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https://www.readbyqxmd.com/read/29334293/dna-barcoding-for-species-identification-in-deep-sea-clams-mollusca-bivalvia-vesicomyidae
#1
Jun Liu, Haibin Zhang
Deep-sea clams (Bivalvia: Vesicomyidae) have been found in reduced environments over the world oceans, but taxonomy of this group remains confusing at species and supraspecific levels due to their high-morphological similarity and plasticity. In the present study, we collected mitochondrial COI sequences to evaluate the utility of DNA barcoding on identifying vesicomyid species. COI dataset identified 56 well-supported putative species/operational taxonomic units (OTUs), approximately covering half of the extant vesicomyid species...
January 15, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29331890/deep-sequence-analysis-reveals-the-ovine-rumen-as-a-reservoir-of-antibiotic-resistance-genes
#2
Thomas C A Hitch, Ben J Thomas, Jessica C A Friedersdorff, Helen Ougham, Christopher J Creevey
Antibiotic resistance is an increasingly important environmental pollutant with direct consequences for human health. Identification of environmental sources of antibiotic resistance genes (ARGs) makes it possible to follow their evolution and prevent their entry into the clinical setting. ARGs have been found in environmental sources exogenous to the original source and previous studies have shown that these genes are capable of being transferred from livestock to humans. Due to the nature of farming and the slaughter of ruminants for food, humans interact with these animals in close proximity, and for this reason it is important to consider the risks to human health...
January 11, 2018: Environmental Pollution
https://www.readbyqxmd.com/read/29330726/ultra-deep-genomic-sequencing-of-hcv-ns5a-resistance-associated-substitutions-in-hcv-hiv-coinfected-patients
#3
Enass A Abdel-Hameed, Susan D Rouster, Ceejay L Boyce, Xiang Zhang, Jacek Biesiada, Mario Medvedovic, Kenneth E Sherman
BACKGROUND AND AIMS: The prevalence of naturally occurring HCV-NS5A resistance-associated substitutions (RAS) to DAA drugs might affect the response to treatment in HCV/HIV coinfected subjects. There are limited data on the frequency of HCV-NS5A naturally occurring drug-RAS at baseline in HCV/HIV coinfected patients when ultra-deep sequencing methodologies are applied. METHODS: HCV-NS5A-RAS were evaluated among 25 subjects in each group. Patients were matched by age, gender, and hepatic fibrosis stage category to control for selection bias...
January 12, 2018: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/29330451/tracheophyte-genomes-keep-track-of-the-deep-evolution-of-the-caulimoviridae
#4
Seydina Issa Diop, Andrew D W Geering, Françoise Alfama-Depauw, Mikaël Loaec, Pierre-Yves Teycheney, Florian Maumus
Endogenous viral elements (EVEs) are viral sequences that are integrated in the nuclear genomes of their hosts and are signatures of viral infections that may have occurred millions of years ago. The study of EVEs, coined paleovirology, provides important insights into virus evolution. The Caulimoviridae is the most common group of EVEs in plants, although their presence has often been overlooked in plant genome studies. We have refined methods for the identification of caulimovirid EVEs and interrogated the genomes of a broad diversity of plant taxa, from algae to advanced flowering plants...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29329546/whole-genome-sequencing-of-genotype-vi-newcastle-disease-viruses-from-formalin-fixed-paraffin-embedded-tissues-from-wild-pigeons-reveals-continuous-evolution-and-previously-unrecognized-genetic-diversity-in-the-u-s
#5
Ying He, Tonya L Taylor, Kiril M Dimitrov, Salman L Butt, James B Stanton, Iryna V Goraichuk, Heather Fenton, Rebecca Poulson, Jian Zhang, Corrie C Brown, Hon S Ip, Marcos Isidoro-Ayza, Claudio L Afonso
BACKGROUND: Newcastle disease viruses (NDV) are highly contagious and cause disease in both wild birds and poultry. A pigeon-adapted variant of genotype VI NDV, often termed pigeon paramyxovirus 1, is commonly isolated from columbids in the United States and worldwide. Complete genomic characterization of these genotype VI viruses circulating in wild columbids in the United States is limited, and due to the genetic variability of the virus, failure of rapid diagnostic detection has been reported...
January 12, 2018: Virology Journal
https://www.readbyqxmd.com/read/29329524/uncovering-the-evolutionary-history-of-neo-xy-sex-chromosomes-in-the-grasshopper-ronderosia-bergii-orthoptera-melanoplinae-through-satellite-dna-analysis
#6
Octavio M Palacios-Gimenez, Diogo Milani, Bernardo Lemos, Elio R Castillo, Dardo A Martí, Erica Ramos, Cesar Martins, Diogo C Cabral-de-Mello
BACKGROUND: Neo-sex chromosome systems arose independently multiple times in evolution, presenting the remarkable characteristic of repetitive DNAs accumulation. Among grasshoppers, occurrence of neo-XY was repeatedly noticed in Melanoplinae. Here we analyzed the most abundant tandem repeats of R. bergii (2n = 22, neo-XY♂) using deep Illumina sequencing and graph-based clustering in order to address the neo-sex chromosomes evolution. RESULTS: The analyses revealed ten families of satDNAs comprising about ~1% of the male genome, which occupied mainly C-positive regions of autosomes...
January 8, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29328655/identification-of-novel-coumestan-derivatives-as-polyketide-synthase-13-inhibitors-against-mycobacterium-tuberculosis
#7
Wei Zhang, Shichun Lun, Shu-Huan Wang, Xingwu Jiang, Fan Yang, Jie Tang, Abigail L Manson, Ashlee M Earl, Hendra Gunosewoyo, William R Bishai, Li-Fang Yu
Inhibition of the mycolic acid pathway has proven a viable strategy in antitubercular drug discovery. The AccA3/AccD4/FadD32/Pks13 complex of Mycobacterium tuberculosis constitutes an essential biosynthetic mechanism for mycolic acids. Small molecules targeting the thioesterase domain of Pks13 have been reported, including a benzofuran-based compound, whose X-ray co-crystal structure has been very recently solved. Its initial inactivity in a serum inhibition titration (SIT) assay led us to further probe other structurally-related benzofurans with the aim to improve their potency and bioavailability...
January 12, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29327637/evidence-of-shallow-mitochondrial-divergence-in-the-slender-armorhead-pentaceros-wheeleri-pisces-pentacerotidae-from-the-emperor-seamount-chain
#8
Seung Eun Bae, Hanna Kim, Seok-Gwan Choi, Jin-Koo Kim
Competitive overexploitation of the slender armorhead, Pentaceros wheeleri, a deep-sea fish inhabiting the Emperor Seamount Chain caused a serious population decline. Therefore, it is urgently necessary to clarify its genetic diversity and connectivity among populations of P. wheeleri for appropriate stock management. For this, we compared 677 base pairs (bp) of mitochondrial (mt) DNA control region (CR) sequences of 80 individuals from three seamounts (the Milwaukee, Kinmei, and Koko Seamounts) in the southern part of the Emperor Seamount Chain...
January 12, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29327117/graphical-classification-of-dna-sequences-of-hla-alleles-by-deep-learning
#9
Jun Miyake, Yuhei Kaneshita, Satoshi Asatani, Seiichi Tagawa, Hirohiko Niioka, Takashi Hirano
Alleles of human leukocyte antigen (HLA)-A DNAs are classified and expressed graphically by using artificial intelligence "Deep Learning (Stacked autoencoder)". Nucleotide sequence data corresponding to the length of 822 bp, collected from the Immuno Polymorphism Database, were compressed to 2-dimensional representation and were plotted. Profiles of the two-dimensional plots indicate that the alleles can be classified as clusters are formed. The two-dimensional plot of HLA-A DNAs gives a clear outlook for characterizing the various alleles...
January 11, 2018: Human Cell
https://www.readbyqxmd.com/read/29326978/seismic-signature-of-active-intrusions-in-mountain-chains
#10
Francesca Di Luccio, Giovanni Chiodini, Stefano Caliro, Carlo Cardellini, Vincenzo Convertito, Nicola Alessandro Pino, Cristiano Tolomei, Guido Ventura
Intrusions are a ubiquitous component of mountain chains and testify to the emplacement of magma at depth. Understanding the emplacement and growth mechanisms of intrusions, such as diapiric or dike-like ascent, is critical to constrain the evolution and structure of the crust. Petrological and geological data allow us to reconstruct magma pathways and long-term magma differentiation and assembly processes. However, our ability to detect and reconstruct the short-term dynamics related to active intrusive episodes in mountain chains is embryonic, lacking recognized geophysical signals...
January 2018: Science Advances
https://www.readbyqxmd.com/read/29326527/treatment-of-a-class-ii-malocclusion-with-deep-overbite-in-an-adult-patient-using-intermaxillary-elastics-and-spee-curve-controlling-with-reverse-and-accentuated-archwires
#11
Fabrício Pinelli Valarelli, Ronaldo Carniel, Paula Patrícia Cotrin-Silva, Mayara Paim Patel, Rodrigo Hermont Cançado, Karina Maria Salvatore Freitas, Marcos Roberto de Freitas
This paper aimed to describe the orthodontic treatment of an adult patient with the following characteristics: asymmetric Class II malocclusion, left subdivision, mandibular midline shifted to the left, mild mandibular anterior crowding, excessive overbite, 4-mm overjet, and a brachycephalic facial pattern. A 31-year-old male patient, treated with fixed preadjusted appliance with Roth prescription, with leveling and alignment NiTi archwire sequence. To correct the asymmetric Class II malocclusion, midline shift as well the overjet and overbite, intermaxillary elastics and accentuated and reversed stainless steel archwires were used, respectively...
October 2017: Contemporary Clinical Dentistry
https://www.readbyqxmd.com/read/29325031/use-of-deep-whole-genome-sequencing-data-to-identify-structure-risk-variants-in-breast-cancer-susceptibility-genes
#12
Xingyi Guo, Jiajun Shi, Qiuyin Cai, Xiao-Ou Shu, Jing He, Wanqing Wen, Jamie Allen, Paul Pharoah, Alison Dunning, David J Hunter, Peter Kraft, Douglas F Easton, Wei Zheng, Jirong Long
Functional disruptions of susceptibility genes by large genomic structure variant (SV) deletions in germlines are known to be associated with cancer risk. However, few studies have been conducted to systematically search for SV deletions in breast cancer susceptibility genes. We analyzed deep (> 30x) whole genome sequencing (WGS) data generated in blood samples from 128 breast cancer patients of Asian and European descent with either a strong family history of breast cancer or early cancer onset disease...
January 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29322618/genome-enabled-metabolic-reconstruction-of-dominant-chemosynthetic-colonizers-in-deep-sea-massive-sulfide-deposits
#13
Shingo Kato, Takazo Shibuya, Yoshihiro Takaki, Miho Hirai, Takuro Nunoura, Katsuhiko Suzuki
Deep-sea massive sulfide deposits remaining after ceasing of hydrothermal activity potentially provide energy for a chemosynthetic ecosystem in the dark, cold marine environments. Although yet-uncultivated bacteria in the phylum Nitrospirae and the class Deltaproteobacteria are known to dominate the microbial communities of sulfide deposits at and below the seafloor, their metabolic capabilities remain largely elusive. Here, we reveal the metabolic potential of these yet-uncultivated bacteria in hydrothermally inactive sulfide deposits collected at the Southern Mariana Trough by seafloor drilling...
January 10, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29322437/deep-computational-circular-rna-analytics-from-rna-seq-data
#14
Tobias Jakobi, Christoph Dieterich
Circular RNAs (circRNAs) have been first described as "scrambled exons" in the 1990s. CircRNAs originate from back splicing or exon skipping of linear RNA templates and have continuously gained attention in recent years due to the availability of high-throughput whole-transcriptome sequencing methods. Numerous manuscripts describe thousands of circRNAs throughout uni- and multicellular eukaryote species and demonstrated that they are conserved, stable, and abundant in specific tissues or conditions. This manuscript provides a walk-through of our bioinformatics toolbox, which covers all aspects of in silico circRNA analysis, starting from raw sequencing data and back-splicing junction discovery to circRNA quantitation and reconstruction of internal the circRNA structure...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29321648/comparative-analysis-of-mirna-expression-profiles-in-transgenic-and-non-transgenic-rice-using-mirna-seq
#15
Cheng Peng, Xiaoyun Chen, Xiaofu Wang, Xiaoli Xu, Wei Wei, Congmao Wang, Junfeng Xu
Safety assessment for genetically modified organisms (GMOs) is required before their release. To date, miRNAs that play important roles in eukaryotic gene regulation have not been considered in the current assessment system. In this study, we identified 6 independent Bt and EPSPS GM rice lines using PCR and immune strip. We analyzed the expression levels of Cry1Ac and EPSPS using quantitative real-time PCR and western blot. Further, miRNAs from the developing seeds of the 6 GM rice lines and the wild-type line were investigated using deep sequencing and bioinformatic approaches...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321642/profiling-of-metabolome-and-bacterial-community-dynamics-in-ensiled-medicago-sativa-inoculated-without-or-with-lactobacillus-plantarum-or-lactobacillus-buchneri
#16
X S Guo, W C Ke, W R Ding, L M Ding, D M Xu, W W Wang, P Zhang, F Y Yang
Using gas chromatography mass spectrometry and the PacBio single molecule with real-time sequencing technology (SMRT), we analyzed the detailed metabolomic profiles and microbial community dynamics involved in ensiled Medicago sativa (alfalfa) inoculated without or with the homofermenter Lactobacillus plantarum or heterofermenter Lactobacillus buchneri. Our results revealed that 280 substances and 102 different metabolites were present in ensiled alfalfa. Inoculation of L. buchneri led to remarkable up-accumulation in concentrations of 4-aminobutyric acid, some free amino acids, and polyols in ensiled alfalfa, whereas considerable down-accumulation in cadaverine and succinic acid were observed in L...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321591/respiratory-syncytial-virus-infection-changes-cargo-composition-of-exosome-released-from-airway-epithelial-cells
#17
Harendra Singh Chahar, Tiziana Corsello, Andrzej S Kudlicki, Narayana Komaravelli, Antonella Casola
Exosomes are microvesicles known to carry biologically active molecules, including RNA, DNA and proteins. Viral infections can induce profound changes in exosome composition, and exosomes have been implicated in viral transmission and pathogenesis. No information is current available regarding exosome composition and function during infection with Respiratory Syncytial Virus (RSV), the most important cause of lower respiratory tract infections in children. In this study, we characterized exosomes released from RSV-infected lung carcinoma-derived A549 cells...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29320424/a-retrospective-examination-of-feline-leukemia-subgroup-characterization-viral-interference-assays-to-deep-sequencing
#18
REVIEW
Elliott S Chiu, Edward A Hoover, Sue VandeWoude
Feline leukemia virus (FeLV) was the first feline retrovirus discovered, and is associated with multiple fatal disease syndromes in cats, including lymphoma. The original research conducted on FeLV employed classical virological techniques. As methods have evolved to allow FeLV genetic characterization, investigators have continued to unravel the molecular pathology associated with this fascinating agent. In this review, we discuss how FeLV classification, transmission, and disease-inducing potential have been defined sequentially by viral interference assays, Sanger sequencing, PCR, and next-generation sequencing...
January 10, 2018: Viruses
https://www.readbyqxmd.com/read/29318861/-clinical-trials-for-treatment-of-allergic-rhinitis-with-heat-sensitive-moxibustion-and-its-regularity-of-heat-sensitization-acupoint-distribution
#19
Yu-Fen Lin, Jian-Min Lu, Yan-Na Su, Ze-Bin Zhong, Zuo-Dan Zhang
OBJECTIVE: To observe the clinical effect of heat sensitive moxibustion (HSM) and its regularity of acupoint heat-sensitization in the treatment of allergic rhinitis (AR) patients. METHODS: Seventy patients with AR were randomly divided into HSM and manual acupuncture groups (n=35/group). For patients of the HSM group, acupoints Yintang (EX-HN 3), bilateral Yingxiang (LI 20), Shangxing (GV 23), Tongtian (BL 7), Feishu (BL 13), Hegu (LI 4), etc. were used, and for patients of the manual acupuncture group, bilateral LI 20 and LI 4, Bitong (EX-HN 8) and EX-HN 3 were needled and stimulated with uniform reinforcing-reducing needling method...
December 25, 2017: Zhen Ci Yan Jiu, Acupuncture Research
https://www.readbyqxmd.com/read/29317639/tectonically-triggered-sediment-and-carbon-export-to-the-hadal-zone
#20
Rui Bao, Michael Strasser, Ann P McNichol, Negar Haghipour, Cameron McIntyre, Gerold Wefer, Timothy I Eglinton
Sediments in deep ocean trenches may contain crucial information on past earthquake history and constitute important sites of carbon burial. Here we present 14C data on bulk organic carbon (OC) and its thermal decomposition fractions produced by ramped pyrolysis/oxidation for a core retrieved from the >7.5 km-deep Japan Trench. High-resolution 14C measurements, coupled with distinctive thermogram characteristics of OC, reveal hemipelagic sedimentation interrupted by episodic deposition of pre-aged OC in the trench...
January 9, 2018: Nature Communications
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