-genome-and-transcriptome-analysis-reveals-distinctive-surface-characteristics-and-unique-physiological-potentials-of-pseudomonas-aeruginosa-atcc-27853
#8
Huiluo Cao, Yong Lai, Salim Bougouffa, Zeling Xu, Aixin Yan
BACKGROUND: Pseudomonas aeruginosa ATCC 27853 was isolated from a hospital blood specimen in 1971 and has been widely used as a model strain to survey antibiotics susceptibilities, biofilm development, and metabolic activities of Pseudomonas spp.. Although four draft genomes of P. aeruginosa ATCC 27853 have been sequenced, the complete genome of this strain is still lacking, hindering a comprehensive understanding of its physiology and functional genome. RESULTS: Here we sequenced and assembled the complete genome of P...
June 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28584301/high-resolution-profiling-of-coral-associated-bacterial-communities-using-full-length-16s-rrna-sequence-data-from-pacbio-smrt-sequencing-system
#9
Wirulda Pootakham, Wuttichai Mhuantong, Thippawan Yoocha, Lalita Putchim, Chutima Sonthirod, Chaiwat Naktang, Nalinee Thongtham, Sithichoke Tangphatsornruang
Coral reefs are a complex ecosystem consisting of coral animals and a vast array of associated symbionts including the dinoflagellate Symbiodinium, fungi, viruses and bacteria. Several studies have highlighted the importance of coral-associated bacteria and their fundamental roles in fitness and survival of the host animal. The scleractinian coral Porites lutea is one of the dominant reef-builders in the Indo-West Pacific. Currently, very little is known about the composition and structure of bacterial communities across P...
June 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28577213/evaluation-of-the-impact-of-ul54-gene-deletion-on-the-global-transcription-and-dna-replication-of-pseudorabies-virus
#10
Zsolt Csabai, Irma F Takács, Michael Snyder, Zsolt Boldogkői, Dóra Tombácz
Pseudorabies virus (PRV) is an animal alphaherpesvirus with a wide host range. PRV has 67 protein-coding genes and several non-coding RNA molecules, which can be classified into three temporal groups, immediate early, early and late classes. The ul54 gene of PRV and its homolog icp27 of herpes simplex virus have a multitude of functions, including the regulation of viral DNA synthesis and the control of the gene expression. Therefore, abrogation of PRV ul54 function was expected to exert a significant effect on the global transcriptome and on DNA replication...
June 2, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28572318/complete-genome-sequences-of-two-geographically-distinct-legionella-micdadei-clinical-isolates
#11
Amy J Osborne, Bethany R Jose, Jasper Perry, Zoe Smeele, Jack Aitken, Paul P Gardner, Sandy Slow
Legionella is a highly diverse genus of intracellular bacterial pathogens that cause Legionnaire's disease (LD), an often severe form of pneumonia. Two L. micdadei sp. clinical isolates, obtained from patients hospitalized with LD from geographically distinct areas, were sequenced using PacBio SMRT cell technology, identifying incomplete phage regions, which may impact virulence.
June 1, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28572312/four-complete-paenibacillus-larvae-genome-sequences
#12
Douglas W Dingman
Four complete genome sequences of genetically distinct Paenibacillus larvae strains have been determined. Pacific BioSciences single-molecule real-time (SMRT) sequencing technology was used as the sole method of sequence determination and assembly. The chromosomes exhibited a G+C content of 44.1 to 44.2% and a molecular size range of 4.29 to 4.67 Mbp.
June 1, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28569259/revealing-complete-complex-kir-haplotypes-phased-by-long-read-sequencing-technology
#13
D Roe, C Vierra-Green, C-W Pyo, K Eng, R Hall, R Kuang, S Spellman, S Ranade, D E Geraghty, M Maiers
The killer cell immunoglobulin-like receptor (KIR) region of human chromosome 19 contains up to 16 genes for natural killer (NK) cell receptors that recognize human leukocyte antigen (HLA)/peptide complexes and other ligands. The KIR proteins fulfill functional roles in infections, pregnancy, autoimmune diseases and transplantation. However, their characterization remains a constant challenge. Not only are the genes highly homologous due to their recent evolution by tandem duplications, but the region is structurally dynamic due to frequent transposon-mediated recombination...
June 1, 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28558786/lost-in-plasmids-next-generation-sequencing-and-the-complex-genome-of-the-tick-borne-pathogen-borrelia-burgdorferi
#14
G Margos, S Hepner, C Mang, D Marosevic, S E Reynolds, S Krebs, A Sing, M Derdakova, M A Reiter, V Fingerle
BACKGROUND: Borrelia (B.) burgdorferi sensu lato, including the tick-transmitted agents of human Lyme borreliosis, have particularly complex genomes, consisting of a linear main chromosome and numerous linear and circular plasmids. The number and structure of plasmids is variable even in strains within a single genospecies. Genes on these plasmids are known to play essential roles in virulence and pathogenicity as well as host and vector associations. For this reason, it is essential to explore methods for rapid and reliable characterisation of molecular level changes on plasmids...
May 30, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28547825/dual-redundant-sequencing-strategy-full-length-gene-characterisation-of-1056-novel-and-confirmatory-hla-alleles
#15
V Albrecht, C Zweiniger, V Surendranath, K Lang, G Schöfl, A Dahl, S Winkler, V Lange, I Böhme, A H Schmidt
The high-throughput department of DKMS Life Science Lab encounters novel human leukocyte antigen (HLA) alleles on a daily basis. To characterise these alleles, we have developed a system to sequence the whole gene from 5'- to 3'-UTR for the HLA loci A, B, C, DQB1 and DPB1 for submission to the European Molecular Biology Laboratory - European Nucleotide Archive (EMBL-ENA) and the IPD-IMGT/HLA Database. Our workflow is based on a dual redundant sequencing strategy. Using shotgun sequencing on an Illumina MiSeq instrument and single molecule real-time (SMRT) sequencing on a PacBio RS II instrument, we are able to achieve highly accurate HLA full-length consensus sequences...
May 25, 2017: HLA
https://www.readbyqxmd.com/read/28529883/smrt-sequencing-data-for-garcinia-mangostana-l-variety-mesta
#16
Mohd Razik Midin, Kok-Keong Loke, Maria Madon, Mohd Shukor Nordin, Hoe-Han Goh, Normah Mohd Noor
The "Queen of Fruits" mangosteen (Garcinia mangostana L.) produces commercially important fruits with desirable taste of flesh and pericarp rich in xanthones with medicinal properties. To date, only limited knowledge is available on the cytogenetics and genome sequences of a common variety of mangosteen (Abu Bakar et al., 2016 [1]). Here, we report the first single-molecule real-time (SMRT) sequencing data from whole genome sequencing of mangosteen of Mesta variety. Raw reads of the SMRT sequencing project can be obtained from SRA database with the accession numbers SRX2718652 until SRX2718659...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28528545/discovery-and-biosynthesis-of-gladiolin-a-burkholderia-gladioli-antibiotic-with-promising-activity-against-mycobacterium-tuberculosis
#17
Lijiang Song, Matthew Jenner, Joleen Masschelein, Cerith Jones, Matthew J Bull, Simon R Harris, Ruben C Hartkoorn, Anthony Vocat, Isolda Romero-Canelon, Paul Coupland, Gordon Webster, Matthew Dunn, Rebecca Weiser, Christopher Paisey, Stewart T Cole, Julian Parkhill, Eshwar Mahenthiralingam, Gregory L Challis
An antimicrobial activity screen of Burkholderia gladioli BCC0238, a clinical isolate from a cystic fibrosis patient, led to the discovery of gladiolin, a novel macrolide antibiotic with potent activity against Mycobacterium tuberculosis H37Rv. Gladiolin is structurally related to etnangien, a highly unstable antibiotic from Sorangium cellulosum that is also active against Mycobacteria. Like etnangien, gladiolin was found to inhibit RNA polymerase, a validated drug target in M. tuberculosis. However, gladiolin lacks the highly labile hexaene moiety of etnangien and was thus found to possess significantly increased chemical stability...
June 5, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28464822/a-high-quality-assembly-of-the-nile-tilapia-oreochromis-niloticus-genome-reveals-the-structure-of-two-sex-determination-regions
#18
Matthew A Conte, William J Gammerdinger, Kerry L Bartie, David J Penman, Thomas D Kocher
BACKGROUND: Tilapias are the second most farmed fishes in the world and a sustainable source of food. Like many other fish, tilapias are sexually dimorphic and sex is a commercially important trait in these fish. In this study, we developed a significantly improved assembly of the tilapia genome using the latest genome sequencing methods and show how it improves the characterization of two sex determination regions in two tilapia species. RESULTS: A homozygous clonal XX female Nile tilapia (Oreochromis niloticus) was sequenced to 44X coverage using Pacific Biosciences (PacBio) SMRT sequencing...
May 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28455781/reduction-in-fecal-microbiota-diversity-and-short-chain-fatty-acid-producers-in-methicillin-resistant-staphylococcus-aureus-infected-individuals-as-revealed-by-pacbio-single-molecule-real-time-sequencing-technology
#19
J Zhao, L Nian, L Y Kwok, T Sun, J Zhao
Methicillin-resistant Staphylococcus aureus (MRSA) may cause potentially lethal infections. Increasing evidence suggests that the gut microbiota is associated with human health. Yet, whether patients with MRSA infections carry specific signatures in their fecal microbiota composition has not been determined. Thus, this study aimed to compare the fecal microbiota profile of MRSA-positive patients (n=15) with individuals without MRSA infection (n=15) by using the PacBio single molecule, real-time (SMRT) DNA sequencing system and real-time quantitative polymerase chain reaction (qPCR)...
April 28, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/28438580/first-complete-genome-sequence-of-bacillus-glycinifermentans-b-27
#20
Kai Bernd Stadermann, Jochen Blom, Claudia Borgmeier, Natalie Sciberras, Sandra Herbold, Maike Kipker, Guido Meurer, Stella Molck, Daniel Petri, Stefan Pelzer, Jessica Schneider
The first complete genome sequence of Bacillus glycinifermentans B-27 was determined by SMRT sequencing generating a genome sequence with a total length of 4,607,442 bases. Based on this sequence 4738 protein-coding sequences were predicted and used to identify gene clusters that are related to the production of secondary metabolites such as Lichenysin, Bacillibactin and Bacitracin. This genomic potential combined with the ability of B. glycinifermentans B-27 to grown in bile containing media might contribute to a future application of this strain as probiotic in productive livestock potentially inhibiting competing and pathogenic organisms...
April 21, 2017: Journal of Biotechnology
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