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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
#1
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/28623264/structural-characterization-of-the-smrt-corepressor-interacting-with-histone-deacetylase-7
#2
Danielle C Desravines, Itziar Serna Martin, Robert Schneider, Philippe J Mas, Nataliia Aleksandrova, Malene Ringkjøbing Jensen, Martin Blackledge, Darren J Hart
The 2525 amino acid SMRT corepressor is an intrinsically disordered hub protein responsible for binding and coordinating the activities of multiple transcription factors and chromatin modifying enzymes. Here we have studied its interaction with HDAC7, a class IIa deacetylase that interacts with the corepressor complex together with the highly active class I deacetylase HDAC3. The binding site of class IIa deacetylases was previously mapped to an approximate 500 amino acid region of SMRT, with recent implication of short glycine-serine-isoleucine (GSI) containing motifs...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28620408/quality-control-of-the-traditional-patent-medicine-yimu-wan-based-on-smrt-sequencing-and-dna-barcoding
#3
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
#4
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
#5
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
#6
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/28577282/estrogen-receptor-%C3%AE-modulation-of-the-er%C3%AE-p53-loop-regulating-gene-expression-proliferation-and-apoptosis-in-breast-cancer
#7
Wenwen Lu, Benita S Katzenellenbogen
Estrogen receptor α (ERα) is a crucial transcriptional regulator in breast cancer, but estrogens mediate their effects through two estrogen receptors, ERα and ERβ, subtypes that have contrasting regulatory actions on gene expression and the survival and growth of breast cancer cells. Here, we examine the impact of ERβ on the ERα-p53 loop in breast cancer. We found that ERβ attenuates ERα-induced cell proliferation, increases apoptosis, and reverses transcriptional activation and repression by ERα. Further, ERβ physically interacts with p53, reduces ERα-p53 binding, and antagonizes ERα-p53-mediated transcriptional regulation...
June 2, 2017: Hormones & Cancer
https://www.readbyqxmd.com/read/28577213/evaluation-of-the-impact-of-ul54-gene-deletion-on-the-global-transcription-and-dna-replication-of-pseudorabies-virus
#8
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
#9
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
#10
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
#11
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
#12
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/28554803/integrated-omics-approaches-to-characterize-a-nuclear-receptor-corepressor-associated-histone-deacetylase-in-mouse-skeletal-muscle
#13
REVIEW
Yingyun Gong, Rui Cao, Guolian Ding, Sungguan Hong, Wenjun Zhou, Wenyun Lu, Manashree Damle, Bin Fang, Chuhan C Wang, Justin Qian, Natasha Lie, Cristina Lanzillotta, Joshua D Rabinowitz, Zheng Sun
Nuclear receptors regulate gene expression by differentially binding to coactivators or corepressors in a ligand-dependent manner, which further recruits a set of epigenome-modifying enzymes that remodel chromatin conformation. Histone acetylation is a major epigenomic change controlled by histone acetyltransferases (HATs) and histone deacetylases (HDACs). HDAC3 is the only HDAC that confers the enzymatic activity to the complexes nucleated by nuclear receptor corepressors NCoR and SMRT. To address the metabolic function of HDAC3, we have deleted it specifically in mouse skeletal muscles...
May 26, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28547825/dual-redundant-sequencing-strategy-full-length-gene-characterisation-of-1056-novel-and-confirmatory-hla-alleles
#14
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
#15
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
#16
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/28493531/ternary-complex-of-human-ror%C3%AE-ligand-binding-domain-inverse-agonist-and-smrt-peptide-shows-a-unique-mechanism-of-corepressor-recruitment
#17
Masato Noguchi, Akihiro Nomura, Ken Murase, Satoki Doi, Keishi Yamaguchi, Kazuyuki Hirata, Makoto Shiozaki, Shintaro Hirashima, Masayuki Kotoku, Takayuki Yamaguchi, Yoshiaki Katsuda, Ruo Steensma, Xioalin Li, Haiyan Tao, Bruno Tse, Morgan Fenn, Robert Babine, Erin Bradley, Paul Crowe, Scott Thacher, Tsuyoshi Adachi, Masafumi Kamada
Retinoid-related orphan receptor gamma (RORγ) directly controls the differentiation of Th17 cell and the production of interleukin-17, which plays an integral role in autoimmune diseases. To obtain insight into RORγ, we have determined the first crystal structure of a ternary complex containing RORγ ligand-binding domain (LBD) bound with a novel synthetic inhibitor and a repressor peptide, 22-mer peptide from silencing mediator of retinoic acid and thyroid hormone receptor (SMRT). Comparison of a binary complex of nonliganded (apo) RORγ-LBD with a nuclear receptor co-activator (NCoA-1) peptide has shown that our inhibitor displays a unique mechanism different from those caused by natural inhibitor, ursolic acid (UA)...
May 11, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28475868/glucocorticoid-receptor-megatrans-switching-mediates-the-repression-of-an-er%C3%AE-regulated-transcriptional-program
#18
Feng Yang, Qi Ma, Zhijie Liu, Wenbo Li, Yuliang Tan, Chunyu Jin, Wubin Ma, Yiren Hu, Jia Shen, Kenneth A Ohgi, Francesca Telese, Wen Liu, Michael G Rosenfeld
The molecular mechanisms underlying the opposing functions of glucocorticoid receptors (GRs) and estrogen receptor α (ERα) in breast cancer development remain poorly understood. Here we report that, in breast cancer cells, liganded GR represses a large ERα-activated transcriptional program by binding, in trans, to ERα-occupied enhancers. This abolishes effective activation of these enhancers and their cognate target genes, and it leads to the inhibition of ERα-dependent binding of components of the MegaTrans complex...
May 4, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28475176/sly-regulates-genes-involved-in-chromatin-remodeling-and-interacts-with-tbl1xr1-during-sperm-differentiation
#19
Charlotte Moretti, Maria-Elisabetta Serrentino, Côme Ialy-Radio, Marion Delessard, Tatiana A Soboleva, Frederic Tores, Marjorie Leduc, Patrick Nitschké, Joel R Drevet, David J Tremethick, Daniel Vaiman, Ayhan Kocer, Julie Cocquet
Sperm differentiation requires unique transcriptional regulation and chromatin remodeling after meiosis to ensure proper compaction and protection of the paternal genome. Abnormal sperm chromatin remodeling can induce sperm DNA damage, embryo lethality and male infertility, yet, little is known about the factors which regulate this process. Deficiency in Sly, a mouse Y chromosome-encoded gene expressed only in postmeiotic male germ cells, has been shown to result in the deregulation of hundreds of sex chromosome-encoded genes associated with multiple sperm differentiation defects and subsequent male infertility...
June 2017: Cell Death and Differentiation
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
#20
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
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