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https://www.readbyqxmd.com/read/27911843/impact-of-the-gut-microbiota-on-enhancer-accessibility-in-gut-intraepithelial-lymphocytes
#1
Nicholas P Semenkovich, Joseph D Planer, Philip P Ahern, Nicholas W Griffin, Charles Y Lin, Jeffrey I Gordon
The gut microbiota impacts many aspects of host biology including immune function. One hypothesis is that microbial communities induce epigenetic changes with accompanying alterations in chromatin accessibility, providing a mechanism that allows a community to have sustained host effects even in the face of its structural or functional variation. We used Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) to define chromatin accessibility in predicted enhancer regions of intestinal αβ(+) and γδ(+) intraepithelial lymphocytes purified from germ-free mice, their conventionally raised (CONV-R) counterparts, and mice reared germ free and then colonized with CONV-R gut microbiota at the end of the suckling-weaning transition...
December 1, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27903897/combining-atac-seq-with-nuclei-sorting-for-discovery-of-cis-regulatory-regions-in-plant-genomes
#2
Zefu Lu, Brigitte T Hofmeister, Christopher Vollmers, Rebecca M DuBois, Robert J Schmitz
: Chromatin structure plays a pivotal role in facilitating proper control of gene expression. Transcription factor (TF) binding of cis-elements is often associated with accessible chromatin regions. Therefore, the ability to identify these accessible regions throughout plant genomes will advance understanding of the relationship between TF binding, chromatin status and the regulation of gene expression. Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) is a recently developed technique used to map open chromatin zones in animal genomes...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27900529/effectiveness-of-pit-and-fissure-sealants-bonded-with-different-adhesive-systems-a-prospective-randomized-controlled-trial
#3
Gizem Erbas Unverdi, Stephan Atilla Atac, Zafer Cavit Cehreli
OBJECTIVES: To evaluate and compare the clinical retention of a resin-based fissure sealant placed with an intermediate layer of etch-and-rinse (ER) or self-etch (SE) adhesives. MATERIALS AND METHODS: Two hundred twenty-eight sealants were placed in 57 children with previously unsealed, caries-free permanent first molars, employing a split-mouth design. The teeth were randomized into four groups (n = 57 teeth/groups) according to the adhesive system placed under the tested sealant (Delton FS+; Dentsply)...
November 30, 2016: Clinical Oral Investigations
https://www.readbyqxmd.com/read/27900485/serum-glutathione-peroxidase-xanthine-oxidase-and-superoxide-dismutase-activities-and-malondialdehyde-levels-in-patients-with-parkinson-s-disease
#4
Burcu Gökçe Çokal, Mustafa Yurtdaş, Selda Keskin Güler, Hafize Nalan Güneş, Ceyla Ataç Uçar, Bilal Aytaç, Zahide Esra Durak, Tahir Kurtuluş Yoldaş, İlker Durak, Hikmet Can Çubukçu
Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by loss of dopaminergic (DA) neurons in the substantia nigra pars compacta (SNpc). Oxidative stress has been hypothesized to play a major role in the development of PD in various studies. This study assessed to investigate oxidative and anti-oxidative status in PD patients. We evaluated oxidant/antioxidant status by measuring serum malondialdehyde (MDA) levels, xanthine oxidase (XO) activities, and activities of antioxidant enzymes, namely, glutathione peroxidase (GSH-Px) and superoxide dismutase (SOD)...
November 30, 2016: Neurological Sciences
https://www.readbyqxmd.com/read/27896813/transcriptional-and-post-transcriptional-regulation-of-histone-variant-h2a-z-during-sea-urchin-development
#5
Mihai Hajdu, Jasmine Calle, Andrea Puno, Aminat Haruna, César Arenas-Mena
Histone variant H2A.Z promotes chromatin accessibility at transcriptional regulatory elements and is developmentally regulated in metazoans. We characterize the transcriptional and post-transcriptional regulation of H2A.Z in the purple sea urchin Strongylocentrotus purpuratus. H2A.Z depletion by antisense translation-blocking morpholino oligonucleotides during early development causes developmental collapse, in agreement with its previously demonstrated general role in transcriptional multipotency. During H2A...
November 29, 2016: Development, Growth & Differentiation
https://www.readbyqxmd.com/read/27895806/genome-wide-epigenomic-profiling-for-biomarker-discovery
#6
REVIEW
René A M Dirks, Hendrik G Stunnenberg, Hendrik Marks
A myriad of diseases is caused or characterized by alteration of epigenetic patterns, including changes in DNA methylation, post-translational histone modifications, or chromatin structure. These changes of the epigenome represent a highly interesting layer of information for disease stratification and for personalized medicine. Traditionally, epigenomic profiling required large amounts of cells, which are rarely available with clinical samples. Also, the cellular heterogeneity complicates analysis when profiling clinical samples for unbiased genome-wide biomarker discovery...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27888827/excision-of-recurrent-synovial-sarcoma-of-the-infratemporal-fossa
#7
Fakih Cihat Eravcı, Mehmet Düzlü, Mehmet Ekrem Zorlu, Metin Yılmaz, Mustafa Sancar Ataç
Synovial sarcoma is a soft tissue sarcoma especially encountered in the lower extremities. The infratemporal fossa is quite a rare location. Since it is a closed location, combined approaches and multidisciplinary planning always need to be considered. This case emphasizes the high-grade character of synovial sarcoma, which causes it to recur often. The difficulty of clear surgical margins in the infratemporal fossa adds to synovial sarcoma a second challenging issue. Therefore, the need of complementary therapy is essential...
September 2016: Kulak Burun Boğaz Ihtisas Dergisi: KBB, Journal of Ear, Nose, and Throat
https://www.readbyqxmd.com/read/27846204/epigenomics-massive-atac
#8
Joshua M Finkelstein
No abstract text is available yet for this article.
November 15, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27837368/comparison-of-neutrophil-lymphocyte-ratio-nlr-in-parkinson-s-disease-subtypes
#9
Ceyla Ataç Uçar, Burcu Gökçe Çokal, Hanzade Aybüke Ünal Artık, Levent Ertuğrul İnan, Tahir Kurtuluş Yoldaş
It has been hypothesized that chronic inflammation may play an important role in the development and progression of the neurodegeneration of Idiopathic Parkinson's disease (IPD). Neutrophil-lymphocyte ratio (NLR) is a marker that indicates the peripheral inflammation. There is only one study regarding NLR and IPD. In this study, we assessed to investigate NLR in patients with IPD, comparing the results with controls and to determine whether there is a difference in NLR levels in subgroups of IPD (akinetic-rigid and tremor-dominant) differ in their levels of NLR...
November 11, 2016: Neurological Sciences
https://www.readbyqxmd.com/read/27832532/assay-for-transposase-accessible-chromatin-with-high-throughput-sequencing-atac-seq-protocol-for-zebrafish-embryos
#10
Canan Doganli, Melissa Sandoval, Sean Thomas, Daniel Hart
Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) is a useful method to map genome-wide chromatin accessibility and nucleosome positioning. Genome-wide sequencing is performed utilizing adapter sequences inserted by a prokaryotic transposase, Tn5, into the accessible regions of chromatin. Here we describe the use of ATAC-seq in the zebrafish embryo and thereby the applicability of this approach in whole vertebrate embryos.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27789702/cistrome-data-browser-a-data-portal-for-chip-seq-and-chromatin-accessibility-data-in-human-and-mouse
#11
Shenglin Mei, Qian Qin, Qiu Wu, Hanfei Sun, Rongbin Zheng, Chongzhi Zang, Muyuan Zhu, Jiaxin Wu, Xiaohui Shi, Len Taing, Tao Liu, Myles Brown, Clifford A Meyer, X Shirley Liu
Chromatin immunoprecipitation, DNase I hypersensitivity and transposase-accessibility assays combined with high-throughput sequencing enable the genome-wide study of chromatin dynamics, transcription factor binding and gene regulation. Although rapidly accumulating publicly available ChIP-seq, DNase-seq and ATAC-seq data are a valuable resource for the systematic investigation of gene regulation processes, a lack of standardized curation, quality control and analysis procedures have hindered extensive reuse of these data...
October 26, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27755413/coronal-split-corpus-osteotomy-of-the-mandible-a-modified-visor-osteotomy-technique-for-bone-volume-enhancement
#12
Mustafa Sancar Ataç, Yeliz Kilinç
The bony augmentation of severely atrophied mandible is generally required for the purposes of prosthetic rehabilitations. The treatment strategies have been well defined in the literature ranging from osteotomy techniques to distraction osteogenesis. Visor osteotomy is the milestone of the reconstructive surgery for the atrophied mandible which has received some modifications. In the present study, the authors describe a new modification of visor osteotomy in which a complete coronal split osteotomy down to the inferior border at the mental region has been performed...
October 14, 2016: Journal of Craniofacial Surgery
https://www.readbyqxmd.com/read/27749837/atac-see-reveals-the-accessible-genome-by-transposase-mediated-imaging-and-sequencing
#13
Xingqi Chen, Ying Shen, Will Draper, Jason D Buenrostro, Ulrike Litzenburger, Seung Woo Cho, Ansuman T Satpathy, Ava C Carter, Rajarshi P Ghosh, Alexandra East-Seletsky, Jennifer A Doudna, William J Greenleaf, Jan T Liphardt, Howard Y Chang
Spatial organization of the genome plays a central role in gene expression, DNA replication, and repair. But current epigenomic approaches largely map DNA regulatory elements outside of the native context of the nucleus. Here we report assay of transposase-accessible chromatin with visualization (ATAC-see), a transposase-mediated imaging technology that employs direct imaging of the accessible genome in situ, cell sorting, and deep sequencing to reveal the identity of the imaged elements. ATAC-see revealed the cell-type-specific spatial organization of the accessible genome and the coordinated process of neutrophil chromatin extrusion, termed NETosis...
October 17, 2016: Nature Methods
https://www.readbyqxmd.com/read/27678375/genome-wide-identification-of-drosophila-dorso-ventral-enhancers-by-differential-histone-acetylation-analysis
#14
Nina Koenecke, Jeff Johnston, Bjoern Gaertner, Malini Natarajan, Julia Zeitlinger
BACKGROUND: Drosophila dorso-ventral (DV) patterning is one of the best-understood regulatory networks to date, and illustrates the fundamental role of enhancers in controlling patterning, cell fate specification, and morphogenesis during development. Histone acetylation such as H3K27ac is an excellent marker for active enhancers, but it is challenging to obtain precise locations for enhancers as the highest levels of this modification flank the enhancer regions. How to best identify tissue-specific enhancers in a developmental system de novo with a minimal set of data is still unclear...
September 27, 2016: Genome Biology
https://www.readbyqxmd.com/read/27600491/authentication-and-characterisation-of-a-new-oesophageal-adenocarcinoma-cell-line-mfd-1
#15
Edwin Garcia, Annette Hayden, Charles Birts, Edward Britton, Andrew Cowie, Karen Pickard, Massimiliano Mellone, Clarisa Choh, Mathieu Derouet, Patrick Duriez, Fergus Noble, Michael J White, John N Primrose, Jonathan C Strefford, Matthew Rose-Zerilli, Gareth J Thomas, Yeng Ang, Andrew D Sharrocks, Rebecca C Fitzgerald, Timothy J Underwood
New biological tools are required to understand the functional significance of genetic events revealed by whole genome sequencing (WGS) studies in oesophageal adenocarcinoma (OAC). The MFD-1 cell line was isolated from a 55-year-old male with OAC without recombinant-DNA transformation. Somatic genetic variations from MFD-1, tumour, normal oesophagus, and leucocytes were analysed with SNP6. WGS was performed in tumour and leucocytes. RNAseq was performed in MFD-1, and two classic OAC cell lines FLO1 and OE33...
September 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27586354/do-c-reactive-protein-level-white-blood-cell-count-and-pain-location-guide-the-selection-of-patients-for-computed-tomography-imaging-in-non-traumatic-acute-abdomen
#16
E Ozan, G K Atac, T Evrin, K Alisar, L O Sonmez, A Alhan
The value of abdominal computed tomography in non-traumatic abdominal pain has been well established. On the other hand, to manage computed tomography, appropriateness has become more of an issue as a result of the concomitant increase in patient radiation exposure with increased computed tomography use. The purpose of this study was to investigate whether C-reactive protein, white blood cell count, and pain location may guide the selection of patients for computed tomography in non-traumatic acute abdomen...
September 2, 2016: Emergency Radiology
https://www.readbyqxmd.com/read/27545347/the-spectrum-and-regulatory-landscape-of-intestinal-innate-lymphoid-cells-are-shaped-by-the-microbiome
#17
Meital Gury-BenAri, Christoph A Thaiss, Nicolas Serafini, Deborah R Winter, Amir Giladi, David Lara-Astiaso, Maayan Levy, Tomer Meir Salame, Assaf Weiner, Eyal David, Hagit Shapiro, Mally Dori-Bachash, Meirav Pevsner-Fischer, Erika Lorenzo-Vivas, Hadas Keren-Shaul, Franziska Paul, Alon Harmelin, Gérard Eberl, Shalev Itzkovitz, Amos Tanay, James P Di Santo, Eran Elinav, Ido Amit
Innate lymphoid cells (ILCs) are critical modulators of mucosal immunity, inflammation, and tissue homeostasis, but their full spectrum of cellular states and regulatory landscapes remains elusive. Here, we combine genome-wide RNA-seq, ChIP-seq, and ATAC-seq to compare the transcriptional and epigenetic identity of small intestinal ILCs, identifying thousands of distinct gene profiles and regulatory elements. Single-cell RNA-seq and flow and mass cytometry analyses reveal compartmentalization of cytokine expression and metabolic activity within the three classical ILC subtypes and highlight transcriptional states beyond the current canonical classification...
August 25, 2016: Cell
https://www.readbyqxmd.com/read/27534422/association-of-the-monocyte-to-hdl-cholesterol-ratio-with-thrombus-burden-in-patients-with-st-segment-elevation-myocardial-infarction
#18
Arif Arısoy, Fatih Altunkaş, Kayıhan Karaman, Metin Karayakalı, Ataç Çelik, Köksal Ceyhan, Çağrı Zorlu
Intracoronary thrombus burden is associated with some adverse events and poor prognosis in patients with ST-segment elevation myocardial infarction (STEMI). Identifying predictors of the intracoronary thrombus burden may contribute to the management of STEMI. In this study, we evaluated whether monocyte count to high-density lipoprotein cholesterol ratio (MHR) is a predictor of intracoronary thrombus burden in patients with STEMI. The study population consisted of 414 patients with STEMI who underwent primary percutaneous coronary intervention (PCI)...
August 16, 2016: Clinical and Applied Thrombosis/hemostasis
https://www.readbyqxmd.com/read/27513249/investigation-of-enteropathogenic-escherichia-coli-and-shiga-toxin-producingescherichia-coli-associated-with-hemolytic-uremic-syndrome-in-%C3%A4-zmir-province-turkey
#19
Elif Bozçal, Gürkan Yiğittürk, Ataç Uzel, Sabire Şöhret Aydemir
BACKGROUND/AIM: The purpose of this study was to investigate Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic Escherichia coli (EPEC) strains originating from diarrheagenic patients. MATERIALS AND METHODS: A total of 102 patients with diarrhea between October 2012 and January 2013 were enrolled in this study. Multiplex and standard polymerase chain reactions were performed to detect and distinguish STEC and EPEC strains. O serotyping of EPEC was carried out by monovalent antisera...
2016: Turkish Journal of Medical Sciences
https://www.readbyqxmd.com/read/27443938/assay-for-transposase-accessible-chromatin-and-circularized-chromosome-conformation-capture-two-methods-to-explore-the-regulatory-landscapes-of-genes-in-zebrafish
#20
A Fernández-Miñán, J Bessa, J J Tena, J L Gómez-Skarmeta
Accurate transcriptional control of genes is fundamental for the correct functioning of organs and developmental processes. This control depends on the interplay between the promoter of genes and other noncoding sequences, whose interaction is mediated by 3D chromatin arrangements. Thus, the detailed description of transcriptional regulatory landscapes is essential to understand the mechanisms of transcriptional regulation. However, to achieve that, two important challenges have to be faced: (1) the identification of the noncoding sequences that contribute to gene transcription and (2) the association of these sequences to the respective genes they control...
2016: Methods in Cell Biology
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