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https://www.readbyqxmd.com/read/29162709/ehrlichia-chaffeensis-and-its-invasin-etpe-block-reactive-oxygen-species-generation-by-macrophages-in-a-dnase-x-dependent-manner
#1
Omid Teymournejad, Mingqun Lin, Yasuko Rikihisa
The obligatory intracellular pathogen Ehrlichia chaffeensis lacks most genes that confer resistance to oxidative stress but can block reactive oxygen species (ROS) generation by host monocytes-macrophages. Bacterial and host molecules responsible for this inhibition have not been identified. To infect host cells, Ehrlichia uses the C terminus of its surface invasin, entry-triggering protein of Ehrlichia (EtpE; EtpE-C), which directly binds the mammalian cell surface receptor glycosylphosphatidylinositol-anchored protein DNase X...
November 21, 2017: MBio
https://www.readbyqxmd.com/read/29157262/immunoproteomic-analysis-of-the-excretory-secretory-products-of-trichinella-pseudospiralis-adult-worms-and-newborn-larvae
#2
Yang Wang, Xue Bai, Haichao Zhu, Xuelin Wang, Haining Shi, Bin Tang, Pascal Boireau, Xuepeng Cai, Xuenong Luo, Mingyuan Liu, Xiaolei Liu
BACKGROUND: The nematode Trichinella pseudospiralis is an intracellular parasite of mammalian skeletal muscle cells and exists in a non-encapsulated form. Previous studies demonstrated that T. pseudospiralis could induce a lower host inflammatory response. Excretory-secretory (ES) proteins as the most important products of host-parasite interaction may play the main functional role in alleviating host inflammation. However, the ES products of T. pseudospiralis early stage are still unknown...
November 21, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/29156107/hemodynamic-force-triggers-rapid-netosis-within-sterile-thrombotic-occlusions
#3
X Yu, J Tan, S L Diamond
BACKGROUND: Neutrophil extracellular traps (NETs) are released when neutrophils encounter infectious pathogens, especially during sepsis. Additionally, NETosis occurs during venous and arterial thrombosis, disseminated intravascular coagulation, and trauma. OBJECTIVE: We tested if hemodynamic forces trigger NETosis during sterile thrombosis. METHODS: NETs were imaged with Sytox-green during microfluidic perfusion of Factor XIIa-inhibited or thrombin-inhibited human whole blood over fibrillar collagen (± tissue factor)...
November 20, 2017: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/29155775/mapping-genome-wide-accessible-chromatin-in-primary-human-t-lymphocytes-by-atac-seq
#4
Ivana Grbesa, Miriam Tannenbaum, Avital Sarusi-Portuguez, Michal Schwartz, Ofir Hakim
Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) is a method used for the identification of open (accessible) regions of chromatin. These regions represent regulatory DNA elements (e.g., promoters, enhancers, locus control regions, insulators) to which transcription factors bind. Mapping the accessible chromatin landscape is a powerful approach for uncovering active regulatory elements across the genome. This information serves as an unbiased approach for discovering the network of relevant transcription factors and mechanisms of chromatin structure that govern gene expression programs...
November 13, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29148971/convergence-of-topological-domain-boundaries-insulators-and-polytene-interbands-revealed-by-high-resolution-mapping-of-chromatin-contacts-in-the-early-drosophila-melanogaster-embryo
#5
Michael R Stadler, Jenna E Haines, Michael Eisen
High-throughput assays of three-dimensional interactions of chromosomes have shed considerable light on the structure of animal chromatin. Despite this progress, the precise physical nature of observed structures and the forces that govern their establishment remain poorly understood. Here we present high resolution Hi-C data from early Drosophila embryos. We demonstrate that boundaries between topological domains of various sizes map to DNA elements that resemble classical insulator elements: short genomic regions sensitive to DNase digestion that are strongly bound by known insulator proteins and are frequently located between divergent promoters...
November 17, 2017: ELife
https://www.readbyqxmd.com/read/29147695/synthesis-of-an-ethyleneimine-tetrahedral-dna-nanostructure-complex-and-its-potential-application-as-a-multi-functional-delivery-vehicle
#6
Taoran Tian, Tao Zhang, Tengfei Zhou, Shiyu Lin, Sirong Shi, Yunfeng Lin
Nowadays, DNA nanostructures are extensively researched for their biocompatibility, editable functionality, and structural stability. Tetrahedral DNA nanostructures (TDNs), widely known for their membrane permeability, are regarded as potential candidates for drug delivery. However, the stability and membrane permeability of TDNs call for further enhancement if in vivo usage is ascribed. To overcome the drawbacks of TDNs, ethylene imine (PEI, 25 kDa, branched)-a classic cationic polymer in the field of gene delivery-was applied...
November 17, 2017: Nanoscale
https://www.readbyqxmd.com/read/29137181/structure-and-functional-analysis-of-promoters-from-two-liver-isoforms-of-cpt-i-in-grass-carp-ctenopharyngodon-idella
#7
Yi-Huan Xu, Zhi Luo, Kun Wu, Yao-Fang Fan, Wen-Jing You, Li-Han Zhang
Carnitine palmitoyltransferase I (CPT I) is a key enzyme involved in the regulation of lipid metabolism and fatty acid β-oxidation. To understand the transcriptional mechanism of CPT Iα1b and CPT Iα2a genes, we cloned the 2695-bp and 2631-bp regions of CPT Iα1b and CPT Iα2a promoters of grass carp (Ctenopharyngodon idella), respectively, and explored the structure and functional characteristics of these promoters. CPT Iα1b had two transcription start sites (TSSs), while CPT Iα2a had only one TSS. DNase I foot printing showed that the CPT Iα1b promoter was AT-rich and TATA-less, and mediated basal transcription through an initiator (INR)-independent mechanism...
November 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29135282/genome-wide-dna-methylation-drives-human-embryonic-stem-cell-erythropoiesis-by-remodeling-gene-expression-dynamics
#8
Zhijing Liu, Qiang Feng, Pengpeng Sun, Yan Lu, Minlan Yang, Xiaowei Zhang, Xiangshu Jin, Yulin Li, Shi-Jiang Lu, Chengshi Quan
AIM: To investigate the role of DNA methylation during erythrocyte production by human embryonic stem cells (hESCs). METHODS: We employed an erythroid differentiation model from hESCs, and then tracked the genome-wide DNA methylation maps and gene expression patterns through an Infinium HumanMethylation450K BeadChip and an Ilumina Human HT-12 v4 Expression Beadchip, respectively. RESULTS: A negative correlation between DNA methylation and gene expression was substantially enriched during the later differentiation stage and was present in both the promoter and the gene body...
November 14, 2017: Epigenomics
https://www.readbyqxmd.com/read/29128838/transfection-of-plasmid-dna-by-nanocarriers-containing-a-gemini-cationic-lipid-with-an-aromatic-spacer-or-its-monomeric-counterpart
#9
María Martínez-Negro, Ana L Barrán-Berdón, Clara Aicart-Ramos, María L Moyá, Conchita Tros de Ilarduya, Emilio Aicart, Elena Junquera
This study performed a biophysical characterization (electrochemistry, structure and morphology) and assessment of the biological activity and cell biocompatibility of GCL/DOPE-pDNA lipoplexes comprised of plasmid DNA and a mixed lipid formed by a DOPE zwitterionic lipid and a gemini cationic lipid N-N'-(1,3-phenylene bis (methylene)) bis (N,N-dimethyl-N-(1-dodecyl) ammonium dibromide (12PH12) containing an aromatic spacer or its monomeric counterpart surfactant, N-benzyl-N,N-dimethyl-N-(1-dodecyl) ammonium bromide (12PH)...
November 8, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/29126307/universal-correction-of-enzymatic-sequence-bias-reveals-molecular-signatures-of-protein-dna-interactions
#10
André L Martins, Ninad M Walavalkar, Warren D Anderson, Chongzhi Zang, Michael J Guertin
Coupling molecular biology to high-throughput sequencing has revolutionized the study of biology. Molecular genomics techniques are continually refined to provide higher resolution mapping of nucleic acid interactions and structure. Sequence preferences of enzymes can interfere with the accurate interpretation of these data. We developed seqOutBias to characterize enzymatic sequence bias from experimental data and scale individual sequence reads to correct intrinsic enzymatic sequence biases. SeqOutBias efficiently corrects DNase-seq, TACh-seq, ATAC-seq, MNase-seq and PRO-seq data...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29126175/conventional-and-pioneer-modes-of-glucocorticoid-receptor-interaction-with-enhancer-chromatin-in-vivo
#11
Thomas A Johnson, Razvan V Chereji, Diana A Stavreva, Stephanie A Morris, Gordon L Hager, David J Clark
Glucocorticoid hormone plays a major role in metabolism and disease. The hormone-bound glucocorticoid receptor (GR) binds to a specific set of enhancers in different cell types, resulting in unique patterns of gene expression. We have addressed the role of chromatin structure in GR binding by mapping nucleosome positions in mouse adenocarcinoma cells. Before hormone treatment, GR-enhancers exist in one of three chromatin states: (i) Nucleosome-depleted enhancers that are DNase I-hypersensitive, associated with the Brg1 chromatin remodeler and flanked by nucleosomes incorporating histone H2A...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29122734/gene-editing-of-mps-i-human-fibroblasts-by-co-delivery-of-a-crispr-cas9-plasmid-and-a-donor-oligonucleotide-using-nanoemulsions-as-nonviral-carriers
#12
Roselena Silvestri Schuh, Talita Giacomet de Carvalho, Roberto Giugliani, Ursula Matte, Guilherme Baldo, Helder Ferreira Teixeira
Mucopolysaccharidosis type I (MPS I) is an inherited disease caused by the deficiency of alpha-L-iduronidase (IDUA). This study shows the use of nanoemulsions co-complexed with the plasmid of CRISPR/Cas9 system and a donor oligonucleotide aiming at MPS I gene editing in vitro. Nanoemulsions composed of MCT, DOPE, DOTAP, DSPE-PEG, and water were prepared by high-pressure homogenization. The DNA was complexed by adsorption or encapsulation of preformed DNA/DOTAP complexes with nanoemulsions at +4/ -1 charge ratio...
November 6, 2017: European Journal of Pharmaceutics and Biopharmaceutics
https://www.readbyqxmd.com/read/29121402/incorporating-functional-genomic-information-to-enhance-polygenic-signal-and-identify-variants-involved-in-gene-by-environment-interaction-for-young-adult-alcohol-problems
#13
Jessica E Salvatore, Jeanne E Savage, Peter Barr, Aaron R Wolen, Fazil Aliev, Eero Vuoksimaa, Antti Latvala, Lea Pulkkinen, Richard J Rose, Jaakko Kaprio, Danielle M Dick
BACKGROUND: Characterizing aggregate genetic risk for alcohol misuse and identifying variants involved in gene-by-environment interaction (G×E) effects has so far been a major challenge. We hypothesized that functional genomic information could be used to enhance detection of polygenic signal underlying alcohol misuse, and to prioritize identification of single nucleotide polymorphisms (SNPs) most likely to exhibit G×E effects. METHODS: We examined these questions in the young adult FinnTwin12 sample (n=1170)...
November 9, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/29118967/cold-perfusion-decellularization-of-whole-organ-porcine-pancreas-supports-human-fetal-pancreatic-cell-attachment-and-expression-of-endocrine-and-exocrine-markers
#14
Erik Elebring, Vijay K Kuna, Niclas Kvarnström, Suchitra Sumitran-Holgersson
Despite progress in the field of decellularization and recellularization, the outcome for pancreas has not been adequate. This might be due to the challenging dual nature of pancreas with both endocrine and exocrine tissues. We aimed to develop a novel and efficient cold-perfusion method for decellularization of porcine pancreas and recellularize acellular scaffolds with human fetal pancreatic stem cells. Decellularization of whole porcine pancreas at 4°C with sodium deoxycholate, Triton X-100 and DNase efficiently removed cellular material, while preserving the extracellular matrix structure...
January 2017: Journal of Tissue Engineering
https://www.readbyqxmd.com/read/29118755/apoptotic-cells-induced-signaling-for-immune-homeostasis-in-macrophages-and-dendritic-cells
#15
REVIEW
Uriel Trahtemberg, Dror Mevorach
Inefficient and abnormal clearance of apoptotic cells (efferocytosis) contributes to systemic autoimmune disease in humans and mice, and inefficient chromosomal DNA degradation by DNAse II leads to systemic polyarthritis and a cytokine storm. By contrast, efficient clearance allows immune homeostasis, generally leads to a non-inflammatory state for both macrophages and dendritic cells (DCs), and contributes to maintenance of peripheral tolerance. As many as 3 × 10(8) cells undergo apoptosis every hour in our bodies, and one of the primary "eat me" signals expressed by apoptotic cells is phosphatidylserine (PtdSer)...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29117135/zno-nanoparticles-protect-rna-from-degradation-better-than-dna
#16
Jayden McCall, Joshua J Smith, Kelsey N Marquardt, Katelin R Knight, Hunter Bane, Alice Barber, Robert K DeLong
Gene therapy and RNA delivery require a nanoparticle (NP) to stabilize these nucleic acids when administered in vivo. The presence of degradative hydrolytic enzymes within these environments limits the nucleic acids' pharmacologic activity. This study compared the effects of nanoscale ZnO and MgO in the protection afforded to DNA and RNA from degradation by DNase, serum or tumor homogenate. For double-stranded plasmid DNA degradation by DNase, our results suggest that the presence of MgO NP can protect DNA from DNase digestion at an elevated temperature (65 °C), a biochemical activity not present in ZnO NP-containing samples at any temperature...
November 8, 2017: Nanomaterials
https://www.readbyqxmd.com/read/29108278/epstein-barr-virus-brlf1-induces-genomic-instability-and-progressive-malignancy-in-nasopharyngeal-carcinoma-cells
#17
Sheng-Yen Huang, Chung-Chun Wu, Yu-Jhen Cheng, Sheng-Ping Chou, Yun-Jin Jiang, Kuo-Chang Chu, Ching-Hwa Tsai, Su-Fang Lin, Jen-Yang Chen
Nasopharyngeal carcinoma (NPC) is a serious health problem in China and Southeast Asia. Relapse is the major cause of mortality, but mechanisms of relapse are mysterious. Epstein-Barr virus (EBV) reactivation and host genomic instability (GI) have correlated with NPC development. Previously, we reported that lytic early genes DNase and BALF3 induce genetic alterations and progressive malignancy in NPC cells, implying lytic proteins may be required for NPC relapse. In this study, we show that immediate early gene BRLF1 induces chromosome mis-segregation and genomic instability in the NPC cells...
October 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/29077896/mirtrans-a-resource-of-transcriptional-regulation-on-micrornas-for-human-cell-lines
#18
Xu Hua, Rongjun Tang, Xiuxiu Xu, Zhi Wang, Qi Xu, Luxiao Chen, Edgar Wingender, Jie Li, Chenyu Zhang, Jin Wang
The cell-specific information of transcriptional regulation on microRNAs (miRNAs) is crucial to the precise understanding of gene regulations in various physiological and pathological processes existed in different tissues and cell types. The database, mirTrans, provides comprehensive information about cell-specific transcription of miRNAs including the transcriptional start sites (TSSs) of miRNAs, transcription factor (TF) to miRNA regulations and miRNA promoter sequences. mirTrans also maps the experimental H3K4me3 and DHS (DNase-I hypersensitive site) marks within miRNA promoters and expressed sequence tags (ESTs) within transcribed regions...
October 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29076707/evaluation-of-probiotic-attributes-of-lactobacillus-sp-isolated-from-cow-and-buffalo-curd-samples-collected-from-kandy
#19
M F Shuhadha, G J Panagoda, T Madhujith, N W Jayawardana
Introduction: Curd is a potential source of probiotic Lactobacillus species. Methods: This study was carried out to isolate and characterise Lactobacillus species available in curd samples sold in the market. Nine curd samples prepared using cow or buffalo milk were obtained from a local market in the Kandy district. Results: Seven isolates (LB 1-7) were identified based on their colony morphology and biochemical characteristics and evaluated for probiotic attributes such as low pH tolerance, resistance to bile salts, antimicrobial activity against Escherichia coli and Pseudomonas aeruginosa, antibiotic activity against erythromycin, chloramphenicol and norfloxacin, haemolytic activity and DNase activity...
September 30, 2017: Ceylon Medical Journal
https://www.readbyqxmd.com/read/29074739/genome-wide-discovery-of-active-regulatory-elements-and-transcription-factor-footprints-in-caenorhabditis-elegans-using-dnase-seq
#20
Paul Sternberg, Margaret Ho, Porfirio Quintero-Cadena
Deep sequencing of size-selected DNase I-treated chromatin (DNase-seq) allows high resolution measurement of chromatin accessibility to DNase I cleavage, permitting identification of de novo active cis-regulatory modules (CRMs) and individual transcription factor (TF) binding sites. We adapted DNase-seq to nuclei isolated from C. elegans embryos and L1 arrest larvae to generate high-resolution maps of TF binding. Over half of embryonic DNase I hypersensitive sites (DHSs) were annotated as noncoding, with 24% in intergenic, 12% in promoters and 28% in introns, with similar statistics observed in L1 arrest larvae...
October 26, 2017: Genome Research
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