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https://www.readbyqxmd.com/read/29224164/hairpin-bisulfite-sequencing-synchronous-methylation-analysis-on-complementary-dna-strands-of-individual-chromosomes
#1
Pascal Giehr, Jörn Walter
The accurate and quantitative detection of 5-methylcytosine is of great importance in the field of epigenetics. The method of choice is usually bisulfite sequencing because of the high resolution and the possibility to combine it with next generation sequencing. Nevertheless, also this method has its limitations. Following the bisulfite treatment DNA strands are no longer complementary such that in a subsequent PCR amplification the DNA methylation patterns information of only one of the two DNA strand is preserved...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224163/methylation-sensitive-high-resolution-melting-ms-hrm
#2
Dianna Hussmann, Lise Lotte Hansen
Methylation-Sensitive High Resolution Melting (MS-HRM) is an in-tube, PCR-based method to detect methylation levels at specific loci of interest. A unique primer design facilitates a high sensitivity of the assays enabling detection of down to 0.1-1% methylated alleles in an unmethylated background.Primers for MS-HRM assays are designed to be complementary to the methylated allele, and a specific annealing temperature enables these primers to anneal both to the methylated and the unmethylated alleles thereby increasing the sensitivity of the assays...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224147/comprehensive-whole-dna-methylome-analysis-by-integrating-medip-seq-and-mre-seq
#3
Xiaoyun Xing, Bo Zhang, Daofeng Li, Ting Wang
Understanding the role of DNA methylation often requires accurate assessment and comparison of these modifications in a genome-wide fashion. Sequencing-based DNA methylation profiling provides an unprecedented opportunity to map and compare complete DNA CpG methylomes. These include whole genome bisulfite sequencing (WGBS), Reduced-Representation Bisulfite-Sequencing (RRBS), and enrichment-based methods such as MeDIP-seq, MBD-seq, and MRE-seq. An investigator needs a method that is flexible with the quantity of input DNA, provides the appropriate balance among genomic CpG coverage, resolution, quantitative accuracy, and cost, and comes with robust bioinformatics software for analyzing the data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224144/low-input-whole-genome-bisulfite-sequencing-using-a-post-bisulfite-adapter-tagging-approach
#4
Julian R Peat, Sébastien A Smallwood
The epigenetic mark 5-methylcytosine confers heritable regulation of gene expression that can be dynamically modulated during transitions in cell fate. With the development of high-throughput sequencing technologies, it is now possible to obtain comprehensive genome-wide maps of the mammalian DNA methylation landscape, but the application of these techniques to limited material remains challenging. Here, we present an optimized protocol to perform whole-genome bisulfite sequencing on low inputs (100-5000 somatic cells) using a post-bisulfite adapter tagging approach...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29223532/new-insights-into-the-influence-of-monofluorination-on-dimyristoylphosphatidylcholine-membrane-properties-a-solid-state-nmr-study
#5
Marie-Claude Gagnon, Erik Strandberg, Anne S Ulrich, Jean-François Paquin, Michèle Auger
Solid-state 19F NMR spectroscopy is a method of choice to study the interactions between lipid membranes and other molecules such as peptides, proteins or drugs. Numerous fluorine-labeled NMR probes have been developed over the last few years, especially fluorine-labeled peptides. In order to develop a new kind of NMR reporter molecule and a complementary approach to fluorine-labeling of peptides, we synthesized six monofluorinated derivatives of the lipid dimyristoylphosphatidylcholine (F-DMPC), with the fluorine atom located along the acyl chain linked to the central glycerol position...
December 6, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29223449/anti-hsv-2-activity-of-peganum-harmala-l-and-isolation-of-the-active-compound
#6
Roudaina Benzekri, Lamjed Bouslama, Adele Papetti, Majdi Hammami, Abderrazak Smaoui, Ferid Limam
Genital herpes is a sexually transmitted disease caused by herpes simplex virus type 2 (HSV-2). Nucleoside analogues such as acyclovir (ACV) are the usual therapy for treating HSV infection. However, the overuse of this drug has led to the emergence of resistant strains. Therefore, the search for new alternative or complementary molecules to overcome this obstacle is needed. In this objective, Peganum harmala was investigated for its HSV-2 activity. The organic extracts of the different plant organs were evaluated for their cytotoxicity on Vero cells by the MTT test and anti HSV-2 activity by plaque reduction assay...
December 6, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29223400/a-new-comprehensive-method-for-detection-of-livestock-related-pathogenic-viruses-using-a-target-enrichment-system
#7
Mami Oba, Shinobu Tsuchiaka, Tsutomu Omatsu, Yukie Katayama, Konosuke Otomaru, Teppei Hirata, Hiroshi Aoki, Yoshiteru Murata, Shinji Makino, Makoto Nagai, Tetsuya Mizutani
We tested usefulness of a target enrichment system SureSelect, a comprehensive viral nucleic acid detection method, for rapid identification of viral pathogens in feces samples of cattle, pigs and goats. This system enriches nucleic acids of target viruses in clinical/field samples by using a library of biotinylated RNAs with sequences complementary to the target viruses. The enriched nucleic acids are amplified by PCR and subjected to next generation sequencing to identify the target viruses. In many samples, SureSelect target enrichment method increased efficiencies for detection of the viruses listed in the biotinylated RNA library...
December 6, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29223067/dissection-of-resistance-to-microdochium-nivale-in-lolium-multiflorum-festuca-arundinacea-introgression-forms
#8
Agnieszka Płażek, Ewa Pociecha, Adam Augustyniak, Katarzyna Masajada, Michał Dziurka, Joanna Majka, Dawid Perlikowski, Izabela Pawłowicz, Arkadiusz Kosmala
The potential of resistance to Microdochium nivale is still not recognized for numerous plant species. The forage grasses of Lolium-Festuca complex are important for grass-biomass production in the temperate regions. Lolium multiflorum is a grass with a high forage quality and productivity but also a relatively low resistance to M. nivale. On the contrary, F. arundinacea has a higher potential of resistance but simultaneously a significantly lower forage quality. These two species cross with each other and the intergeneric hybrids possess complementary characters of both genera...
December 5, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29222687/chrysophyllum-cainito-apple-star-a-fruit-with-gastroprotective-activity-in-experimental-ulcer-models
#9
Roseane Leandra da Rosa, Camila Leandra de Almeida, Lincon Bordigon Somensi, Thaise Boeing, Luisa Nathália Bolda Mariano, Clarissa de Medeiros Amorim Krueger, Priscila de Souza, Valdir Cechinel Filho, Luisa Mota da Silva, Sérgio Faloni de Andrade
The gastroprotective potential of the methanolic extracts from peels (MEPe), seeds (MESe) and pulp (MEPu) of Chrysophyllum cainito L. (Sapotaceae) fruits was evaluated in mice using ethanol/HCl- and indomethacin-induced ulcer, as well as the antiulcer effect of the juice and flour from this fruit. The lowest oral gastroprotective dose of MEPe, MESe and MEPu against ethanol/HCl was 3, 3 and 10 mg/kg, respectively. Moreover, all extracts increased mucin secretion at 176, 198 and 193%. Intraperitoneal administration of MEPe (0...
December 8, 2017: Inflammopharmacology
https://www.readbyqxmd.com/read/29222161/detection-of-proteome-diversity-resulted-from-alternative-splicing-is-limited-by-trypsin-cleavage-specificity
#10
Xiaojing Wang, Simona G Codreanu, Bo Wen, Kai Li, Matthew Chambers, Daniel C Liebler, Bing Zhang
Alternative splicing dramatically increases transcriptome complexity but its contribution to proteome diversity remains controversial. Exon-exon junction spanning peptides provide direct evidence for the translation of specific splice isoforms and are critical for delineating protein isoform complexity. Here we found that junction-spanning peptides are underrepresented in publicly available mass spectrometry-based shotgun proteomics data sets. Further analysis showed that evolutionarily conserved preferential nucleotide usage at exon boundaries increases the occurrence of lysine- and arginine-coding triplets at the end of exons...
December 8, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29222062/evolutionary-history-of-the-cobalamin-independent-methionine-synthase-gene-family-across-the-land-plants
#11
Hugo Vianna Silva Rody, Luiz Orlando de Oliveira
Plants are successful paleopolyploids. The wide diversity of land plants is driven strongly by their gene duplicates undergoing distinct evolutionary fates after duplication. We used genomic resources from 35 model plant species to unravel the evolutionary fate of gene copies (paralogs) of the cobalamin-independent methionine synthase (metE) gene family across the land plants. To explore genealogical relationships and characterize positive selection as a driving force in the evolution of metE paralogs within a single species, we carried out complementary analyses on genomic data of 32 genotypes of soybean...
December 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29221989/differential-targeting-of-membrane-lipid-domains-by-caffeic-acid-and-its-ester-derivatives
#12
Hugo A L Filipe, Carla Sousa, Joaquim T Marquês, Diogo Vila-Viçosa, António de Granada Flor, Ana S Viana, M Soledade C S Santos, Miguel Machuqueiro, Rodrigo F M de Almeida
Phenolic acids have been associated to a wide range of important health benefits underlain by a common molecular mechanism of action. Considering that significant membrane permeation is prevented by their hydrophilic character, we hypothesize that their main effects result from the interplay with cell membrane surface. This hypothesis was tested using the paradigmatic caffeic acid (CA) and two of its ester derivatives, rosmarinic (RA) and chlorogenic (CGA) acids, for which we predict, based on molecular dynamics simulations, a shallow location in phospholipid bilayers dependent on the protonation-state...
December 5, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/29221966/lesion-magnetic-susceptibility-response-to-hyperoxic-challenge-a-biomarker-for-malignant-brain-tumor-microenvironment
#13
Pinar Senay Özbay, Sonja Stieb, Cristina Rossi, Oliver Riesterer, Andreas Boss, Tobias Weiss, Felix Kuhn, Klaas Paul Pruessmann, Daniel Nanz
BACKGROUND AND PURPOSE: Quantitative susceptibility mapping has been previously used to differentiate lesions in patients with brain tumors. The aim of this work was to characterize the response of magnetic susceptibility differences in malignant brain tumors and surrounding edema to hyperoxic and hypercapnic respiratory challenges. METHODS: Images of malignant brain tumor patients (2 glioblastoma multiforme, 2 anaplastic astrocytoma, 1 brain metastasis) with clinical MRI exams (contrast-enhanced T1w) were acquired at 3T...
December 5, 2017: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/29221588/eau-thermale-d%C3%A2-av%C3%A3-ne-et-dermatite-atopique-av%C3%A3-ne%C3%A2-s-thermal-water-and-atopic-dermatitis
#14
D Guerrero, E Garrigue
Atopic dermatitis (AD) is the most frequent disease treated at the Avène hydrotherapy center. Children represent a large part of the population due to the high prevalence of AD in early childhood. Avène thermal spring water (ATSW) has been known for its therapeutic effects since the middle of the 18th century. It has been greatly studied over the last decades, with a comprehensive fundamental, pharmaco-clinical and clinical approach. Cohort studies using the Scoring Atopic Dermatitis (SCORAD) clinical score and the Dermatology Life Quality Index (DLQI) or the Children's Dermatology Life Quality Index [CDLQI]) quality of life scores, allowed to confirm the clinical results obtained from the previous studies...
January 2017: Annales de Dermatologie et de Vénéréologie
https://www.readbyqxmd.com/read/29221505/the-politics-of-socioeconomic-status-how-socioeconomic-status-may-influence-political-attitudes-and-engagement
#15
REVIEW
Jazmin L Brown-Iannuzzi, Kristjen B Lundberg, Stephanie McKee
Socioeconomic status is hypothesized to be one factor informing political attitudes and actions. Presumably, this relationship is rooted in economic self-interest, with individuals preferring policies that would benefit them financially. In addition, these economic policy preferences are assumed to translate into political action. However, the relationships between socioeconomic status and political attitudes and behavior, as well as the psychological mechanisms associated with those relationships, are not straightforward...
December 2017: Current Opinion in Psychology
https://www.readbyqxmd.com/read/29221475/a-critical-realist-evaluation-of-a-music-therapy-intervention-in-palliative-care
#16
Sam Porter, Tracey McConnell, Mike Clarke, Jenny Kirkwood, Naomi Hughes, Lisa Graham-Wisener, Joan Regan, Miriam McKeown, Kerry McGrillen, Joanne Reid
BACKGROUND: Music therapy is increasingly used as an adjunct therapy to support symptom management in palliative care. However, studies to date have paid little attention to the processes that lead to changes in patient outcomes. To fill this gap, we examined the processes and experiences involved in the introduction of music therapy as an adjunct complementary therapy to palliative care in a hospice setting in the United Kingdom (UK). METHODS: Using a realistic evaluation approach, we conducted a qualitative study using a variety of approaches...
December 8, 2017: BMC Palliative Care
https://www.readbyqxmd.com/read/29221410/trapping-and-escape-in-a-turbid-medium
#17
P L Krapivsky, S Redner
We investigate the absorption of diffusing molecules in a fluid-filled spherical beaker that contains many small reactive traps. The molecules are absorbed either by hitting a trap or by escaping via the beaker walls. In the physical situation where the number N of traps is large and their radii a are small compared to the beaker radius R, the fraction of molecules E that escape to the beaker wall and the complementary fraction T that eventually are absorbed by the traps depend only on the dimensionless parameter combination λ = Na/R...
December 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29221069/transmission-line-metamaterials-based-on-strongly-coupled-split-ring-complementary-split-ring-resonators
#18
Yu-Jhan Lin, Yu-Han Chang, Wei-Chen Chien, Watson Kuo
We experimentally studied the coupling between a double split ring resonator and a complementary split ring resonator. The greatest coupling occurs when the two resonators are separated by the average ring radius, and the dimensionless coupling is as large as 0.1, allowing a novel planar metamaterial based on this hybrid structure. The coupling strength can be varied up to a factor of 2 by changing the relative orientation of the split ring resonators. A 2×2 waveguide structure with -10 dB coupling factor can be achieved, and showing multi-mode plasmon-induced transparency...
November 27, 2017: Optics Express
https://www.readbyqxmd.com/read/29220541/yoga-for-stroke-rehabilitation
#19
REVIEW
Maggie Lawrence, Francisco T Celestino Junior, Hemilianna Hs Matozinho, Lindsay Govan, Jo Booth, Jane Beecher
BACKGROUND: Stroke is a major health issue and cause of long-term disability and has a major emotional and socioeconomic impact. There is a need to explore options for long-term sustainable interventions that support stroke survivors to engage in meaningful activities to address life challenges after stroke. Rehabilitation focuses on recovery of function and cognition to the maximum level achievable, and may include a wide range of complementary strategies including yoga.Yoga is a mind-body practice that originated in India, and which has become increasingly widespread in the Western world...
December 8, 2017: Cochrane Database of Systematic Reviews
https://www.readbyqxmd.com/read/29220367/periodontitis-is-associated-with-significant-hepatic-fibrosis-in-patients-with-non-alcoholic-fatty-liver-disease
#20
William Alazawi, Eduardo Bernabe, David Tai, Tomasz Janicki, Polychronis Kemos, Salma Samsuddin, Wing-Kin Syn, David Gillam, Wendy Turner
BACKGROUND AND AIMS: Non-alcoholic fatty liver disease (NAFLD) has a bidirectional association with metabolic syndrome. It affects up to 30% of the general population, 70% of individuals with diabetes and 90% with obesity. The main histological hallmark of progressive NAFLD is fibrosis. There is a bidirectional epidemiological link between periodontitis and metabolic syndrome. NAFLD, periodontitis and diabetes share common risk factors, are characterised by inflammation and associated with changes in commensal bacteria...
2017: PloS One
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