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https://www.readbyqxmd.com/read/28724921/saliva-and-tooth-biofilm-bacterial-microbiota-in-adolescents-in-a-low-caries-community
#1
Linda Eriksson, Pernilla Lif Holgerson, Ingegerd Johansson
The oral cavity harbours a complex microbiome that is linked to dental diseases and serves as a route to other parts of the body. Here, the aims were to characterize the oral microbiota by deep sequencing in a low-caries population with regular dental care since childhood and search for association with caries prevalence and incidence. Saliva and tooth biofilm from 17-year-olds and mock bacteria communities were analysed using 16S rDNA Illumina MiSeq (v3-v4) and PacBio SMRT (v1-v8) sequencing including validity and reliability estimates...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28701704/concatseq-a-method-for-increasing-throughput-of-single-molecule-sequencing-by-concatenating-short-dna-fragments
#2
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
#3
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
#4
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/28682810/spectral-temporal-modulated-ripple-discrimination-by-children-with-cochlear-implants
#5
David M Landsberger, Monica Padilla, Amy S Martinez, Laurie S Eisenberg
OBJECTIVES: A postlingually implanted adult typically develops hearing with an intact auditory system, followed by periods of deafness (or near deafness) and adaptation to the implant. For an early implanted child whose brain is highly plastic, the auditory system matures with consistent input from a cochlear implant. It is likely that the auditory system of early implanted cochlear implant users is fundamentally different than postlingually implanted adults. The purpose of this study is to compare the basic psychophysical capabilities and limitations of these two populations on a spectral resolution task to determine potential effects of early deprivation and plasticity...
July 4, 2017: Ear and Hearing
https://www.readbyqxmd.com/read/28679546/untangling-heteroplasmy-structure-and-evolution-of-an-atypical-mitochondrial-genome-by-pacbio-sequencing
#6
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/28645579/anti-androgenic-mechanisms-of-bisphenol-a-involve-androgen-receptor-signaling-pathway
#7
Hui Wang, Zhen Ding, Qiao-Mei Shi, Xing Ge, Heng-Xue Wang, Meng-Xue Li, Gang Chen, Qi Wang, Qiang Ju, Jin-Peng Zhang, Mei-Rong Zhang, Li-Chun Xu
We have shown Bisphenol A (BPA) acts as an androgen receptor (AR) antagonist in the previous study. However, the mechanisms underlying anti-androgenic effects of BPA remain unclear. The objective of this study was to explore whether the AR signaling was involved in AR antagonism of BPA. The Cell Counting Kit-8 (CCK-8) assay and Real-Time Cell Analysis (RTCA) iCELLigence system were applied to analyze the mouse Sertoli cell TM4 proliferation. The mammalian two-hybrid assays were performed to investigate the effects of BPA on the AR amino- and carboxyl-terminal regions (N/C) interaction and the interactions of the AR with steroid receptor coactivator-1 (SRC-1), co-repressors including silencing mediator for thyroid hormone receptors (SMRT) and nuclear receptor co-repressor (NCoR)...
June 20, 2017: Toxicology
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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...
August 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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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