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https://www.readbyqxmd.com/read/29224215/deleterious-variants-in-dchs1-are-prevalent-in-sporadic-cases-of-mitral-valve-prolapse
#1
Alisson Clemenceau, Jean-Christophe Bérubé, Paméla Bélanger, Nathalie Gaudreault, Maxime Lamontagne, Oumhani Toubal, Marie-Annick Clavel, Romain Capoulade, Patrick Mathieu, Philippe Pibarot, Yohan Bosse
BACKGROUND: A recent study identified DCHS1 as a causal gene for mitral valve prolapse. The goal of this study is to investigate the presence and frequency of known and novel variants in this gene in 100 asymptomatic patients with moderate to severe organic mitral regurgitation. METHODS: DNA sequencing assays were developed for two previously identified functional missense variants, namely p.R2330C and p.R2513H, and all 21 exons of DCHS1. Pathogenicity of variants was evaluated in silico...
December 10, 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/29224209/sircle-a-randomised-controlled-cost-comparison-of-self-administered-short-course-isoniazid-and-rifapentine-for-cost-effective-latent-tuberculosis-eradication
#2
Justin T Denholm, Emma S McBryde, Damon Eisen, Alan Street, Elizabeth Matchett, Caroline Chen, Thomas Shultz, Beverly Biggs, Karin Leder
BACKGROUND: Currently, treatment of latent tuberculosis infection (LTBI) in Australia consists most commonly of a 9-month course of isoniazid (9H). A 3-month course of weekly isoniazid and rifapentine (3HP) has been shown to be as effective as 9 months of daily isoniazid, and associated with less hepatotoxicity; however, rifapentine is not currently available in Australia. Introduction of this regimen would have apparent advantages for people with LTBI in Victoria by safely shortening duration of LTBI therapy...
December 2017: Internal Medicine Journal
https://www.readbyqxmd.com/read/29224170/affinity-based-enrichment-techniques-for-the-genome-wide-analysis-of-5-hydroxymethylcytosine
#3
John P Thomson, Richard R Meehan
Since its initial characterization in 2009 there has been a great degree of interest in comparative profiling of 5-hydroxymethylcytosine (5hmC) nucleotides in vertebrate DNA. Through a host of genome-wide studies the distribution of 5hmC has been mapped in a range of cell lines, tissue types and organisms; the majority of which have been generated through affinity-based methods for 5hmC enrichment. Although recent advances in the field have resulted in the ability to investigate the levels of both methylated and hydroxymethylated cytosines at single base resolution, such studies are still relatively cost-prohibitive as well as technically challenging...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224168/tet-assisted-bisulfite-sequencing-tab-seq
#4
Miao Yu, Dali Han, Gary C Hon, Chuan He
5-Hydroxymethylcytosine (5hmC) is a modified form of cytosine, which has recently been found in mammalian cells and tissues. 5hmC is derived from 5-methylcytosine (5mC) by Ten-eleven translocation (TET) family protein-mediated oxidation and may regulate gene expression. Numerous affinity-based profiling methods have been developed to help understand the exact function of 5hmC in the genome. However, these methods have a relatively low resolution (~100 bp) without quantitative information of the modification percentage on each site...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224167/dna-methylation-analysis-of-free-circulating-dna-in-body-fluids
#5
Maria Jung, Glen Kristiansen, Dimo Dietrich
Circulating cell-free DNA in body fluids is an analyte of great interest in basic and clinical research. The analyses of DNA methylation and hydroxymethylation patterns in body fluids might allow one to determine the certain state of a disease, in particular of cancer. DNA methylation biomarkers in liquid biopsies, i.e. blood plasma samples, may help optimizing personalized therapy for individual patients. DNA methylation analyses of specific loci usually require a bisulfite conversion of the DNA, which requires a sufficiently high amount of DNA at the appropriate concentration...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224162/methylation-specific-multiplex-ligation-dependent-probe-amplification-ms-mlpa
#6
Cathy B Moelans, Lilit Atanesyan, Suvi P Savola, Paul J van Diest
This chapter describes a method for the rapid assessment of promoter hypermethylation levels or methylation of imprinted regions in human genomic DNA extracted from various sources using methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA). Multiplex ligation-dependent probe amplification (MLPA) is a powerful and easy-to-perform PCR-based technique that can identify gains, amplifications, losses, deletions, methylation and mutations of up to 55 targets in a single reaction, while requiring only minute quantities of DNA (about 50 ng) extracted from blood, fresh frozen or formalin-fixed paraffin-embedded materials...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224161/quantitative-region-specific-dna-methylation-analysis-by-the-epityper%C3%A2-technology
#7
Sonja Kunze
DNA methylation plays a profound role in development and health as well as development and progression of disease. High-throughput quantitative DNA methylation analysis is therefore crucial for the study of the normal physiology of the epigenome and its dysregulation in disease. Many target areas are identified by a range of emerging genome-wide cytosine methylation techniques, but these whole genome scans usually only provide methylation data for a few individual CpG sites (CpGs) within a region. The EpiTYPER™ assay is a region-specific method for the detection and quantitative analysis of DNA methylation that allows performing a high-resolution scan of selected regions...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224157/quantitative-dna-methylation-analysis-at-single-nucleotide-resolution-by-pyrosequencing%C3%A2
#8
Florence Busato, Emelyne Dejeux, Hafida El Abdalaoui, Ivo Glynne Gut, Jörg Tost
Many protocols for gene-specific DNA methylation analysis are either labor intensive, not quantitative and/or limited to the measurement of the methylation status of only one or very few CpG positions. Pyrosequencing is a real-time sequencing technology that overcomes these limitations. After bisulfite modification of genomic DNA, a region of interest is amplified by PCR with one of the two primers being biotinylated. The PCR generated template is rendered single-stranded and a pyrosequencing primer is annealed to analyze quantitatively cytosine methylation...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224154/large-scale-targeted-dna-methylation-analysis-using-bisulfite-padlock-probes
#9
Dinh Diep, Nongluk Plongthongkum, Kun Zhang
Bisulfite padlock probes (BSPP) are a method for the targeted quantification of DNA methylation in mammalian genomes. They can simultaneously characterize the level of methylcytosine modification in a large number of targeted regions at single-base resolution. A major advantage of BSPP is that it allows the flexible capture of an arbitrary subset of genomic regions (hundreds to hundreds of thousands of genomic loci) in single-tube reactions. Large number of samples can be processed efficiently and converted into multiplexed sequencing libraries with only three enzymatic steps, without the conventional library preparation procedures...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224153/multiplexed-dna-methylation-analysis-of-target-regions-using-microfluidics-fluidigm
#10
Martyna Adamowicz, Klio Maratou, Timothy J Aitman
Whole genome shotgun bisulfite sequencing is a method used to generate genome-wide methylation profiles. There are many available protocols to validate the results of this genome-wide method, but they mostly share the limitation of measuring methylation at a small number of CpG positions in small numbers of samples. We developed a multiplexed DNA methylation analysis protocol, which allows for the simultaneous quantitative measurement of cytosine methylation at single nucleotide resolution in 48 PCR amplicons and 48 samples utilizing the microfluidic system established by Fluidigm...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224152/microdroplet-pcr-for-highly-multiplexed-targeted-bisulfite-sequencing
#11
H Kiyomi Komori, Sarah A LaMere, Traver Hart, Steven R Head, Ali Torkamani, Daniel R Salomon
Many methods exist for examining CpG DNA methylation. However, many of these are qualitative, laborious to apply to a large number of genes simultaneously, or are not easy to target to specific regions of interest. Microdroplet PCR-based bisulfite sequencing allows for quantitative single base resolution analysis of investigator selected regions of interest. Following bisulfite conversion of genomic DNA, targeted microdroplet PCR is conducted with custom primer libraries. Samples are then fragmented, concatenated, and sequenced by high-throughput sequencing...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224149/nucleosome-occupancy-and-methylome-sequencing-nome-seq
#12
Fides D Lay, Theresa K Kelly, Peter A Jones
Various methodologies are available to interrogate specific components of epigenetic mechanisms such as DNA methylation or nucleosome occupancy at both the locus-specific and the genome-wide level. It has become increasingly clear, however, that comprehension of the functional interactions between epigenetic mechanisms is critical for understanding how cellular transcription programs are regulated or deregulated during normal and disease development. The Nucleosome Occupancy and Methylome sequencing (NOMe-seq) assay allows us to directly measure the relationship between DNA methylation and nucleosome occupancy by taking advantage of the methyltransferase M...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224147/comprehensive-whole-dna-methylome-analysis-by-integrating-medip-seq-and-mre-seq
#13
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/29224143/multiplexed-reduced-representation-bisulfite-sequencing-with-magnetic-bead-fragment-size-selection
#14
William P Accomando, Karin B Michels
Reduced representation bisulfite sequencing (RRBS) is a technique for assessing genome-wide DNA methylation in an organism whose genome has been fully sequenced. It allows researchers to target gene regions with particular CpG densities, thereby selecting the desired genomic contexts. Here, we describe an approach that uses magnetic beads to accomplish this selection. In addition, the use of indexed, methylated adapters enables up to 12 samples to be pooled, and subjected to multiplexed RRBS in a single-sequencing lane...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224132/treatment-of-mild-to-moderate-hypoglycemia-in-patients-with-type-1-diabetes-treated-with-insulin-pump-therapy-are-current-recommendations-effective
#15
Véronique Gingras, Katherine Desjardins, Mohamed Raef Smaoui, Valérie Savard, Virginie Messier, Ahmad Haidar, Laurent Legault, Rémi Rabasa-Lhoret
AIMS: Mild-to-moderate hypoglycemia (blood glucose < 4.0 mmol/L) is recommended to be treated with 15 g of carbohydrates and to repeat the treatment if hypoglycemia persists after 15 min. This recommendation was established before intensive insulin therapy and based on studies using insulin with different pharmacokinetic profiles from actual insulin analogs showing that 15 g of glucose increases blood glucose by ~ 1.5 mmol/L in 15 min. We aimed to explore the effect of current recommended treatment of mild-to-moderate hypoglycemia in type 1 diabetes (T1D) participants and factors associated with treatment effectiveness...
December 9, 2017: Acta Diabetologica
https://www.readbyqxmd.com/read/29224131/characterization-of-tomato-leaf-curl-purple-vein-virus-a-new-monopartite-new-world-begomovirus-infecting-tomato-in-northeast-brazil
#16
M A Macedo, L C Albuquerque, M R Maliano, J O Souza, M R Rojas, A K Inoue-Nagata, R L Gilbertson
A new begomovirus species was identified from tomato plants with upward leaf curling and purple vein symptoms, which was first identified in the Piaui state of Northeast (NE) Brazil in 2014. Tomato leaf samples were collected in 2014 and 2016, and PCR with degenerate primers revealed begomovirus infection. Rolling circle amplification and restriction enzyme digestion indicated a single genomic DNA of ~ 2.6 kb. Cloning and sequencing revealed a genome organization similar to DNA-A components of New World (NW) bipartite begomoviruses, with no DNA-B...
December 9, 2017: Archives of Virology
https://www.readbyqxmd.com/read/29224117/heated-communities-large-inter-and-intraspecific-variation-in-heat-tolerance-across-trophic-levels-of-a-soil-arthropod-community
#17
Oscar Franken, Milou Huizinga, Jacintha Ellers, Matty P Berg
Temperature extremes are predicted to increase in frequency, intensity and duration under global warming and are believed to significantly affect community composition and functioning. However, the effect of extreme climatic events on communities remains difficult to predict, especially because species can show dissimilar responses to abiotic changes, which may affect the outcome of species interactions. To anticipate community responses we need knowledge on within and among species variation in stress tolerance...
December 9, 2017: Oecologia
https://www.readbyqxmd.com/read/29224116/chemical-shift-assignments-of-the-partially-deuterated-fyn-sh2-sh3-domain
#18
Fabien Kieken, Karine Loth, Nico van Nuland, Peter Tompa, Tom Lenaerts
Src Homology 2 and 3 (SH2 and SH3) are two key protein interaction modules involved in regulating the activity of many proteins such as tyrosine kinases and phosphatases by respective recognition of phosphotyrosine and proline-rich regions. In the Src family kinases, the inactive state of the protein is the direct result of the interaction of the SH2 and the SH3 domain with intra-molecular regions, leading to a closed structure incompetent with substrate modification. Here, we report the 1H, 15N and 13C backbone- and side-chain chemical shift assignments of the partially deuterated Fyn SH3-SH2 domain and structural differences between tandem and single domains...
December 9, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/29224077/gene-profiling-and-t-cell-receptor-sequencing-from-antigen-specific-cd4-t-cells
#19
Marie Holt, Anne Costanzo, Louis Gioia, Brian Abe, Andrew I Su, Luc Teyton
The paucity of pathogenic T cells in circulating blood limits the information delivered by bulk analysis. Toward diagnosis and monitoring of treatments of autoimmune diseases, we have devised single-cell analysis approaches capable of identifying and characterizing rare circulating CD4 T cells.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224072/snp-discovery-from-single-and-multiplex-genome-assemblies-of-non-model-organisms
#20
Phillip A Morin, Andrew D Foote, Christopher M Hill, Benoit Simon-Bouhet, Aimee R Lang, Marie Louis
Population genetic studies of non-model organisms often rely on initial ascertainment of genetic markers from a single individual or a small pool of individuals. This initial screening has been a significant barrier to beginning population studies on non-model organisms (Aitken et al., Mol Ecol 13:1423-1431, 2004; Morin et al., Trends Ecol Evol 19:208-216, 2004). As genomic data become increasingly available for non-model species, SNP ascertainment from across the genome can be performed directly from published genome contigs and short-read archive data...
2018: Methods in Molecular Biology
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