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https://www.readbyqxmd.com/read/28430818/comparative-genomics-of-burkholderia-multivorans-a-ubiquitous-pathogen-with-a-highly-conserved-genomic-structure
#1
Charlotte Peeters, Vaughn S Cooper, Philip J Hatcher, Bart Verheyde, Aurélien Carlier, Peter Vandamme
The natural environment serves as a reservoir of opportunistic pathogens. A well-established method for studying the epidemiology of such opportunists is multilocus sequence typing, which in many cases has defined strains predisposed to causing infection. Burkholderia multivorans is an important pathogen in people with cystic fibrosis (CF) and its epidemiology suggests that strains are acquired from non-human sources such as the natural environment. This raises the central question of whether the isolation source (CF or environment) or the multilocus sequence type (ST) of B...
2017: PloS One
https://www.readbyqxmd.com/read/28424528/elucidation-of-quantitative-structural-diversity-of-remarkable-rearrangement-regions-shufflons-in-inci2-plasmids
#2
Tsuyoshi Sekizuka, Michiko Kawanishi, Mamoru Ohnishi, Ayaka Shima, Kengo Kato, Akifumi Yamashita, Mari Matsui, Satowa Suzuki, Makoto Kuroda
A multiple DNA inversion system, the shufflon, exists in incompatibility (Inc) I1 and I2 plasmids. The shufflon generates variants of the PilV protein, a minor component of the thin pilus. The shufflon is one of the most difficult regions for de novo genome assembly because of its structural diversity even in an isolated bacterial clone. We determined complete genome sequences, including those of IncI2 plasmids carrying mcr-1, of three Escherichia coli strains using single-molecule, real-time (SMRT) sequencing and Illumina sequencing...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28415976/smrt-genome-assembly-corrects-reference-errors-resolving-the-genetic-basis-of-virulence-in-mycobacterium-tuberculosis
#3
Afif Elghraoui, Samuel J Modlin, Faramarz Valafar
BACKGROUND: The genetic basis of virulence in Mycobacterium tuberculosis has been investigated through genome comparisons of virulent (H37Rv) and attenuated (H37Ra) sister strains. Such analysis, however, relies heavily on the accuracy of the sequences. While the H37Rv reference genome has had several corrections to date, that of H37Ra is unmodified since its original publication. RESULTS: Here, we report the assembly and finishing of the H37Ra genome from single-molecule, real-time (SMRT) sequencing...
April 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28400415/recombination-dependent-replication-and-gene-conversion-homogenize-repeat-sequences-and-diversify-plastid-genome-structure
#4
Tracey A Ruhlman, Jin Zhang, John C Blazier, Jamal S M Sabir, Robert K Jansen
PREMISE OF THE STUDY: There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements...
April 11, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28396297/the-co-regulators-src-1-and-smrt-are-involved-in-interleukin-6-induced-androgen-receptor-activation
#5
Qi Wang, Hui Wang, Qiang Ju, Zhen Ding, Xing Ge, Qiao-Mei Shi, Ji-Long Zhou, Xiao-Long Zhou, Jin-Peng Zhang, Mei-Rong Zhang, Hong-Min Yu, Li-Chun Xu
BACKGROUND: The androgen receptor (AR) can be stimulated by interleukin-6 (IL-6) in the absence of androgens to induce prostate cancer progression. The purpose of this study was to investigate whether the co-activator steroid receptor coactivator-1 (SRC-1) and co-repressor silencing mediator for retinoid and thyroid hormone receptors (SMRT) are involved in IL-6-induced AR activation. METHODS: The effects of IL-6 on LNCaP cell proliferation were monitored using real-time cell analysis (RTCA) iCELLigence system...
November 1, 2016: European Cytokine Network
https://www.readbyqxmd.com/read/28388540/transcriptional-regulation-of-mixed-lineage-kinase-3-by-estrogen-and-its-implication-in-er-positive-breast-cancer-pathogenesis
#6
Navin Viswakarma, Rakesh Sathish Nair, Gautam Sondarva, Subhasis Das, Lucas Ibrahimi, Zhiyong Chen, Subhash Sinha, Basabi Rana, Ajay Rana
Mixed Lineage Kinase 3 (MLK3), also called as MAP3K11 is a tightly regulated MAP3K member but its cellular function is still not fully understood. Earlier we reported post-translational regulation of MLK3 by estrogen (E2) that inhibited the kinase activity and favored survival of ER+ breast cancer cells. Here we report that MLK3 is also transcriptionally downregulated by E2 in ER+ breast cancer cells. Publicly available data and in situ hybridization of human breast tumors showed significant down regulation of MLK3 transcripts in ER+ tumors...
March 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28381259/halc-high-throughput-algorithm-for-long-read-error-correction
#7
Ergude Bao, Lingxiao Lan
BACKGROUND: The third generation PacBio SMRT long reads can effectively address the read length issue of the second generation sequencing technology, but contain approximately 15% sequencing errors. Several error correction algorithms have been designed to efficiently reduce the error rate to 1%, but they discard large amounts of uncorrected bases and thus lead to low throughput. This loss of bases could limit the completeness of downstream assemblies and the accuracy of analysis. RESULTS: Here, we introduce HALC, a high throughput algorithm for long read error correction...
April 5, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28369806/identification-of-microbial-profile-of-koji-using-single-molecule-real-time-sequencing-technology
#8
Wenyan Hui, Qiangchuan Hou, Chenxia Cao, Haiyan Xu, Yi Zhen, Lai-Yu Kwok, Tiansong Sun, Heping Zhang, Wenyi Zhang
Koji is a kind of Japanese traditional fermented starter that has been used for centuries. Many fermented foods are made from koji, such as sake, miso, and soy sauce. This study used the single molecule real-time sequencing technology (SMRT) to investigate the bacterial and fungal microbiota of 3 Japanese koji samples. After SMRT analysis, a total of 39121 high-quality sequences were generated, including 14354 bacterial and 24767 fungal sequence reads. The high-quality gene sequences were assigned to 5 bacterial and 2 fungal plyla, dominated by Proteobacteria and Ascomycota, respectively...
March 29, 2017: Journal of Food Science
https://www.readbyqxmd.com/read/28364362/advantages-of-genome-sequencing-by-long-read-sequencer-using-smrt-technology-in-medical-area
#9
REVIEW
Kazuma Nakano, Akino Shiroma, Makiko Shimoji, Hinako Tamotsu, Noriko Ashimine, Shun Ohki, Misuzu Shinzato, Maiko Minami, Tetsuhiro Nakanishi, Kuniko Teruya, Kazuhito Satou, Takashi Hirano
PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions...
March 31, 2017: Human Cell
https://www.readbyqxmd.com/read/28361880/genomic-structure-of-the-horse-major-histocompatibility-complex-class-ii-region-resolved-using-pacbio-long-read-sequencing-technology
#10
Agnese Viļuma, Sofia Mikko, Daniela Hahn, Loren Skow, Göran Andersson, Tomas F Bergström
The mammalian Major Histocompatibility Complex (MHC) region contains several gene families characterized by highly polymorphic loci with extensive nucleotide diversity, copy number variation of paralogous genes, and long repetitive sequences. This structural complexity has made it difficult to construct a reliable reference sequence of the horse MHC region. In this study, we used long-read single molecule, real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio) to sequence eight Bacterial Artificial Chromosome (BAC) clones spanning the horse MHC class II region...
March 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28348836/evolution-of-a-zoonotic-pathogen-investigating-prophage-diversity-in-enterohaemorrhagic-escherichia-coli-o157-by-long-read-sequencing
#11
Sharif Shaaban, Lauren A Cowley, Sean P McAteer, Claire Jenkins, Timothy J Dallman, James L Bono, David L Gally
Enterohaemorrhagic Escherichia coli (EHEC) O157 is a zoonotic pathogen for which colonization of cattle and virulence in humans is associated with multiple horizontally acquired genes, the majority present in active or cryptic prophages. Our understanding of the evolution and phylogeny of EHEC O157 continues to develop primarily based on core genome analyses; however, such short-read sequences have limited value for the analysis of prophage content and its chromosomal location. In this study, we applied Single Molecule Real Time (SMRT) sequencing, using the Pacific Biosciences long-read sequencing platform, to isolates selected from the main sub-clusters of this clonal group...
December 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28348241/structure-of-the-mecp2-tblr1-complex-reveals-a-molecular-basis-for-rett-syndrome-and-related-disorders
#12
Valdeko Kruusvee, Matthew J Lyst, Ceitidh Taylor, Žygimantė Tarnauskaitė, Adrian P Bird, Atlanta G Cook
Rett syndrome (RTT) is an X-linked neurological disorder caused by mutations in the methyl-CpG-binding protein 2 (MeCP2) gene. The majority of RTT missense mutations disrupt the interaction of the MeCP2 with DNA or the nuclear receptor corepressor (NCoR)/silencing mediator of retinoic acid and thyroid receptors (SMRT) corepressor complex. Here, we show that the "NCoR/SMRT interaction domain" (NID) of MeCP2 directly contacts transducin-beta like 1 (TBL1) and TBL1 related (TBLR1), two paralogs that are core components of NCoR/SMRT...
March 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28344213/over-expression-of-tbl1xr1-indicates-poor-prognosis-of-serous-epithelial-ovarian-cancer
#13
Ming Ma, Nina Yu
Transducin (β)-like 1 X-linked receptor 1 (TBL1XR1) is a core component of the NCoR/SMRT transcription co-repressor complex, and its role in regulating cancer progression has been reported. Serous epithelial ovarian cancer (EOC) is the most common histological type of EOC. Here we explored the significance of TBL1XR1 expression in predicting outcomes of patients with serous EOC. Real-time quantitative PCR analysis showed that the expression level of TBL1XR1 mRNA was significantly higher in EOC tissues compared with adjacent non-tumorous tissues...
2017: Tohoku Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28336599/complete-genome-sequence-and-methylome-analysis-of-acinetobacter-calcoaceticus-65
#14
Alexey Fomenkov, Tamas Vincze, Sergey K Degtyarev, Richard J Roberts
Acinetobacter calcoaceticus 65 is the original source strain for the restriction enzyme Acc65I. Its complete sequence and full methylome were determined using single-molecule real-time (SMRT) sequencing.
March 23, 2017: Genome Announcements
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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