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single cell methylation

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https://www.readbyqxmd.com/read/28212413/scarless-deletion-of-up-to-seven-methyl-accepting-chemotaxis-genes-with-an-optimized-method-highlights-key-function-of-chem-in-salmonella-typhimurium
#1
Stefanie Hoffmann, Christiane Schmidt, Steffi Walter, Jennifer K Bender, Roman G Gerlach
Site-directed scarless mutagenesis is an essential tool of modern pathogenesis research. We describe an optimized two-step protocol for genome editing in Salmonella enterica serovar Typhimurium to enable multiple sequential mutagenesis steps in a single strain. The system is based on the λ Red recombinase-catalyzed integration of a selectable antibiotics resistance marker followed by replacement of this cassette. Markerless mutants are selected by expressing the meganuclease I-SceI which induces double-strand breaks in bacteria still harboring the resistance locus...
2017: PloS One
https://www.readbyqxmd.com/read/28210718/synthesis-and-epr-spectroscopic-characterization-of-the-perchlorotriarylmethyl-tricarboxylic-acid-radical-ptmtc-and-its-13-c-labelled-analogue-13c-ptmtc
#2
Marwa Elewa, Nadica Maltar-Strmečki, Mohamed M Said, Hosam A El Shihawy, Mohamed El-Sadek, Juliane Frank, Simon Drescher, Malte Drescher, Karsten Mäder, Dariush Hinderberger, Peter Imming
A hydrophilic tris(tetrachlorotriaryl)methyl (tetrachloro-TAM) radical labelled 50% with (13)C at the central carbon atom was prepared. The mixture of isotopologue radicals was characterised by continuous wave and pulsed X-band electron paramagnetic spectroscopy (EPS). For the pharmaceutical and medical applications planned, the quantitative influence of oxygen, viscosity, temperature and pH on EPR line widths was studied in aqueous buffer, DMSO, water-methanol and water-glycerol mixtures. Under in vivo conditions, pH can be disregarded...
February 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28209776/distance-dependent-gradient-in-nmdar-driven-spine-calcium-signals-along-tapering-dendrites
#3
Alison S Walker, Guilherme Neves, Federico Grillo, Rachel E Jackson, Mark Rigby, Cian O'Donnell, Andrew S Lowe, Gema Vizcay-Barrena, Roland A Fleck, Juan Burrone
Neurons receive a multitude of synaptic inputs along their dendritic arbor, but how this highly heterogeneous population of synaptic compartments is spatially organized remains unclear. By measuring N-methyl-d-aspartic acid receptor (NMDAR)-driven calcium responses in single spines, we provide a spatial map of synaptic calcium signals along dendritic arbors of hippocampal neurons and relate this to measures of synapse structure. We find that quantal NMDAR calcium signals increase in amplitude as they approach a thinning dendritic tip end...
February 16, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28205560/alkb-homolog-3-mediated-trna-demethylation-promotes-protein-synthesis-in-cancer-cells
#4
Yuko Ueda, Ikumi Ooshio, Yasuyuki Fusamae, Kaori Kitae, Megumi Kawaguchi, Kentaro Jingushi, Hiroaki Hase, Kazuo Harada, Kazumasa Hirata, Kazutake Tsujikawa
The mammalian AlkB homolog (ALKBH) family of proteins possess a 2-oxoglutarate- and Fe(II)-dependent oxygenase domain. A similar domain in the Escherichia coli AlkB protein catalyzes the oxidative demethylation of 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) in both DNA and RNA. AlkB homolog 3 (ALKBH3) was also shown to demethylate 1-meA and 3-meC (induced in single-stranded DNA and RNA by a methylating agent) to reverse the methylation damage and retain the integrity of the DNA/RNA. We previously reported the high expression of ALKBH3 in clinical tumor specimens and its involvement in tumor progression...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28203244/pistil-transcriptome-analysis-to-disclose-genes-and-gene-products-related-to-aposporous-apomixis-in-hypericum-perforatum-l
#5
Giulio Galla, Sara Zenoni, Linda Avesani, Lothar Altschmied, Paride Rizzo, Timothy F Sharbel, Gianni Barcaccia
Unlike sexual reproduction, apomixis encompasses a number of reproductive strategies, which permit maternal genome inheritance without genetic recombination and syngamy. The key biological features of apomixis are the circumvention of meiosis (i.e., apomeiosis), the differentiation of unreduced embryo sacs and egg cells, and their autonomous development in functional embryos through parthenogenesis, and the formation of viable endosperm either via fertilization-independent means or following fertilization with a sperm cell...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28202014/defensive-changes-in-maize-leaves-induced-by-feeding-of-mediterranean-corn-borer-larvae
#6
Rogelio Santiago, Ana Cao, Ana Butrón, Ana López-Malvar, Víctor M Rodríguez, Germán V Sandoya, Rosa A Malvar
BACKGROUND: Plants can respond to insect attack via defense mechanisms that reduce insect performance. In this study, we examined the effects of several treatments applied to two maize genotypes (one resistant, one susceptible) on the subsequent growth and survival of Sesamia nonagrioides Lef. (Mediterranean corn borer, MCB) larvae. The treatments were infestation with MCB larvae, application of MCB regurgitant upon wounding, wounding alone, or exposure to methyl jasmonate, and they were applied at the V6-V8 stage of maize development...
February 15, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28199463/effect-of-methyl-aminolevulinate-photodynamic-therapy-with-and-without-ablative-fractional-laser-treatment-in-patients-with-microinvasive-squamous-cell-carcinoma-a-randomized-clinical-trial
#7
Seung-Hwan Choi, Ki-Ho Kim, Ki-Hoon Song
Importance: Surgical excision is the standard treatment for cutaneous squamous cell carcinoma (SCC). However, microinvasive SCC (Clark level II) is limited to the papillary dermis, and it should be differentiated from invasive SCC. Ablative fractional laser-primed photodynamic therapy (AFL-PDT) may have enhanced efficacy. Objective: To compare 1 session of AFL-PDT with 2 sessions of conventional methyl aminolevulinate-PDT (MAL-PDT) for the treatment of microinvasive SCC...
February 15, 2017: JAMA Dermatology
https://www.readbyqxmd.com/read/28196677/molecular-modeling-docking-and-dynamics-simulations-of-the-dioclea-lasiophylla-mart-ex-benth-seed-lectin-an-edematogenic-and-hypernociceptive-protein
#8
Vanir Reis Pinto-Junior, Vinicius Jose Silva Osterne, Mayara Queiroz Santiago, Claudia Figueiredo Lossio, Celso Shiniti Nagano, Cintia Renata Costa Rocha, Jessica Catarine Frutuoso Nascimento, Francisco Lucas Faustino Nascimento, Ivanice Bezerra Silva, Antonia Simoni Oliveira, Jorge Luis Almeida Correia, Rodrigo Bainy Leal, Ana Maria Sampaio Assreuy, Benildo Sousa Cavada, Kyria Santiago Nascimento
Lectins are proteins, or glycoproteins, capable of reversibly binding to specific mono- or oligosaccharides via a noncatalytic domain. The Diocleinae subtribe presents lectins with high structural similarity, but different effects based on biological activity assays. This variability results from small structural differences. Therefore, in this context, the present study aimed to perform a structural analysis of the lectin from Dioclea lasiophylla Mart. ex Benth seeds (DlyL) and evaluate its inflammatory effect...
February 11, 2017: Biochimie
https://www.readbyqxmd.com/read/28194108/novel-sulfur-metabolites-of-garlic-attenuate-cardiac-hypertrophy-and-remodeling-through-induction-of-na-k-atpase-expression
#9
Tarak N Khatua, Roshan M Borkar, Soheb A Mohammed, Amit K Dinda, R Srinivas, Sanjay K Banerjee
Epidemiologic studies show an inverse correlation between garlic consumption and progression of cardiovascular disease. However, the molecular basis for the beneficial effect of garlic on the heart is not known. Therefore, the objective of the present study was to (1) investigate the effect of raw garlic on isoproterenol (Iso) induced cardiac hypertrophy (2) find the active metabolites of garlic responsible for the beneficial effect. Cardiac hypertrophy was induced in rats by subcutaneous single injection of Iso 5 mg kg(-1) day(-1) for 15 days and the effect of garlic (250 mg/kg/day orally) was evaluated...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28193626/autologous-heat-shock-protein-peptide-vaccination-for-newly-diagnosed-glioblastoma-impact-of-peripheral-pd-l1-expression-on-response-to-therapy
#10
Orin Bloch, Michael Lim, Michael E Sughrue, Ricardo J Komotar, John M Abrahams, Donald M O'Rourke, Anthony D'Ambrosio, Jeffrey N Bruce, Andrew T Parsa
PURPOSE: Standard therapy for newly diagnosed glioblastoma (GBM) is surgical resection, followed by concurrent radiotherapy and temozolomide chemotherapy. In this phase 2 clinical trial, the addition of an autologous heat shock protein vaccine to standard therapy was evaluated. Tumor-induced immunosuppression, mediated by expression of PD-L1 on tumor and circulating immune cells, may impact the efficacy of vaccination. Expression of PD-L1 on peripheral myeloid cells was evaluated for the first time as a predictor of survival...
February 13, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28192709/tetrazolylmethyl-quinolines-design-docking-studies-synthesis-anticancer-and-antifungal-analyses
#11
Saba Kauser J Shaikh, Ravindra R Kamble, Shilpa M Somagond, H C Devarajegowda, Sheshagiri R Dixit, Shrinivas D Joshi
A new series of 2,5 and 1,5-regioisomers of the tetrazolyl group viz., 3-[(5-benzyl/benzylthio-2H-tetrazol-2-yl) methyl]-2-chloro-6-substituted quinoline 6h-q and 3-[(5-benzyl/benzylthio-1H-tetrazol-1-yl) methyl]-2-chloro-6-substituted quinolines 7h-q were synthesized. Docking studies of all these compounds with DNA as target using PDB: 1AU5 and 453D revealed that the compounds 6h and 6i act as covalent cross linker on the DNA helix of the former and intercalate the latter both with higher C score values. Another set of docking studies in the active pocket of dihydrofolate reductase and N-myristoyl transferase as targets to assess antifungal activity revealed that compounds 6k, 6l, 6p and 7q (with bromo and fluro substituents) showcases different binding modes and hydrogen bonding...
February 1, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28190803/characterization-of-a-novel-rhamnose-containing-acidic-glycosphingolipid-from-the-ascidian-halocynthia-aurantium
#12
Hisao Kojima, Ryota Shinohara, Saki Itonori, Masahiro Ito
Halocynthia aurantium, an edible ascidian species belonging to Urochordata, was subjected to structural characterization of acidic glycosphingolipids to investigate these molecules in ascidians: sulfatide from Ciona intestinalis and the glucuronic acid-containing acidic glycosphingolipid from H. roretzi. Acidic glycosphingolipids containing three or five sugars were isolated from soft parts of the ascidian H. aurantium by chloroform-methanol extraction, mild-alkaline hydrolysis, precipitation with cold acetone, and subsequent column chromatography using a DEAE-Sephadex A-25 column, a Florisil column, and an Iatrobead column...
February 10, 2017: Journal of Oleo Science
https://www.readbyqxmd.com/read/28186757/thieno-3-2-b-pyrrole-5-carboxamides-as-new-reversible-inhibitors-of-histone-lysine-demethylase-kdm1a-lsd1-part-2-structure-based-drug-design-and-structure-activity-relationship
#13
Paola Vianello, Luca Sartori, Federica Amigoni, Anna Cappa, Giovanni Fagá, Raimondo Fattori, Elena Legnaghi, Giuseppe Ciossani, Andrea Mattevi, Giuseppe Meroni, Loris Moretti, Valentina Cecatiello, Sebastiano Pasqualato, Alessia Romussi, Florian Thaler, Paolo Trifiró, Oronza A Botrugno, Manuela Villa, Paola Dessanti, Saverio Minucci, Stefania Vultaggio, Elisa Zagarrí, Mario Varasi, Ciro Mercurio
The balance of methylation levels at histone H3 lysine 4 (H3K4) is regulated by KDM1A (LSD1). KDM1A is overexpressed in several tumor types, thus representing an emerging target for the development of novel cancer therapeutics. We have previously described (Part 1) the identification of thieno[3,2-b]pyrrole-5-carboxamides, as novel reversible inhibitors of KDM1A, whose preliminary exploration resulted in compound 2 with biochemical IC50 = 160 nM. We now report the structure-guided optimization of this chemical series, based on multiple ligand/KDM1A-CoRest co-crystal structures, which led to several extremely potent inhibitors...
February 10, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28182018/genome-wide-base-resolution-mapping-of-dna-methylation-in-single-cells-using-single-cell-bisulfite-sequencing-scbs-seq
#14
Stephen J Clark, Sébastien A Smallwood, Heather J Lee, Felix Krueger, Wolf Reik, Gavin Kelsey
DNA methylation (DNAme) is an important epigenetic mark in diverse species. Our current understanding of DNAme is based on measurements from bulk cell samples, which obscures intercellular differences and prevents analyses of rare cell types. Thus, the ability to measure DNAme in single cells has the potential to make important contributions to the understanding of several key biological processes, such as embryonic development, disease progression and aging. We have recently reported a method for generating genome-wide DNAme maps from single cells, using single-cell bisulfite sequencing (scBS-seq), allowing the quantitative measurement of DNAme at up to 50% of CpG dinucleotides throughout the mouse genome...
March 2017: Nature Protocols
https://www.readbyqxmd.com/read/28178597/determination-of-topiramate-in-dried-blood-spots-using-single-quadrupole-gas-chromatography-mass-spectrometry-after-flash-methylation-with-trimethylanilinium-hydroxide
#15
Roberta Zilles Hahn, Marina Venzon Antunes, Priscila Costa Arnhold, Natalia Bordin Andriguetti, Simone Gasparin Verza, Rafael Linden
Dried blood spots (DBS) sampling obtained from fingerpricks is a promising and patient friendly alternative for obtaining samples for drug quantification, that could be of interest for topiramate (TOP) therapeutic drug monitoring. The aim of this study was to develop and validate a simple and fast GC-MS assay for TOP measurement in dried blood spots (DBS). The method uses a liquid extraction of one 8mm DBS, followed by a flash methylation with TMAH, and separation in a DB-5ms capillary column. Total analytical run time was 15min...
February 1, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28174298/the-startle-disease-mutation-e103k-impairs-activation-of-human-homomeric-%C3%AE-1-glycine-receptors-by-disrupting-an-intersubunit-salt-bridge-across-the-agonist-binding-site
#16
Fatemah Safar, Elliot Hurdiss, Marios Erotocritou, Timo Greiner, Remigijus Lape, Mark W Irvine, Guangyu Fang, David Jane, Rilei Yu, Marc A Dämgen, Philip C Biggin, Lucia G Sivilotti
Glycine receptors (GlyR) belong to the pentameric ligand gated ion channel (pLGIC) superfamily and mediate fast inhibitory transmission in the vertebrate CNS. Disruption of glycinergic transmission by inherited mutations produces startle disease in man. Many startle mutations are in GlyRs and provide useful clues to the function of the channel domains. E103K is one of few startle mutations found in the extracellular agonist binding site of the channel, in loop A of the principal side of the subunit interface...
February 7, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28174249/tracking-the-embryonic-stem-cell-transition-from-ground-state-pluripotency
#17
Tüzer Kalkan, Nelly Olova, Mila Roode, Carla Mulas, Heather J Lee, Isabelle Nett, Hendrik Marks, Rachael Walker, Hendrik G Stunnenberg, Kathryn S Lilley, Jennifer Nichols, Wolf Reik, Paul Bertone, Austin Smith
Mouse embryonic stem (ES) cells are locked into self-renewal by shielding from inductive cues. Release from this ground state in minimal conditions offers a system for delineating developmental progression from naive pluripotency. Here we examined the initial transition process. The ES cell population behaves asynchronously. We therefore exploited a short-half-life Rex1::GFP reporter to isolate cells either side of exit from naive status. Extinction of ES cell identity in single cells is acute. It occurs only after near-complete elimination of naïve pluripotency factors, but precedes appearance of lineage specification markers...
February 7, 2017: Development
https://www.readbyqxmd.com/read/28150904/rationally-developed-organic-salts-of-tolfenamic-acid-and-its-%C3%AE-alanine-derivatives-for-dual-purpose-anti-inflammatory-topical-gel-and-anti-cancer-agent
#18
Parthasarathi Dastidar, Rumana Parveen, Bommagani Sravanthi
A new series of primary ammonium monocarboxylate (PAM) salts of a non-steroidal-anti-Inflammatory-drug (NSAID) namely Tolfenamic acid (TA) and its β-alanine derivative was generated; nearly 67% of the salts in the series showed gelling ability with various solvents including water (biogenic solvent) and methyl salicylate (typically used for topical gel formulations). Gels were characterized by table top and dynamic rheology, electron microscopy etc. Structure-property correlation based on single crystal and powder X-ray diffraction data of several gelator and non-gelator salts revealed intriguing insights...
February 2, 2017: Chemistry, An Asian Journal
https://www.readbyqxmd.com/read/28150704/genome-wide-dna-methylation-reprogramming-in-response-to-inorganic-arsenic-links-inhibition-of-ctcf-binding-dnmt-expression-and-cellular-transformation
#19
Matthew Rea, Meredith Eckstein, Rebekah Eleazer, Caroline Smith, Yvonne N Fondufe-Mittendorf
Chronic low dose inorganic arsenic (iAs) exposure leads to changes in gene expression and epithelial-to-mesenchymal transformation. During this transformation, cells adopt a fibroblast-like phenotype accompanied by profound gene expression changes. While many mechanisms have been implicated in this transformation, studies that focus on the role of epigenetic alterations in this process are just emerging. DNA methylation controls gene expression in physiologic and pathologic states. Several studies show alterations in DNA methylation patterns in iAs-mediated pathogenesis, but these studies focused on single genes...
February 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28137366/somatic-mutations-in-cancer-stochastic-versus-predictable
#20
Barry Gold
The origins of human cancers remain unclear except for a limited number of potent environmental mutagens, such as tobacco and UV light, and in rare cases, familial germ line mutations that affect tumor suppressor genes or oncogenes. A significant component of cancer etiology has been deemed stochastic and correlated with the number of stem cells in a tissue, the number of times the stem cells divide and a low incidence of random DNA polymerase errors that occur during each cell division. While somatic mutations occur during each round of DNA replication, mutations in cancer driver genes are not stochastic...
February 2017: Mutation Research
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