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single cell methylation

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https://www.readbyqxmd.com/read/28644607/electrochemical-exfoliation-of-graphite-in-aqueous-sodium-halide-electrolytes-towards-low-oxygen-content-graphene-for-energy-and-environmental-applications
#1
Jose Maria Munuera, Juan Ignacio Paredes, Marina Enterria, Ana Pagán, Silvia Villar-Rodil, Manuel Fernando R Pereira, J I Martins, José L Figueiredo, Jose Luis Cenis, Amelia Martinez-Alonso, Juan Manuel D Tascon
Graphene and graphene-based materials have shown great promise in many technological applications, but their large-scale production and processing by simple and cost-effective means still constitute significant issues in the path of their widespread implementation. Here, we investigate a straightforward method for the preparation of a ready-to-use and low oxygen content graphene material that is based on electrochemical (anodic) delamination of graphite in aqueous medium with sodium halides as the electrolyte...
June 23, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28638377/a-novel-bromodomain-inhibitor-reverses-hiv-1-latency-through-specific-binding-with-brd4-to-promote-tat-and-p-tefb-association
#2
Huachao Huang, Shuai Liu, Maxime Jean, Sydney Simpson, He Huang, Mark Merkley, Tsuyoshi Hayashi, Weili Kong, Irene Rodríguez-Sánchez, Xiaofeng Zhang, Hailemichael O Yosief, Hongyu Miao, Jianwen Que, James J Kobie, James Bradner, Netty G Santoso, Wei Zhang, Jian Zhu
While combinatory antiretroviral therapy (cART) can effectively reduce HIV-1 viremia, it cannot eliminate HIV-1 infection. In the presence of cART, viral reservoirs remain latent, impeding the cure of HIV-1/AIDS. Recently, latency-reversing agents (LRAs) have been developed with the intent of purging latent HIV-1, providing an intriguing strategy for the eradication of the residual viral reservoirs. Our earlier studies show that the first-generation, methyl-triazolo bromodomain, and extra-terminal domain inhibitor (BETi), JQ1, facilitates the reversal of HIV-1 latency...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28635273/a-direct-bandgap-copper-antimony-halide-perovskite
#3
Brenda Vargas, Estrella Ramos, Enrique Pérez-Gutiérrez, Juan C Alonso, Diego Solis-Ibarra
Since the establishment of perovskite solar cells (PSCs) there has been an intense search for alternative materials to replace lead and improve their stability towards moisture and light. As single-metal perovskite structures have yielded unsatisfactory performances, an alternative is the use of double perovskites that incorporate a combination of metals. To this day, only a handful of these compounds have been synthesized, but most of them have indirect bandgaps and/or do not have bandgaps energies well-suited for photovoltaic applications...
June 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28630425/reconstructing-cell-cycle-pseudo-time-series-via-single-cell-transcriptome-data
#4
Zehua Liu, Huazhe Lou, Kaikun Xie, Hao Wang, Ning Chen, Oscar M Aparicio, Michael Q Zhang, Rui Jiang, Ting Chen
Single-cell mRNA sequencing, which permits whole transcriptional profiling of individual cells, has been widely applied to study growth and development of tissues and tumors. Resolving cell cycle for such groups of cells is significant, but may not be adequately achieved by commonly used approaches. Here we develop a traveling salesman problem and hidden Markov model-based computational method named reCAT, to recover cell cycle along time for unsynchronized single-cell transcriptome data. We independently test reCAT for accuracy and reliability using several data sets...
June 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28630288/intact-pirna-pathway-prevents-l1-mobilization-in-male-meiosis
#5
Simon J Newkirk, Suman Lee, Fiorella C Grandi, Valeriya Gaysinskaya, James M Rosser, Nicole Vanden Berg, Cathryn A Hogarth, Maria C N Marchetto, Alysson R Muotri, Michael D Griswold, Ping Ye, Alex Bortvin, Fred H Gage, Jef D Boeke, Wenfeng An
The PIWI-interacting RNA (piRNA) pathway is essential for retrotransposon silencing. In piRNA-deficient mice, L1-overexpressing male germ cells exhibit excessive DNA damage and meiotic defects. It remains unknown whether L1 expression simply highlights piRNA deficiency or actually drives the germ-cell demise. Specifically, the sheer abundance of genomic L1 copies prevents reliable quantification of new insertions. Here, we developed a codon-optimized L1 transgene that is controlled by an endogenous mouse L1 promoter...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28629864/structure-function-relationships-in-human-d-aspartate-oxidase-characterisation-of-variants-corresponding-to-known-single-nucleotide-polymorphisms
#6
Masumi Katane, Ryo Kanazawa, Risa Kobayashi, Megumi Oishi, Kazuki Nakayama, Yasuaki Saitoh, Tetsuya Miyamoto, Masae Sekine, Hiroshi Homma
D-Aspartate oxidase (DDO) is a degradative enzyme that is stereospecific for the acidic amino acid D-aspartate, an endogenous agonist of the N-methyl-D-aspartate (NMDA) receptor. Dysregulation of NMDA receptor-mediated neurotransmission has been implicated in the onset of various neuropsychiatric disorders including schizophrenia and in chronic pain. Thus, appropriate regulation of the amount of D-aspartate is believed to be important for maintaining proper neural activity in the nervous system. Herein, the effects of the non-synonymous single nucleotide polymorphisms (SNPs) R216Q and S308N on several properties of human DDO were examined...
June 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28621329/single-cell-multi-omics-sequencing-of-mouse-early-embryos-and-embryonic-stem-cells
#7
Fan Guo, Lin Li, Jingyun Li, Xinglong Wu, Boqiang Hu, Ping Zhu, Lu Wen, Fuchou Tang
Single-cell epigenome sequencing techniques have recently been developed. However, the combination of different layers of epigenome sequencing in an individual cell has not yet been achieved. Here, we developed a single-cell multi-omics sequencing technology (single-cell COOL-seq) that can analyze the chromatin state/nucleosome positioning, DNA methylation, copy number variation and ploidy simultaneously from the same individual mammalian cell. We used this method to analyze the reprogramming of the chromatin state and DNA methylation in mouse preimplantation embryos...
June 16, 2017: Cell Research
https://www.readbyqxmd.com/read/28619057/polysaccharide-compositions-of-collenchyma-cell-walls-from-celery-apium-graveolens-l-petioles
#8
Da Chen, Philip J Harris, Ian M Sims, Zoran Zujovic, Laurence D Melton
BACKGROUND: Collenchyma serves as a mechanical support tissue for many herbaceous plants. Previous work based on solid-state NMR and immunomicroscopy suggested collenchyma cell walls (CWs) may have similar polysaccharide compositions to those commonly found in eudicotyledon parenchyma walls, but no detailed chemical analysis was available. In this study, compositions and structures of cell wall polysaccharides of peripheral collenchyma from celery petioles were investigated. RESULTS: This is the first detailed investigation of the cell wall composition of collenchyma from any plant...
June 15, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28618935/heterogeneous-dna-methylation-status-in-same-cell-subpopulations-of-ovarian-cancer-tissues
#9
Qiling Li, Xue Xue, Wenzhi Li, Qi Wang, Lu Han, Tiffany Brunson, Wei Xu, Isfahan Chambers-Harris, Qing Wang, Xu Li, Li Ma, Qing Song
This study aims to explore the heterogeneous DNA methylation differences between individual single ovarian cancer cells isolated from the same formalin-fixed and paraffin-embedded human ovarian cancer tissue. Single cells were isolated by laser microdissection. Whole genome amplification and polymerase chain reaction purification were performed on the converted genomic DNA. Target primers designed for checking DNA methylation were used in polymerase chain reaction reactions to amplify special fragments. Sequencing was performed to analyze the heterogeneous DNA methylation statuses of different single ovarian cancer cells...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28611598/early-paradoxical-increase-of-dopamine-a-neurochemical-study-of-olfactory-bulb-in-asymptomatic-and-symptomatic-mptp-treated-monkeys
#10
Christian Pifl, Harald Reither, Natalia Lopez-Gonzalez Del Rey, Carmen Cavada, Jose A Obeso, Javier Blesa
Parkinson's disease (PD) is a neurodegenerative disease with both motor and non-motor manifestations. Hyposmia is one of the early non-motor symptoms, which can precede motor symptoms by several years. The relationship between hyposmia and PD remains elusive. Olfactory bulb (OB) pathology shows an increased number of olfactory dopaminergic cells, protein aggregates and dysfunction of neurotransmitter systems. In this study we examined tissue levels of dopamine (DA) and serotonin (5-hydroxytryptamine, 5-HT) and their metabolites, of noradrenaline (NA) and of the amino acid neurotransmitters aspartate, glutamate, taurine and γ-aminobutyric acid in OBs of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) treated Macaca fascicularis in different stages, including monkeys who were always asymptomatic, monkeys who recovered from mild parkinsonian signs, and monkeys with stable moderate or severe parkinsonism...
2017: Frontiers in Neuroanatomy
https://www.readbyqxmd.com/read/28609193/dna-methylome-profiling-on-the-infinium-humanmethylation450-array-from-limiting-quantities-of-genomic-dna-from-a-single-small-archived-bloodspot
#11
Kripa Asrani, Gary M Shaw, Jasper Rine, Nicholas J Marini
AIMS: Archived newborn bloodspots are valuable sample collections for genetic and epigenetic disease research. However, they have often been stored for long periods of time, under less than ideal circumstances, and nucleic acid yields can be low, particularly when samples become limiting. We wished to determine whether the quantity and quality of genomic DNA (gDNA) isolated from a single, surgical bloodspot punch (2 mm dia.) were adequate for accurate and reliable DNA methylome profiling on the Illumina HumanMethylation450 array...
June 13, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28605464/strand-specific-cpg-hemimethylation-a-novel-epigenetic-modification-functional-for-genomic-imprinting
#12
Iris Patiño-Parrado, Álvaro Gómez-Jiménez, Noelia López-Sánchez, José M Frade
Imprinted genes are regulated by allele-specific differentially DNA-methylated regions (DMRs). Epigenetic methylation of the CpGs constituting these DMRs is established in the germline, resulting in a 5-methylcytosine-specific pattern that is tightly maintained in somatic tissues. Here, we show a novel epigenetic mark, characterized by strand-specific hemimethylation of contiguous CpG sites affecting the germline DMR of the murine Peg3, but not Snrpn, imprinted domain. This modification is enriched in tetraploid cortical neurons, a cell type where evidence for a small proportion of formylmethylated CpG sites within the Peg3-controlling DMR is also provided...
June 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28605387/a-simple-fractionated-extraction-method-for-the-comprehensive-analysis-of-metabolites-lipids-and-proteins-from-a-single-sample
#13
Mohamed Salem, Michal Bernach, Krzysztof Bajdzienko, Patrick Giavalisco
Understanding of complex biological systems requires the measurement, analysis and integration of multiple compound classes of the living cell, usually determined by transcriptomic, proteomic, metabolomics and lipidomic measurements. In this protocol, we introduce a simple method for the reproducible extraction of metabolites, lipids and proteins from biological tissues using a single aliquot per sample. The extraction method is based on a methyl tert-butyl ether: methanol: water system for liquid: liquid partitioning of hydrophobic and polar metabolites into two immiscible phases along with the precipitation of proteins and other macromolecules as a solid pellet...
June 1, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28598303/caulobacter-rhizosphaerae-sp-nov-a-stalked-bacterium-isolated-from-rhizosphere-soil
#14
Le-Ni Sun, En-Dong Yang, Xue-Ting Hou, Jie-Chao Wei, Zhuo-Xin Yuan, Wei-Yun Wang
The Gram-reaction-negative, aerobic, white- to pale-yellow-coloured and rod-shaped bacterium with a single polar flagellum or a stalk, designated strain 7F14T, was isolated from rhizosphere soil of cultivated watermelon (Citrullus lanatus) collected from Hefei, China. Growth of strain 7F14T was observed at pH 6.0-9.0, 10-30 °C and in the presence of 0-1 % (w/v) NaCl. Cells were catalase-negative and oxidase-positive. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain 7F14T formed a phyletic lineage within the genus Caulobacter of the family Caulobacteraceae and showed the highest 16S rRNA gene sequence similarities to Caulobacter henricii ATCC 15253T (98...
June 9, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28598109/-the-study-of-decitabine-effect-on-the-endometrial-carcinoma-xenografted-in-nude-mice
#15
Ran-Hong Li, Xue-Ping Wang, Hui Liu
OBJECTIVES: To explore the effect of the demethylation drug 5-Aza-CdR on endometrial carcinoma xenografted in nude mice. METHODS: Randomly assigned the mice into decitabine (AZA),cisplatin (DDP),medroxyprogesterone acetate (MPA),AZA+DDP,AZA+MPA,DDP+MPA and model groups (three in each group) after building the models of xenografted tumor by transplanting the HEC-1B cells on nude mice,and dealt them respectively with corresponding drugs (1 μg/g,single or combination) in the experiment groups and normal saline in model group (injected per 3 d,8 injections in total)...
November 2016: Sichuan da Xue Xue Bao. Yi Xue Ban, Journal of Sichuan University. Medical Science Edition
https://www.readbyqxmd.com/read/28595067/pentapeptides-for-the-treatment-of-small-cell-lung-cancer-optimisation-by-n-ind-alkyl-modification-of-the-tryptophan-side-chain
#16
Osama Haitham Abusara, Sally Freeman, Harmesh Singh Aojula
The pentapeptide, tert-Prenyl(4th)-NH2 (DMePhe-DTrp-Phe-DTrp(N-tert-prenyl)-Leu-NH2), has recently been reported by our group to exhibit properties of substance P (SP) antagonist G against small cell lung cancer (SCLC). In this study, we undertook a systematic structure activity investigation to optimise this lead compound to improve its in vitro anti-tumour activity and biocompatibility. A series of d-tryptophan (D-Trp) derivatives were synthesised, with a range of aliphatic N-alkyl chains (methyl to pentyl) on the indole nitrogen (N(ind))...
May 27, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28587138/toxin-variability-estimations-of-68-alexandrium-ostenfeldii-dinophyceae-strains-from-the-netherlands-reveal-a-novel-abundant-gymnodimine
#17
Helge Martens, Urban Tillmann, Kirsi Harju, Carmela Dell'Aversano, Luciana Tartaglione, Bernd Krock
Alexandrium ostenfeldii is a toxic dinoflagellate that has recently bloomed in Ouwerkerkse Kreek, The Netherlands, and which is able to cause a serious threat to shellfish consumers and aquacultures. We used a large set of 68 strains to the aim of fully characterizing the toxin profiles of the Dutch A. ostenfeldii in consideration of recent reports of novel toxins. Alexandrium ostenfeldii is known as a causative species of paralytic shellfish poisoning, and consistently in the Dutch population we determined the presence of several paralytic shellfish toxins (PST) including saxitoxin (STX), GTX2/3 (gonyautoxins), B1 and C1/C2...
May 26, 2017: Microorganisms
https://www.readbyqxmd.com/read/28581523/a-dna-methylation-map-of-human-cancer-at-single-base-pair-resolution
#18
E Vidal, S Sayols, S Moran, A Guillaumet-Adkins, M P Schroeder, R Royo, M Orozco, M Gut, I Gut, N Lopez-Bigas, H Heyn, M Esteller
Although single base-pair resolution DNA methylation landscapes for embryonic and different somatic cell types provided important insights into epigenetic dynamics and cell-type specificity, such comprehensive profiling is incomplete across human cancer types. This prompted us to perform genome-wide DNA methylation profiling of 22 samples derived from normal tissues and associated neoplasms, including primary tumors and cancer cell lines. Unlike their invariant normal counterparts, cancer samples exhibited highly variable CpG methylation levels in a large proportion of the genome, involving progressive changes during tumor evolution...
June 5, 2017: Oncogene
https://www.readbyqxmd.com/read/28578488/17%C3%AE-estradiol-increases-non-cpg-methylation-in-exon-1-of-the-rainbow-trout-oncorhynchus-mykiss-myod-gene
#19
Prasanthi P Koganti, Jian Wang, Beth Cleveland, Jianbo Yao
MyoD is an important myogenic transcription factor necessary for the differentiation of myogenic precursor cells (MPC) to form mature myotubes, a process essential for muscle growth. Epigenetic markers such as CpH methylation are known gene regulators that are important for the differentiation process. In this study, we investigated whether DNA methylation is a potential mechanism associated with the ability of 17β-estradiol (E2) to reduce MyoD gene expression and muscle growth in rainbow trout. Rainbow trout received a single intraperitoneal injection of E2 or the injection vehicle (control)...
June 3, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28576863/evolving-mistranslating-trnas-through-a-phenotypically-ambivalent-intermediate-in-saccharomyces-cerevisiae
#20
Matthew D Berg, Kyle S Hoffman, Julie Genereaux, Safee Mian, Ryan S Trussler, David B Haniford, Patrick O'Donoghue, Christopher J Brandl
The genetic code converts information from nucleic acid into protein. The genetic code was thought to be immutable, yet many examples in nature indicate that variations to the code provide a selective advantage. We used a sensitive selection system involving suppression of a deleterious allele (tti2-L187P) in Saccharomyces cerevisiae to detect mistranslation and identify mechanisms that allow genetic code evolution. Though tRNA(Ser) containing a proline anticodon (UGG) is toxic, using our selection system, we identified four tRNA(Ser)UGG variants, each with a single mutation, that mistranslate at a tolerable level...
June 2, 2017: Genetics
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