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https://www.readbyqxmd.com/read/29434377/single-nucleus-analysis-of-accessible-chromatin-in-developing-mouse-forebrain-reveals-cell-type-specific-transcriptional-regulation
#1
Sebastian Preissl, Rongxin Fang, Hui Huang, Yuan Zhao, Ramya Raviram, David U Gorkin, Yanxiao Zhang, Brandon C Sos, Veena Afzal, Diane E Dickel, Samantha Kuan, Axel Visel, Len A Pennacchio, Kun Zhang, Bing Ren
Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types. Here we report single-nucleus ATAC-seq, a combinatorial barcoding-assisted single-cell assay for transposase-accessible chromatin that is optimized for use on flash-frozen primary tissue samples. We apply this technique to the mouse forebrain through eight developmental stages. Through analysis of more than 15,000 nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell types...
February 12, 2018: Nature Neuroscience
https://www.readbyqxmd.com/read/29429127/tissue-and-strain-specific-effects-of-a-genotoxic-carcinogen-1-3-butadiene-on-chromatin-and-transcription
#2
Jennifer W Israel, Grace A Chappell, Jeremy M Simon, Sebastian Pott, Alexias Safi, Lauren Lewis, Paul Cotney, Hala S Boulos, Wanda Bodnar, Jason D Lieb, Gregory E Crawford, Terrence S Furey, Ivan Rusyn
Epigenetic effects of environmental chemicals are under intense investigation to fill existing knowledge gaps between environmental/occupational exposures and adverse health outcomes. Chromatin accessibility is one prominent mechanism of epigenetic control of transcription, and understanding of the chemical effects on both could inform the causal role of epigenetic alterations in disease mechanisms. In this study, we hypothesized that baseline variability in chromatin organization and transcription profiles among various tissues and mouse strains influence the outcome of exposure to the DNA damaging chemical 1,3-butadiene...
February 10, 2018: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/29420797/octopus-toolkit-a-workflow-to-automate-mining-of-public-epigenomic-and-transcriptomic-next-generation-sequencing-data
#3
Taemook Kim, Hogyu David Seo, Lothar Hennighausen, Daeyoup Lee, Keunsoo Kang
Octopus-toolkit is a stand-alone application for retrieving and processing large sets of next-generation sequencing (NGS) data with a single step. Octopus-toolkit is an automated set-up-and-analysis pipeline utilizing the Aspera, SRA Toolkit, FastQC, Trimmomatic, HISAT2, STAR, Samtools, and HOMER applications. All the applications are installed on the user's computer when the program starts. Upon the installation, it can automatically retrieve original files of various epigenomic and transcriptomic data sets, including ChIP-seq, ATAC-seq, DNase-seq, MeDIP-seq, MNase-seq and RNA-seq, from the gene expression omnibus data repository...
February 6, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29415207/progression-of-calcium-density-in-the-ascending-thoracic-aorta-is-inversely-associated-with-incident-cardiovascular-disease-events
#4
Isac C Thomas, Robyn L McClelland, Matthew A Allison, Joachim H Ix, Erin D Michos, Nketi I Forbang, Wendy S Post, Nathan D Wong, Matthew J Budoff, Michael H Criqui
Aims: Little is known regarding the risk of atherosclerotic cardiovascular disease (ASCVD) conferred by changes in the volume and density of ascending thoracic aorta calcium (ATAC) over time. We evaluated changes in ATAC volume and density scores and incident ASCVD events. Methods and results: The Multi-Ethnic Study of Atherosclerosis is a prospective cohort study of individuals without baseline clinical ASCVD. Ascending thoracic aorta calcium was measured from baseline and follow-up (mean interval 2...
February 5, 2018: European Heart Journal Cardiovascular Imaging
https://www.readbyqxmd.com/read/29415120/impact-of-the-st101-clone-on-fatality-among-patients-with-colistin-resistant-klebsiella-pneumoniae-infection
#5
Fusun Can, Sirin Menekse, Pelin Ispir, Nazli Atac, Ozgur Albayrak, Tuana Demir, Doruk Can Karaaslan, Salih Nafiz Karahan, Mahir Kapmaz, Ozlem Kurt Azap, Funda Timurkaynak, Serap Simsek Yavuz, Seniha Basaran, Fugen Yoruk, Alpay Azap, Safiye Koculu, Nur Benzonana, Nathan A Lack, Mehmet Gönen, Onder Ergonul
Objectives: We describe the molecular characteristics of colistin resistance and its impact on patient mortality. Methods: A prospective cohort study was performed in seven different Turkish hospitals. The genotype of each isolate was determined by MLST and repetitive extragenic palindromic PCR (rep-PCR). Alterations in mgrB were detected by sequencing. Upregulation of pmrCAB, phoQ and pmrK was quantified by RT-PCR. mcr-1 and the genes encoding OXA-48, NDM-1 and KPC were amplified by PCR...
February 3, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29412141/integration-of-human-pancreatic-islet-genomic-data-refines-regulatory-mechanisms-at-type-2-diabetes-susceptibility-loci
#6
Matthias Thurner, Martijn van de Bunt, Jason M Torres, Anubha Mahajan, Vibe Nylander, Amanda J Bennett, Kyle J Gaulton, Amy Barrett, Carla Burrows, Christopher G Bell, Robert Lowe, Stephan Beck, Vardhman K Rakyan, Anna L Gloyn, Mark I McCarthy
Human genetic studies have emphasised the dominant contribution of pancreatic islet dysfunction to development of Type 2 Diabetes (T2D). However, limited annotation of the islet epigenome has constrained efforts to define the molecular mechanisms mediating the, largely regulatory, signals revealed by Genome-Wide Association Studies (GWAS). We characterised patterns of chromatin accessibility (ATAC-seq, n=17) and DNA methylation (whole-genome bisulphite sequencing, n=10) in human islets, generating high-resolution chromatin state maps through integration with established ChIP-seq marks...
February 7, 2018: ELife
https://www.readbyqxmd.com/read/29400509/realization-of-an-electrically-tunable-narrow-bandwidth-atomically-thin-mirror-using-monolayer-mose_-2
#7
Patrick Back, Sina Zeytinoglu, Aroosa Ijaz, Martin Kroner, Atac Imamoğlu
The advent of two-dimensional semiconductors, such as van der Waals heterostructures, propels new research directions in condensed matter physics and enables development of novel devices with unique functionalities. Here, we show experimentally that a monolayer of MoSe_{2} embedded in a charge controlled heterostructure can be used to realize an electrically tunable atomically thin mirror, which effects 87% extinction of an incident field that is resonant with its exciton transition. The corresponding maximum reflection coefficient of 41% is only limited by the ratio of the radiative decay rate to the nonradiative linewidth of exciton transition and is independent of incident light intensity up to 400  W/cm^{2}...
January 19, 2018: Physical Review Letters
https://www.readbyqxmd.com/read/29342231/mapping-gene-regulatory-networks-from-single-cell-omics-data
#8
Mark W E J Fiers, Liesbeth Minnoye, Sara Aibar, Carmen Bravo González-Blas, Zeynep Kalender Atak, Stein Aerts
Single-cell techniques are advancing rapidly and are yielding unprecedented insight into cellular heterogeneity. Mapping the gene regulatory networks (GRNs) underlying cell states provides attractive opportunities to mechanistically understand this heterogeneity. In this review, we discuss recently emerging methods to map GRNs from single-cell transcriptomics data, tackling the challenge of increased noise levels and data sparsity compared with bulk data, alongside increasing data volumes. Next, we discuss how new techniques for single-cell epigenomics, such as single-cell ATAC-seq and single-cell DNA methylation profiling, can be used to decipher gene regulatory programmes...
January 12, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29341143/loss-of-alkaline-ceramidase-inhibits-autophagy-in-arabidopsis-and-plays-an-important-role-during-environmental-stress-response
#9
Ping Zheng, Jian-Xin Wu, Sunil Kumar Sahu, Hong-Yun Zeng, Li-Qun Huang, Zhe Liu, Shi Xiao, Nan Yao
Sphingolipids, a class of bioactive lipids found in cell membranes, can modulate the biophysical properties of the membranes and play a critical role in signal transduction. Sphingolipids are involved in autophagy in humans and yeast, but their role in autophagy in plants is not well understood. In this study, we reported that the AtACER, an alkaline ceramidase that hydrolyzes ceramide to LCB, functions in autophagy process in Arabidopsis. Our empirical data showed that the loss of AtACER inhibited autophagy, while its overexpression promoted autophagy under nutrient, salinity, and oxidative stresses...
January 17, 2018: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29303138/is-age-a-determinant-for-nausea-and-vomiting-in-disabled-patients-after-dental-treatment-under-sedation
#10
Hüseyin Cihad Turgut, Metin Alkan, Gülay Kip, Mustafa Sancar Ataç, Sevil Kahraman Altundağ, Süleyman Bozkaya, Berrin Işik, Mustafa Arslan
BACKGROUND AND AIM: Postoperative nausea and vomiting (PONV) is one of most frequently encountered problems after dental treatment of mentally and/or motor disabled patients under sedation or general anesthesia. In this study, we aimed to investigate whether PONV incidence in disabled patients differs between adults (≥18 years) and children/teenage (<18 years). Also investigating complication rates related with anesthesia protocols were additional objectives of the study. MATERIALS AND METHODS: We retrospectively evaluated anesthesia reports of 664 cases undergone different dental treatment procedures under deep sedation with various anesthetic agents...
November 2017: Nigerian Journal of Clinical Practice
https://www.readbyqxmd.com/read/29296732/chromatin-dynamics-during-the-differentiation-of-long-term-hematopoietic-stem-cells-to-multipotent-progenitors
#11
Xiang Yu, Chao Wu, Dheeraj Bhavanasi, Hong Wang, Brian D Gregory, Jian Huang
ATAC-seq provides genome-wide chromatin state in 3 cell types of hematopoietic stem/progenitor cells.Transcription factor cohorts are associated with dynamic changes of open chromatin during the differentiation of LT/ST-HSCs to MPPs.
June 13, 2017: Blood Advances
https://www.readbyqxmd.com/read/29259032/analysis-of-chromatin-accessibility-in-decidualizing-human-endometrial-stromal-cells
#12
Pavle Vrljicak, Emma S Lucas, Lauren Lansdowne, Raffaella Lucciola, Joanne Muter, Nigel P Dyer, Jan J Brosens, Sascha Ott
Spontaneous decidualization of the endometrium in response to progesterone signaling is confined to menstruating species, including humans and other higher primates. During this process, endometrial stromal cells (EnSCs) differentiate into specialized decidual cells that control embryo implantation. We subjected undifferentiated and decidualizing human EnSCs to an assay for transposase accessible chromatin with sequencing (ATAC-seq) to map the underlying chromatin changes. A total of 185,084 open DNA loci were mapped accurately in EnSCs...
December 19, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29249357/il-10-signaling-remodels-adipose-chromatin-architecture-to-limit-thermogenesis-and-energy-expenditure
#13
Prashant Rajbhandari, Brandon J Thomas, An-Chieh Feng, Cynthia Hong, Jiexin Wang, Laurent Vergnes, Tamer Sallam, Bo Wang, Jaspreet Sandhu, Marcus M Seldin, Aldons J Lusis, Loren G Fong, Melanie Katz, Richard Lee, Stephen G Young, Karen Reue, Stephen T Smale, Peter Tontonoz
Signaling pathways that promote adipose tissue thermogenesis are well characterized, but the limiters of energy expenditure are largely unknown. Here, we show that ablation of the anti-inflammatory cytokine IL-10 improves insulin sensitivity, protects against diet-induced obesity, and elicits the browning of white adipose tissue. Mechanistic studies define bone marrow cells as the source of the IL-10 signal and adipocytes as the target cell type mediating these effects. IL-10 receptor alpha is highly enriched in mature adipocytes and is induced in response to differentiation, obesity, and aging...
December 8, 2017: Cell
https://www.readbyqxmd.com/read/29239690/antibody-drug-conjugates-design-and-development-for-therapy-and-imaging-in-and-beyond-cancer-labex-mabimprove-industrial-workshop-july-27-28-2017-tours-france
#14
Camille Martin, Claire Kizlik-Masson, André Pèlegrin, Hervé Watier, Marie-Claude Viaud-Massuard, Nicolas Joubert
The annual "Antibody Industrial Symposium", co organized by LabEx MAbImprove, MabDesign and Polepharma, was held in Tours, France on June 27-28, 2017. The focus was on antibody-drug-conjugates (ADCs), new entities which realize the hope of Paul Ehrlich's magic bullet. ADCs result from the bioconjugation of a highly cytotoxic drug to a selective monoclonal antibody, which acts as a vector. Building on knowledge gained during the development of three approved ADCs, brentuximab vedotin (Adcetris®), ado trastuzumab emtansine (Kadcyla®) and inotuzumab ozogamicin (Besponsa®), and the many ADCs in development, this meeting addressed strategies and the latest innovations in the field from fundamental research to manufacturing...
December 14, 2017: MAbs
https://www.readbyqxmd.com/read/29232376/che1-aatf-interacts-with-subunits-of-the-histone-acetyltransferase-core-module-of-saga-complexes
#15
Gizem Caliskan, Ikbal C Baris, Ferhan Ayaydin, Melanie J Dobson, Muge Senarisoy, Imre M Boros, Zeki Topcu, Sevil Zencir
General Control Non-derepressible 5 (GCN5) and Alteration/Deficiency in Activation 2 and 3 proteins (ADA2 and ADA3, respectively) are subunits of the Histone AcetylTransferase (HAT) module of SAGA- and ATAC-type co-activators. We previously reported four new interacting partners of human ADA3 identified by screening a human fetal brain cDNA library using yeast two hybrid technology. One of these partners was Apoptosis-Antagonizing Transcription Factor (AATF), also known as Che-1, an RNA polymerase II-binding protein with a number of roles in different cellular processes including regulation of transcription, cell proliferation, cell cycle control, DNA damage responses and apoptosis...
2017: PloS One
https://www.readbyqxmd.com/read/29229750/profiling-of-accessible-chromatin-regions-across-multiple-plant-species-and-cell-types-reveals-common-gene-regulatory-principles-and-new-control-modules
#16
Kelsey A Maher, Marko Bajic, Kaisa Kajala, Mauricio Reynoso, Germain Pauluzzi, Donnelly West, Kristina Zumstein, Margaret Woodhouse, Kerry L Bubb, Michael W Dorrity, Christine Queitsch, Julia Bailey-Serres, Neelima Sinha, Siobhan M Brady, Roger Deal
The transcriptional regulatory structure of plant genomes remains poorly defined relative to animals. It is unclear how many cis-regulatory elements exist, where these elements lie relative to promoters, and how these features are conserved across plant species. We employed the Assay for Transposase-Accessible Chromatin (ATAC-seq) in four plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome...
December 11, 2017: Plant Cell
https://www.readbyqxmd.com/read/29226895/a-late-complication-of-coronary-artery-perforation-during-primary-percutaneous-coronary-intervention-coronary-arteriovenous-fistula
#17
Kayıhan Karaman, Metin Karayakalı, Arif Arısoy, İlker Akar, Ataç Çelik
Coronary artery perforation (CAP) is a rare, but potentially mortal possible complication of percutaneous coronary intervention. There are several treatment options for this complication, including prolonged balloon dilatation, use of a coronary stent graft, and bypass surgery. In this case report, a 65-year-old female patient who was admitted to the catheter laboratory with a diagnosis of acute coronary syndrome, was presented. Coronary angiography revealed total occlusion in the mid segment of the right coronary artery and a drug-eluting stent was implanted under 12 atm of pressure following pre-dilatation with a perfusion balloon...
December 2017: Türk Kardiyoloji Derneği Arşivi: Türk Kardiyoloji Derneğinin Yayın Organıdır
https://www.readbyqxmd.com/read/29220666/chromatin-accessibility-dynamics-during-ipsc-reprogramming
#18
Dongwei Li, Jing Liu, Xuejie Yang, Chunhua Zhou, Jing Guo, Chuman Wu, Yue Qin, Lin Guo, Jiangping He, Shenyong Yu, He Liu, Xiaoshan Wang, Fang Wu, Junqi Kuang, Andrew P Hutchins, Jiekai Chen, Duanqing Pei
Cell-fate decisions remain poorly understood at the chromatin level. Here, we map chromatin remodeling dynamics during induction of pluripotent stem cells. ATAC-seq profiling of MEFs expressing Oct4-Sox2-Klf4 (OSK) reveals dynamic changes in chromatin states shifting from open to closed (OC) and closed to open (CO), with an initial burst of OC and an ending surge of CO. The OC loci are largely composed of genes associated with a somatic fate, while the CO loci are associated with pluripotency. Factors/conditions known to impede reprogramming prevent OSK-driven OC and skew OC-CO dynamics...
December 7, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/29201435/endothelial-nitric-oxide-synthase-gene%C3%A2-polymorphisms-in-patients-with-slow%C3%A2-coronary-flow
#19
Nurzen Sezgin, Abdullah Tekin, Fatma Belgin Atac, Hasibe Verdi, Alpay Turan Sezgin
Background and aims: The aim of this study was to explore potential associations of the intron 4 variable number of tandem repeats (VNTR) and E298A polymorphisms of the endothelial nitric oxide synthase (eNOS) gene with slow coronary flow (SCF). The association between plasma nitrate and nitrite (NO x ) concentrations and eNOS gene polymorphisms was also assessed. Materials and methods: The intron 4 VNTR and E298A polymorphisms of the eNOS gene were evaluated in the isolated DNA blood samples obtained from the SCF patient group (n = 30) and healthy group consisted of age- and sex-matched controls (n = 61)...
September 2017: Interventional Medicine & Applied Science
https://www.readbyqxmd.com/read/29192626/neutrophil-lymphocyte-ratio-predicts-postoperative-pain-after-orthognathic-surgery
#20
H C Turgut, M Alkan, M S Ataç, S K Altundağ, S Bozkaya, B Şimşek, B Işik, M Arslan
BACKGROUND AND AIM: Postoperative pain is well known and usually disturbing complication of surgery. Inflammation plays an important role in the development and progression of postoperative pain. We aimed to investigate possible relationship between preoperatively measured neutrophil-lymphocyte ratio (NLR) - as an inflammation marker - and postoperative analgesic demand in patients underwent orthognathic surgery. MATERIALS AND METHODS: We retrospectively investigated medical and anesthesia records of 177 patients underwent orthognathic surgery...
October 2017: Nigerian Journal of Clinical Practice
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