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https://www.readbyqxmd.com/read/30001693/trumpet-transcriptome-guided-quality-assessment-of-m-6-a-seq-data
#1
Teng Zhang, Shao-Wu Zhang, Lin Zhang, Jia Meng
BACKGROUND: Methylated RNA immunoprecipitation sequencing (MeRIP-seq or m6 A-seq) has been extensively used for profiling transcriptome-wide distribution of RNA N6-Methyl-Adnosine methylation. However, due to the intrinsic properties of RNA molecules and the intricate procedures of this technique, m6 A-seq data often suffer from various flaws. A convenient and comprehensive tool is needed to assess the quality of m6 A-seq data to ensure that they are suitable for subsequent analysis. RESULTS: From a technical perspective, m6 A-seq can be considered as a combination of ChIP-seq and RNA-seq; hence, by effectively combing the data quality assessment metrics of the two techniques, we developed the trumpet R package for evaluation of m6 A-seq data quality...
July 13, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29997100/-efficacy-of-inactivated-autologous-porous-bone-flap-and-bam-bone-induced-artificial-bone-for-repairing-skull-defect-in-rats
#2
Chao-Min Wang, Tie-Jian Liu, Zhen-Hua Song, Xiao-Yu Guo, Da-Nian Wei, Cheng-Yong Liu
OBJECTIVE: To study the effect of BAM bone grafting combined with inactivated autologous porous bone flap in repairing skull defect in rats. METHODS: Seventy-two Wistar rats with skull defect were randomly divided into control group, inactivated autologous bone flap group (AB group), BAM bone-induced artificial bone material group (BAM group), and inactivated autologous bone flap with BAM bone-induced artificial bone group (BAM+AB group). The bone healing was evaluated with micro-CT and the new bone formation was assessed with histological staining at 1, 2, and 3 months after modeling...
June 20, 2018: Nan Fang Yi Ke da Xue Xue Bao, Journal of Southern Medical University
https://www.readbyqxmd.com/read/29996592/antimicrobial-agents-that-inhibit-the-outer-membrane-assembly-machines-of-gram-negative-bacteria
#3
REVIEW
Umji Choi, Chang-Ro Lee
Gram-negative pathogens, such as Klebsiella pneumoniae , Pseudomonas aeruginosa , and Acinetobacter baumannii , pose a serious threat to public health worldwide, due to high rates of antibiotic resistance and the lack of development of novel antimicrobial agents targeting Gram-negative bacteria.The outer membrane (OM) of Gram-negative bacteria is a unique architecture that acts as a potent permeability barrier against toxic molecules, such as antibiotics. The OM is composed of phospholipids, lipopolysaccharide (LPS), outer membrane β-barrel proteins (OMP), and lipoproteins...
April 27, 2018: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29992192/the-quality-sequencing-minimum-qsm-providing-comprehensive-consistent-transparent-next-generation-sequencing-data-quality-assurance
#4
Shazia Mahamdallie, Elise Ruark, Shawn Yost, Márton Münz, Anthony Renwick, Emma Poyastro-Pearson, Ann Strydom, Sheila Seal, Nazneen Rahman
Next generation sequencing (NGS) is routinely used in clinical genetic testing. Quality management of NGS testing is essential to ensure performance is consistently and rigorously evaluated. Three primary metrics are used in NGS quality evaluation: depth of coverage, base quality and mapping quality. To provide consistency and transparency in the utilisation of these metrics we present the Quality Sequencing Minimum (QSM). The QSM defines the minimum quality requirement a laboratory has selected for depth of coverage (C), base quality (B) and mapping quality (M) and can be applied per base, exon, gene or other genomic region, as appropriate...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29991993/implementing-ejtm-3-european-journal-of-translational-myology-mobility-medicine-along-the-silk-road
#5
Paola Arslan, Barbara Ravara
Two main novelties will appear in the second 2018 Issue of the European Journal of Translational Myology demonstrating that the journal is vital and in expansion, one novelty is that the journal is implementing its authorship and readership to broader clinical fields from muscle myology and mobility to clinical medicine and surgery. Consequently, the Editorial Board is also expanding to allow a broader expert evaluation of Authors submitted typescripts. The expanded Editorial Board recently evaluated the option to change the name of the journal from Ejtm to EjtM3 (Myology, Mobility, Medicine), in order to expand the original journal title meaning...
April 24, 2018: European Journal of Translational Myology
https://www.readbyqxmd.com/read/29985130/jnk-signaling-triggers-spermatogonial-dedifferentiation-during-chronic-stress-to-maintain-the-germline-stem-cell-pool-in-the-drosophila-testis
#6
Salvador C Herrera, Erika A Bach
Exhaustion of stem cells is a hallmark of aging. In the Drosophila testis, dedifferentiated germline stem cells (GSCs) derived from spermatogonia increases during lifespan, leading to the model that dedifferentiation counteracts the decline of GSCs in aged males. To test this, we blocked dedifferentiation by mis-expressing the differentiation factor bag of marbles ( bam ) in spermatogonia while lineage-labeling these cells. Strikingly, blocking bam -lineage dedifferentiation under normal conditions in virgin males has no impact on the GSC pool...
July 9, 2018: ELife
https://www.readbyqxmd.com/read/29984394/catabolism-of-the-groundwater-micropollutant-2-6-dichlorobenzamide-beyond-2-6-dichlorobenzoate-is-plasmid-encoded-in-aminobacter-sp-msh1
#7
Jeroen T'Syen, Bart Raes, Benjamin Horemans, Raffaella Tassoni, Baptiste Leroy, Cédric Lood, Vera van Noort, Rob Lavigne, Ruddy Wattiez, Hans-Peter E Kohler, Dirk Springael
Aminobacter sp. MSH1 uses the groundwater micropollutant 2,6-dichlorobenzamide (BAM) as sole source of carbon and energy. In the first step, MSH1 converts BAM to 2,6-dichlorobenzoic acid (2,6-DCBA) by means of the BbdA amidase encoded on the IncP-1β plasmid pBAM1. Information about the genes and degradation steps involved in 2,6-DCBA metabolism in MSH1 or any other organism is currently lacking. Here, we show that the genes for 2,6-DCBA degradation in strain MSH1 reside on a second catabolic plasmid in MSH1, designated as pBAM2...
July 8, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29984240/population-structure-of-leishmania-tropica-causing-anthroponotic-cutaneous-leishmaniasis-in-southern-iran-by-pcr-rflp-of-kinetoplastid-dna
#8
Mohammad Amin Ghatee, Hossein Mirhendi, Masoud Marashifard, Zahra Kanannejad, Walter R Taylor, Iraj Sharifi
Iran is one of the six countries with the most cutaneous leishmaniasis (CL) patients. Understanding better the genotypes of the parasite population in relation to geography and climate is critical to achieving better CL control. We aimed to characterise the population structure of Leishmania tropica , the cause of anthroponotic cutaneous leishmaniasis (ACL), from important foci in southeast (Bam and Kerman) and southwest (Shiraz) Iran. A total of 39 L. tropica isolates from ACL patients from southeast (Bam 14, Kerman 12) and southwest (Shiraz 13) Iran were analysed by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) of the kinetoplast DNA (kDNA) using restriction enzymes Msp I ( HpaII ) and Cla I...
2018: BioMed Research International
https://www.readbyqxmd.com/read/29982625/svengine-an-efficient-and-versatile-simulator-of-genome-structural-variations-with-features-of-cancer-clonal-evolution
#9
Li Charlie Xia, Dongmei Ai, Hojoon Lee, Noemi Andor, Chao Li, Nancy R Zhang, Hanlee P Ji
Background: Simulating genome sequence data with variant features facilitates the development and benchmarking of structural variant analysis programs. However, there are only a few data simulators that provide structural variants in silico and even fewer that provide variants with different allelic fraction and haplotypes. Findings: We developed SVEngine, an open source tool to address this need. SVEngine simulates next generation sequencing data with embedded structural variations...
July 5, 2018: GigaScience
https://www.readbyqxmd.com/read/29980640/fshd-type-2-and-bosma-arhinia-microphthalmia-syndrome-two-faces-of-the-same-mutation
#10
Karlien Mul, Richard J L F Lemmers, Marjolein Kriek, Patrick J van der Vliet, Marlinde L van den Boogaard, Umesh A Badrising, John M Graham, Angela E Lin, Harrison Brand, Steven A Moore, Katherine Johnson, Teresinha Evangelista, Ana Töpf, Volker Straub, Solange Kapetanovic García, Sabrina Sacconi, Rabi Tawil, Stephen J Tapscott, Nicol C Voermans, Baziel G M van Engelen, Corinne G C Horlings, Natalie D Shaw, Silvère M van der Maarel
OBJECTIVE: To determine whether congenital arhinia/Bosma arhinia microphthalmia syndrome (BAMS) and facioscapulohumeral muscular dystrophy type 2 (FSHD2), 2 seemingly unrelated disorders both caused by heterozygous pathogenic missense variants in the SMCHD1 gene, might represent different ends of a broad single phenotypic spectrum associated with SMCHD1 dysfunction. METHODS: We examined and/or interviewed 14 patients with FSHD2 and 4 unaffected family members with N-terminal SMCHD1 pathogenic missense variants to identify BAMS subphenotypes...
July 6, 2018: Neurology
https://www.readbyqxmd.com/read/29966545/rapid-detection-of-listeria-in-ice-cream-in-13-hours-using-the-roka-listeria-detection-assay
#11
Elba Veronica Arias-Rios, Kristina Tenney, Tam Mai, Sam Anderson, Ruth Marie Cantera, Lourdes M Nadala, Sukkyun Han, Harish Janagama, Jasmine M Pando, Brandon Selover, Shao Lei Sung, Cesar Nadala, Mansour Samadpour
> Background: Listeria contamination is a major concern in the ice cream industry; therefore, early and accurate detection is vital. Current detection methods require about a 24 h enrichment period for detection. Objective: Enhance the early detection of Listeria in ice cream using the highly sensitive isothermal ribosomal RNA-based Roka/Atlas Listeria Detection Assay. Methods: The R2 Medium was developed for Listeria enrichment by Molecular Epidemiology, Inc. (Seattle, WA). Comparative growth curve studies were performed on the new R2 Medium for Listeria and the currently validated media for the Roka Listeria Detection Assay...
July 2, 2018: Journal of AOAC International
https://www.readbyqxmd.com/read/29965761/interactions-of-long-chain-perfluorotelomer-alcohol-and-perfluorinated-hydrocarbons-with-model-decomposer-membranes
#12
Aneta Wojcik, Paulina Perczyk, Pawel Wydro, Michał Flasiński, Marcin Broniatowski
Perfluorinated hydrocarbons and their polar derivatives are produced annually in high quantities and find multiple industrial and technological applications due to their chemical and physical durability, significant hydro- and lipophobicity and excellent surface activity. Unfortunately, multiple perfluorinated compounds are recognized as persistent organic pollutants as they are completely non-biodegradable and accumulate in soils and sediments. In our studies we applied Langmuir monolayers formed by different structural phospholipids as models of soil bacteria and fungi membranes and investigated the effects exerted by long chain perfluorinated pollutants: perfluorotelomer alcohol and two structurally different perfluorinated hydrocarbons on the artificial membranes...
July 2, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29959250/itraq-based-global-proteomic-analysis-of-salmonella-enterica-serovar-typhimurium-in-response-to-desiccation-low-a-w-and-thermal-treatment
#13
Alice Maserati, Antonio Lourenco, Francisco Diez-Gonzalez, Ryan C Fink
In this study, the changes in the global proteome of Salmonella in response to desiccation and thermal treatment were investigated by iTRAQ multiplex technique. A Salmonella Typhimurium strain was dried, equilibrated at high (1.0) and low (0.11) water activity (aw ), and thermally treated at 75°C. The proteomes were characterized after every treatment. The proteomes of the different treatments differed in the expression of 175 proteins. Based on their proteomic expression profiles, samples were clustered into two major groups, "dry" samples and "moist" samples...
June 29, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29946516/impact-of-tobacco-cessation-on-tuberculosis-control
#14
EDITORIAL
Tara Singh Bam
No abstract text is available yet for this article.
June 21, 2018: Public Health Action
https://www.readbyqxmd.com/read/29945233/appreci8-a-pipeline-for-precise-variant-calling-integrating-8-tools
#15
Sarah Sandmann, Mohsen Karimi, Aniek O de Graaf, Christian Rohde, Stefanie Göllner, Julian Varghese, Jan Ernsting, Gunilla Walldin, Bert A van der Reijden, Carsten Müller-Tidow, Luca Malcovati, Eva Hellström-Lindberg, Joop H Jansen, Martin Dugas
Motivation: The application of next-generation sequencing in research and particularly in clinical routine requires valid variant calling results. However, evaluation of several commonly used tools has pointed out that not a single tool meets this requirement. False positive as well as false negative calls necessitate additional experiments and extensive manual work. Intelligent combination and output filtration of different tools could significantly improve the current situation. Results: We developed appreci8, an automatic variant calling pipeline for calling single nucleotide variants and short indels by combining and filtering the output of eight open-source variant calling tools, based on a novel artifact- and polymorphism score...
June 26, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29941590/inhibitor-of-intramembrane-protease-rsep-blocks-the-%C3%AF-e-response-causing-lethal-accumulation-of-unfolded-outer-membrane-proteins
#16
Anna Konovalova, Marcin Grabowicz, Carl J Balibar, Juliana C Malinverni, Ronald E Painter, Daniel Riley, Paul A Mann, Hao Wang, Charles G Garlisi, Brad Sherborne, Nathan W Rigel, Dante P Ricci, Todd A Black, Terry Roemer, Thomas J Silhavy, Scott S Walker
The outer membrane (OM) of Gram-negative bacteria forms a robust permeability barrier that blocks entry of toxins and antibiotics. Most OM proteins (OMPs) assume a β-barrel fold, and some form aqueous channels for nutrient uptake and efflux of intracellular toxins. The Bam machine catalyzes rapid folding and assembly of OMPs. Fidelity of OMP biogenesis is monitored by the σE stress response. When OMP folding defects arise, the proteases DegS and RseP act sequentially to liberate σE into the cytosol, enabling it to activate transcription of the stress regulon...
June 25, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29927245/nitrogen-rich-copper-ii-bromate-complexes-an-exotic-class-of-primary-explosives-%C3%A2
#17
Maximilian H H Wurzenberger, Norbert Szimhardt, Jörg Stierstorfer
Because of the ongoing very challenging search for potential replacements of the currently used toxic lead-based primary explosives, new synthetic strategies have to be developed. In particular, the smart concept of energetic coordination compounds (ECC) has proven to hold great potential to solve this difficult and complex problem. The herein-described approach combines the exotic and neglected class of copper(II) bromate ECC with different environmentally friendly nitrogen-rich heterocycles, which exhibit the energetic properties of powerful primary explosives...
June 21, 2018: Inorganic Chemistry
https://www.readbyqxmd.com/read/29907615/characterization-of-the-plp-dependent-transaminase-initiating-azasugar-biosynthesis
#18
Jeffrey M Arciola, Nicole A Horenstein
Biosynthesis of the azasugar 1-deoxynojirimycin (DNJ) critically involves a transamination in the first committed step. Here we identify the azasugar biosynthetic cluster signature in Paenibacillus polymyxa SC2 ( Ppo ), homologous to that reported in Bacillus amyloliquefaciens FZB42 ( Bam ) and report the characterization of the aminotransferase GabT1 (named from Bam ). GabT1 from Ppo exhibits a specific activity of 4.9 nmol/min/mg at 30 °C (pH 7.5), a somewhat promiscuous amino donor selectivity, and curvilinear steady-state kinetics that do not reflect the predicted ping pong behavior typical of aminotransferases...
June 15, 2018: Biochemical Journal
https://www.readbyqxmd.com/read/29906272/correction-coupled-effects-of-oil-spill-and-hurricane-on-saltmarsh-terrestrial-arthropods
#19
Wokil Bam, Linda M Hooper-Bui, Rachel M Strecker, Puspa L Adhikari, Edward B Overton
[This corrects the article DOI: 10.1371/journal.pone.0194941.].
2018: PloS One
https://www.readbyqxmd.com/read/29899524/microrna-30-modulates-metabolic-inflammation-by-regulating-notch-signaling-in-adipose-tissue-macrophages
#20
Kathryn Miranda, Xiaoming Yang, Marpe Bam, E Angela Murphy, Prakash S Nagarkatti, Mitzi Nagarkatti
BACKGROUND/OBJECTIVES: Obesity is a pandemic disorder that is characterized by accumulation of adipose tissue and chronic low-grade inflammation that is driven primarily by adipose tissue macrophages (ATMs). While ATM polarization from pro-(M1) to anti-(M2) inflammatory phenotype influences insulin sensitivity and energy expenditure, the mechanisms of such a switch are unclear. In the current study, we identified epigenetic pathways including microRNAs (miR) in ATMs that regulate obesity-induced inflammation...
June 13, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
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