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https://www.readbyqxmd.com/read/29224170/affinity-based-enrichment-techniques-for-the-genome-wide-analysis-of-5-hydroxymethylcytosine
#1
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/29224167/dna-methylation-analysis-of-free-circulating-dna-in-body-fluids
#2
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/29224154/large-scale-targeted-dna-methylation-analysis-using-bisulfite-padlock-probes
#3
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/29224149/nucleosome-occupancy-and-methylome-sequencing-nome-seq
#4
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/29224070/genome-wide-analysis-of-dna-methylation-in-single-cells-using-a-post-bisulfite-adapter-tagging-approach
#5
Heather J Lee, Sébastien A Smallwood
DNA methylation is an epigenetic mark implicated in the regulation of key biological processes. Using high-throughput sequencing technologies and bisulfite-based approaches, it is possible to obtain comprehensive genome-wide maps of the mammalian DNA methylation landscape with a single-nucleotide resolution and absolute quantification. However, these methods were only applicable to bulk populations of cells. Here, we present a protocol to perform whole-genome bisulfite sequencing on single cells (scBS-Seq) using a post-bisulfite adapter tagging approach...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29223141/molecular-and-functional-characterization-of-choline-transporter-like-proteins-in-esophageal-cancer-cells-and-potential-therapeutic-targets
#6
Fumiaki Nagashima, Ryohta Nishiyama, Beniko Iwao, Yuiko Kawai, Chikanao Ishii, Tsuyoshi Yamanaka, Hiroyuki Uchino, Masato Inazu
In this study, we examined the molecular and functional characterization of choline uptake in the human esophageal cancer cells. In addition, we examined the influence of various drugs on the transport of [3H]choline, and explored the possible correlation between the inhibition of choline uptake and apoptotic cell death. We found that both choline transporter-like protein 1 (CTL1) and CTL2 mRNAs and proteins were highly expressed in esophageal cancer cell lines (KYSE series). CTL1 and CTL2 were located in the plasma membrane and mitochondria, respectively...
December 8, 2017: Biomolecules & Therapeutics
https://www.readbyqxmd.com/read/29216714/fabrication-of-hyperbranched-block-statistical-copolymer-based-prodrug-with-dual-sensitivities-for-controlled-release
#7
Luping Zheng, Yunfei Wang, Xianshuo Zhang, Liwei Ma, Baoyan Wang, Xiangling Ji, Hua Wei
Dendrimer with hyperbranched structure and multivalent surface is regarded as one of the most promising candidates close to the ideal drug delivery systems, but the clinical translation and scale-up production of dendrimer has been hampered significantly by the synthetic difficulties. Therefore there is considerable scope for the development of novel hyperbranched polymer that can not only address the drawbacks of dendrimer but maintain its advantages. The reversible addition-fragmentation chain transfer self-condensing vinyl polymerization (RAFT-SCVP) technique has enabled facile preparation of segmented hyperbranched polymer (SHP) by using chain transfer monomer (CTM)-based double-head agent during the past decade...
December 7, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29216382/improving-crispr-cas-specificity-with-chemical-modifications-in-single-guide-rnas
#8
Daniel E Ryan, David Taussig, Israel Steinfeld, Smruti M Phadnis, Benjamin D Lunstad, Madhurima Singh, Xuan Vuong, Kenji D Okochi, Ryan McCaffrey, Magdalena Olesiak, Subhadeep Roy, Chong Wing Yung, Bo Curry, Jeffrey R Sampson, Laurakay Bruhn, Douglas J Dellinger
CRISPR systems have emerged as transformative tools for altering genomes in living cells with unprecedented ease, inspiring keen interest in increasing their specificity for perfectly matched targets. We have developed a novel approach for improving specificity by incorporating chemical modifications in guide RNAs (gRNAs) at specific sites in their DNA recognition sequence ('guide sequence') and systematically evaluating their on-target and off-target activities in biochemical DNA cleavage assays and cell-based assays...
December 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29215886/bibenzyl-based-meroterpenoid-enantiomers-from-the-chinese-liverwort-radula-sumatrana
#9
Xiao Wang, Lin Li, Rongxiu Zhu, Jiaozhen Zhang, Jinchuan Zhou, Hongxiang Lou
Six new pairs of bibenzyl-based meroterpenoid enantiomers, (±)-rasumatranin A-D (1-4) and (±)-radulanin M and N (5 and 6), and six known compounds were isolated from the adnascent Chinese liverwort, Radula sumatrana. Their structures were elucidated based on spectroscopic data and chiral phase HPLC-ECD analyses. The structures of 1 and 7 were also confirmed by single-crystal X-ray diffraction analysis. Cytotoxicity tests of the isolated compounds showed that 6-hydroxy-3-methyl-8-phenylethylbenzo[b]oxepin-5-one (8) showed activity against the human cancer cell lines MCF-7, PC-3, and SMMC-7721, with IC50 values of 3...
December 7, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/29200710/identification-of-hepatoprotective-constituents-in-limonium-tetragonum-and-development-of-simultaneous-analysis-method-using-high-performance-liquid-chromatography
#10
Jae Sun Lee, Yun Na Kim, Na-Hyun Kim, Jeong-Doo Heo, Min Hye Yang, Jung-Rae Rho, Eun Ju Jeong
Background: Limonium tetragonum, a naturally salt-tolerant halophyte, has been studied recently and is of much interest to researchers due to its potent antioxidant and hepatoprotective activities. Objective: In the present study, we attempted to elucidate bioactive compounds from ethyl acetate (EtOAc) soluble fraction of L. tetragonum extract. Furthermore, the simultaneous analysis method of bioactive EtOAc fraction of L. tetragonum has been developed using high-performance liquid chromatography (HPLC)...
October 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/29197629/pharmacological-modulation-of-hypoxia-induced-respiratory-neuroplasticity
#11
REVIEW
Sara Turner, Kristi Streeter, John Greer, Gordon S Mitchell, David D Fuller
Hypoxia elicits complex cell signaling mechanisms in the respiratory control system that can produce long-lasting changes in respiratory motor output. In this article, we review experimental approaches used to elucidate signaling pathways associated with hypoxia, and summarize current hypotheses regarding the intracellular signaling pathways evoked by intermittent exposure to hypoxia. We review data showing that pharmacological treatments can enhance neuroplastic responses to hypoxia. Original data are included to show that pharmacological modulation of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) function can reveal a respiratory neuroplastic response to a single, brief hypoxic exposure in anesthetized mice...
November 29, 2017: Respiratory Physiology & Neurobiology
https://www.readbyqxmd.com/read/29182515/sesquiterpenes-from-the-saudi-red-sea-litophyton-arboreum-with-their-cytotoxic-and-antimicrobial-activities
#12
Lamia T Abou El-Kassem, Usama W Hawas, Samy K El-Desouky, Radwan Al-Farawati
A new pseudoguaiane-type sesquiterpene named litopharbol (1) was isolated from the methanolic extract of the Red Sea soft coral Litophyton arboreum, along with known sesquiterpenoids alismol (2), alismorientol B (3), teuhetenone A (4), and calamusin I (5); steroid, 24-methyl-cholesta-5,24(28)-diene-3β-ol (6), alkyl glyceryl ether, chimyl alcohol (7); sphingolipid, erythro-N-dodecanoyl-docosasphinga-(4E,8E)-dienine (8); and nitrogenous bases, thymine (9) and thymidine (10). The structures were determined on the basis of nuclear magnetic resonance (NMR) spectroscopic (1D and 2D NMR data including heteronuclear single quantum coherence spectroscopy, heteronuclear multiple-bond correlation spectroscopy, and nuclear Overhauser effect spectroscopy) and mass spectrometric analyses...
November 28, 2017: Zeitschrift Für Naturforschung. C, A Journal of Biosciences
https://www.readbyqxmd.com/read/29178065/how-far-can-mitochondrial-dna-drive-the-disease
#13
Hongzhi Sun, Weibin Shi, Xiangdong Wang
Mitochondria are one of the dominant drivers for producing cellular energy to meet a large number of biological functions, of which the mitochondrial DNA (mtDNA) is the control center of energetic driving force and the dominant driver of mitochondrial molecular diversification. mtDNA transcription generates the necessary RNAs to regulate the extent and nature of mtRNA post-transcriptional modifications and the activity of nucleus-encoded enzymes. With a special focus on mtDNA, the current volume aims to overview the biology and structures of mtDNA, regulatory roles of mtDNA in lung diseases, or involvement of mtDNA in metabolism...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29176845/minimal-2-o-methyl-phosphorothioate-linkage-modification-pattern-of-synthetic-guide-rnas-for-increased-stability-and-efficient-crispr-cas9-gene-editing-avoiding-cellular-toxicity
#14
Megan Basila, Melissa L Kelley, Anja van Brabant Smith
Since its initial application in mammalian cells, CRISPR-Cas9 has rapidly become a preferred method for genome engineering experiments. The Cas9 nuclease is targeted to genomic DNA using guide RNAs (gRNA), either as the native dual RNA system consisting of a DNA-targeting CRISPR RNA (crRNA) and a trans-activating crRNA (tracrRNA), or as a chimeric single guide RNA (sgRNA). Entirely DNA-free CRISPR-Cas9 systems using either Cas9 protein or Cas9 mRNA and chemically synthesized gRNAs allow for transient expression of CRISPR-Cas9 components, thereby reducing the potential for off-targeting, which is a significant advantage in therapeutic applications...
2017: PloS One
https://www.readbyqxmd.com/read/29175600/forensic-dna-methylation-profiling-from-minimal-traces-how-low-can-we-go
#15
Jana Naue, Huub C J Hoefsloot, Ate D Kloosterman, Pernette J Verschure
Analysis of human DNA methylation (DNAm) can provide additional investigative leads in crime cases, e.g. the type of tissue or body fluid, the chronological age of an individual, and differentiation between identical twins. In contrast to the genetic profile, the DNAm level is not the same in every cell. At the single cell level, DNAm represents a binary event at a defined CpG site (methylated versus non-methylated). The DNAm level from a DNA extract however represents the average level of methylation of the CpG of interest of all molecules in the forensic sample...
November 13, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29171222/-molecular-regulative-mechanisms-of-aging-and-interventional-effects-of-chinese-herbal-medicine
#16
REVIEW
Bu-Hui Liu, Yi-Huang Gu, Yue Tu, Wei-Ming He, Wei Wu, Ying-Lu Liu, Zi-Yue Wan, Yi-Gang Wan
Aging is a gradual process during the loss of functions in cells,organs and tissues by time. The molecular mechanisms of aging-related theories include the classical ones such as telomere,oxygen radical and nonenzymatic glycosylation,as well as the newly proposed ones such as DNA methylation,mitochondrial DNA (mtDNA)and autophagy. The latest study showed the anti-aging effect of autophagy in hematopoietic stem cells. In recent years,based on the molecular regulative mechanisms of aging,a number of the promising anti-aging drugs have been found,including nicotinamide mononucleotide(NMN)and FOXO4-DRI,a peptide of anti-aging...
August 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29161231/epigenetic-regulation-mechanisms-of-microrna-expression
#17
Sara Morales, Mariano Monzo, Alfons Navarro
MicroRNAs (miRNAs) are single-stranded RNAs of 18-25 nucleotides that regulate gene expression at the post-transcriptional level. They are involved in many physiological and pathological processes, including cell proliferation, apoptosis, development and carcinogenesis. Because of the central role of miRNAs in the regulation of gene expression, their expression needs to be tightly controlled. Here, we summarize the different mechanisms of epigenetic regulation of miRNAs, with a particular focus on DNA methylation and histone modification...
November 21, 2017: Biomolecular Concepts
https://www.readbyqxmd.com/read/29155286/sulfur-mustard-induced-epigenetic-modifications-over-time-a-pilot-study
#18
Thilo Simons, Dirk Steinritz, Birgit Bölck, Annette Schmidt, Tanja Popp, Horst Thiermann, Thomas Gudermann, Wilhelm Bloch, Kai Kehe
The chemical warfare agent sulfur mustard (SM) can cause long-term health effects that may occur even years after a single exposure. The underlying pathophysiology is unknown, but epigenetic mechanisms are discussed as feasible explanation. "Epigenetics" depicts regulation of gene function without affecting the DNA sequence itself. DNA-methylation and covalent histone modifications (methylation or acetylation) are regarded as important processes. In the present in vitro study using early endothelial cells (EEC), we analyzed SM-induced DNA methylation over time and compared results to an in vivo skin sample that was obtained approx...
November 16, 2017: Toxicology Letters
https://www.readbyqxmd.com/read/29154989/targeting-bromodomain-and-extraterminal-proteins-in-breast-cancer
#19
REVIEW
Jennifer M Sahni, Ruth A Keri
Breast cancer is a collection of distinct tumor subtypes that are driven by unique gene expression profiles. These transcriptomes are controlled by various epigenetic marks that dictate which genes are expressed and suppressed. During carcinogenesis, extensive restructuring of the epigenome occurs, including aberrant acetylation, alteration of methylation patterns, and accumulation of epigenetic readers at oncogenes. As epigenetic alterations are reversible, epigenome-modulating drugs could provide a mechanism to silence numerous oncogenes simultaneously...
November 15, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/29143354/synthesis-and-biological-properties-of-radiohalogenated-%C3%AE-%C3%AE-disubstituted-amino-acids-for-pet-and-spect-imaging-of-amino-acid-transporters-aats
#20
Mark M Goodman, Weiping Yu, Nashwa Jarkas
Fluorine-18 and iodine-123 labeled non-natural alicyclic and methyl branched disubstituted α,α-amino acids are a diverse and useful class of tumor imaging agents suitable for positron emission tomography (PET) and single photon emission computed tomography (SPECT). These tracers target the increased expression of the cell membrane amino acid transporter systems L, ASC and A exhibited by many human tumor cells. The most established clinical use for these radiolabeled amino acids is imaging primary and recurrent gliomas, and primary, recurrent and metastatic prostate cancer...
November 16, 2017: Journal of Labelled Compounds & Radiopharmaceuticals
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