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ChIP assay

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https://www.readbyqxmd.com/read/29039944/3d-printed-micro-flow-injection-analysis-platform-for-on-line-magnetic-nanoparticle-sorptive-extraction-of-antimicrobials-in-biological-specimens-as-a-front-end-to-liquid-chromatographic-assays
#1
Han Wang, David J Cocovi-Solberg, Bin Hu, Manuel Miró
In this work, the concept of 3D printed microflow injection (3D-µFI) embodying a dedicated multi-functional 3D-printed stator onto a rotary microvalve along with a mesofluidic sample preparation platform is proposed for the first time. A transparent 3D-printed stereolithographic mesofluidic chip device accommodating polyaniline (PANI) decorated magnetic nanoparticles (32.5±3.8 mg) is harnessed to in-line sorptive microextraction as a front end to liquid chromatography with peak focusing. As a proof of concept application, the 3D-µFI assembly was resorted to matrix clean-up and automatic programmable-flow determination of organic emerging contaminants (4-hydroxybenzoate analogs and triclosan as antimicrobial model analytes) in human saliva and urine samples...
October 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29036458/metabolic-syndrome-induces-over-expression-of-the-human-at1r-a-haplotype-dependent-effect-with-implications-on-cardio-renal-function
#2
Sudhir Jain, Nitin Puri, Anita Rana, Natalie Sirianni, Brahmaraju Mopidevi, Ashok Kumar
Background: The transcriptional regulation of the human AT1R gene in pathophysiologies, like the metabolic syndrome, is poorly understood. The human AT1R gene has polymorphisms in its promoter that can be arranged in two haplotypes. Variants -810T, -713T, -214A, and -153A always occur together (Hap-I) and variants -810A, -713G, -214C, and -153G form Hap-II. We have hypothesized that high fat diet will alter cellular transcriptional milieu and increase hAT1R gene expression in a haplotype-dependent manner...
October 5, 2017: American Journal of Hypertension
https://www.readbyqxmd.com/read/29028630/ezh2-regulates-dental-pulp-inflammation-by-direct-effect-on-inflammatory-factors
#3
Tianqian Hui, Peng A, Yuan Zhao, Jing Yang, Ling Ye, Chenglin Wang
OBJECTIVE: Pulpitis is a multi-factorial disease that could be caused by complex interactions between genetics, epigenetics and environmental factors. We aimed to evaluate the role of Enhancer of Zeste Homolog 2 (EZH2) in the inflammatory response of human dental pulp cells (HDPCs) and dental pulp tissues. METHODS: The expressions of inflammatory cytokines in HDPCs treated by EZH2 complex or EZH2 siRNA with or without rhTNF-α were examined by quantitative real-time polymerase chain reaction (q-PCR)...
October 7, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/29027171/chromatin-immunoprecipitation-assay-in-the-hyperthermoacidophilic-crenarchaeon-sulfolobus-acidocaldarius
#4
Kun Wang, Ann-Christin Lindås
Chromatin immunoprecipitation (ChIP) is a powerful method used for identifying genome-wide DNA-protein interactions in vivo. A large number of essential intracellular processes such as DNA replication, transcription regulation, chromatin stability, and others are all dependent on protein interactions with DNA. The DNA fragments enriched from the ChIP assay are analyzed by downstream applications, for example, microarray hybridization (ChIP-chip), quantitative PCR (ChIP-qPCR), or deep sequencing (ChIP-seq). This chapter presents a stepwise protocol for ChIP performed in hyperthermophilic archaea that we have successfully used in the hyperthermoacidophilic crenarchaeon Sulfolobus acidocaldarius...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29027168/chip-re-chip-co-occupancy-analysis-by-sequential-chromatin-immunoprecipitation
#5
Timothy V Beischlag, Gratien G Prefontaine, Oliver Hankinson
Chromatin immunoprecipitation (ChIP) exploits the specific interactions between DNA and DNA-associated proteins. It can be used to examine a wide range of experimental parameters. A number of proteins bound at the same genomic location can identify a multi-protein chromatin complex where several proteins work together to regulate gene transcription or chromatin configuration. In many instances, this can be achieved using sequential ChIP; or simply, ChIP-re-ChIP. Whether it is for the examination of specific transcriptional or epigenetic regulators, or for the identification of cistromes, the ability to perform a sequential ChIP adds a higher level of power and definition to these analyses...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29027162/how-to-combine-chip-with-qpcr
#6
Patrik Asp
Chromatin immunoprecipitation (ChIP) coupled with quantitative PCR (qPCR) has in the last 15 years become a basic mainstream tool in genomic research. Numerous commercially available ChIP kits, qPCR kits, and real-time PCR systems allow for quick and easy analysis of virtually anything chromatin-related as long as there is an available antibody. However, the highly accurate quantitative dimension added by using qPCR to analyze ChIP samples significantly raises the bar in terms of experimental accuracy, appropriate controls, data analysis, and data presentation...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29027161/considerations-on-experimental-design-and-data-analysis-of-chromatin-immunoprecipitation-experiments
#7
Antonio Jordán-Pla, Neus Visa
Arguably one of the most valuable techniques to study chromatin organization, ChIP is the method of choice to map the contacts established between proteins and genomic DNA. Ever since its inception, more than 30 years ago, ChIP has been constantly evolving, improving, and expanding its capabilities and reach. Despite its widespread use by many laboratories across a wide variety of disciplines, ChIP assays can be sometimes challenging to design, and are often sensitive to variations in practical implementation...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29026848/drug-induced-sialorrhea-and-microfluidic-chip-electrophoretic-analysis-of-engorged-adult-female-tick-saliva-of-haemaphysalis-longicornis-acari-ixodidae
#8
Mohammad Saiful Islam, Myung Jo You
BACKGROUND: The aim of the present study was to induce salivation in Haemaphysalis longicornis to increase saliva production and to characterize the collection of proteins present in the collected saliva using on-chip-electrophoresis. METHODS: Saliva of adult female engorged H. longicornis was collected by treatment with 0.2% dopamine hydrochloride. All protein samples were characterized by SDS-PAGE electrophoresis using a microfluidic High Sensitivity Protein Assay 250 kit by 2100 Bioanalyzer (Agilent Technologies, USA) under non-reducing conditions...
March 2017: Journal of Arthropod-borne Diseases
https://www.readbyqxmd.com/read/29025258/microrna-373-inhibits-cell-proliferation-and-invasion-via-targeting-brf2-in-human-non-small-cell-lung-cancer-a549-cell-line
#9
Lei Wang, Junfeng Qu, Li Zhou, Fei Liao, Ju Wang
Purpose: The purpose of this study was to investigate the biological role and mechanism of miR-373 targeting of TFIIB-related factor 2 (BRF2) in the regulation of non-small cell lung cancer (NSCLC) cells. Methods: miRNA microarray chip analysis of four paired NSCLC and adjacent non-tumor tissues was performed. Quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting were used to detect the expression levels of miR-373 and BRF2 in NSCLC tissues and cell lines...
October 12, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/29022910/long-non-coding-rna-myd88-promotes-growth-and-metastasis-in-hepatocellular-carcinoma-via-regulating-myd88-expression-through-h3k27-modification
#10
Xiaoliang Xu, Yin Yin, Junwei Tang, Yu Xie, Zhuo Han, Xudong Zhang, Qiaoyu Liu, Xihu Qin, Xinli Huang, Beicheng Sun
Enhanced Myd88 expression has been found in various parenchymal tumors especially in hepatocellular carcinoma with little mechanism of its upregulation known. A lot of long non-coding RNAs are reported to regulate the protein-coding genes which have location association through various mechanisms. In our study we confirmed a new long non-coding RNA Myd88 aberrant upregulated in HCC located upstream of Myd88 and verified a positive regulation relationship between them indicating that Lnc-Myd88 might participate in the enhanced expression of Myd88 in HCC...
October 12, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/29017567/impairment-of-igf2-gene-expression-in-prostate-cancer-is-triggered-by-epigenetic-dysregulation-of-igf2-dmr0-and-its-interaction-with-klf4
#11
Undraga Schagdarsurengin, Angela Lammert, Natalie Schunk, Diana Sheridan, Stefan Gattenloehner, Klaus Steger, Florian Wagenlehner, Temuujin Dansranjavin
BACKGROUND: Human cancer cells often exhibit impaired IGF2 expression and the underlying mechanisms are multifaceted and complex. Besides the well-known imprinting control region IGF2/H19-ICR, the involvement of a differentially methylated region in the promoter P0 of IGF2 gene (IGF2-DMR0) has been suggested. Here, we evaluate several mechanisms potentially leading to up- and/or down-regulation of IGF2 expression in prostate cancer and present a novel role of Kruppel-like factor 4 (KLF4) as a transcriptional regulator of IGF2 binding in IGF2-DMR0...
October 10, 2017: Cell Communication and Signaling: CCS
https://www.readbyqxmd.com/read/29017500/nf-%C3%AE%C2%BAb-potentiates-tumor-growth-by-suppressing-a-novel-target-lpts
#12
Dongbo Liu, Hongping Miao, Yuanyin Zhao, Xia Kang, Shenglan Shang, Wei Xiang, Rongchen Shi, Along Hou, Rui Wang, Kun Zhao, Yingzhe Liu, Yue Ma, Huan Luo, Hongming Miao, Fengtian He
BACKGROUND: Chronic inflammation is causally linked to the carcinogenesis and progression of most solid tumors. LPTS is a well-identified tumor suppressor by inhibiting telomerase activity and cancer cell growth. However, whether and how LPTS is regulated by inflammation signaling is still incompletely elucidated. METHODS: Real-time PCR and western blotting were used to determine the expression of p65 and LPTS. Reporter gene assay, electrophoretic mobility shift assay and chromatin immunoprecipitation were performed to decipher the regulatory mechanism between p65 and LPTS...
October 10, 2017: Cell Communication and Signaling: CCS
https://www.readbyqxmd.com/read/28994807/dry-film-photoresist-based-electrochemical-microfluidic-biosensor-platform-device-fabrication-on-chip-assay-preparation-and-system-operation
#13
Richard Bruch, André Kling, Gerald A Urban, Can Dincer
In recent years, biomarker diagnostics became an indispensable tool for the diagnosis of human disease, especially for the point-of-care diagnostics. An easy-to-use and low-cost sensor platform is highly desired to measure various types of analytes (e.g., biomarkers, hormones, and drugs) quantitatively and specifically. For this reason, dry film photoresist technology - enabling cheap, facile, and high-throughput fabrication - was used to manufacture the microfluidic biosensor presented here. Depending on the bioassay used afterwards, the versatile platform is capable of detecting various types of biomolecules...
September 19, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28994579/dual-amplification-fluorescence-assay-for-alpha-fetal-protein-utilizing-immuno-hybridization-chain-reaction-and-metal-enhanced-fluorescence-of-carbon-nanodots
#14
Dangdang Xu, Cui Liu, Chengyu Li, Chongyang Song, Yafeng Kang, Chu-Bo Qi, Yi Lin, Dai-Wen Pang, Hong-Wu Tang
As an emerging fascinating fluorescent nanomaterial, carbon nanodots (CDs) have attracted much attention due to their unique properties such as small size, antiphotobleaching and biocompatibility. However, its use in biomedical analysis is limited due to its low quantum yield. Herein, we constructed a dual amplification fluorescence sensor by incorporating immuno-hybridization chain reaction (HCR) and metal-enhanced fluorescence (MEF) of CDs for the detection of alpha fetal protein (AFP). The immuno-plasmonic slide and detection antibodies conjugated oligonucleotide initiator are served to capture and probe AFP molecules, respectively...
October 10, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28992614/serum-and-glucocorticoid-inducible-kinase-1-sensitive-survival-proliferation-and-migration-of-rhabdomyosarcoma-cells
#15
Evi Schmid, Matias Julian Stagno, Jing Yan, Sabine Schleicher, Willi Yu, Sabina Honisch, Florian Lang, Jörg Fuchs, Guido Seitz
BACKGROUND/AIMS: Rhabdomyosarcoma, the most common pediatric soft tissue sarcoma, may show an intrinsic refractoriness to standard chemotherapy in advanced tumor stages, which is associated with poor prognosis. Cellular mechanisms conferring tumor cell survival and therapy resistance in many tumor types include the serum & glucocorticoid inducible kinase (SGK) 1 pathway, a kinase expressed ubiquitously with particularly strong expression in skeletal muscle and some tumor types. The present study explored whether SGK1 is expressed in rhabdomyosarcoma and, if so, whether this kinase impacts on tumor cell survival, proliferation and migration...
October 9, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28992113/two-transcriptional-activators-of-n-acetylserotonin-o-methyltransferase-2-and-melatonin-biosynthesis-in-cassava
#16
Yunxie Wei, Guoyin Liu, Yujing Bai, Feiyu Xia, Chaozu He, Haitao Shi
Similar to the situation in animals, melatonin biosynthesis is regulated by four sequential enzymatic steps in plants. Although the melatonin synthesis genes have been identified in various plants, the upstream transcription factors of them remain unknown. In this study on cassava (Manihot esculenta), we found that MeWRKY79 and heat-shock transcription factor 20 (MeHsf20) targeted the W-box and the heat-stress elements (HSEs) in the promoter of N-acetylserotonin O-methyltransferase 2 (MeASMT2), respectively...
August 26, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28991925/next-generation-elisa-diagnostic-assay-for-chagas-disease-based-on-the-combination-of-short-peptidic-epitopes
#17
Juan Mucci, Santiago J Carmona, Romina Volcovich, Jaime Altcheh, Estefanía Bracamonte, Jorge D Marco, Morten Nielsen, Carlos A Buscaglia, Fernán Agüero
Chagas Disease, caused by the protozoan Trypanosoma cruzi, is a major health and economic problem in Latin America for which no vaccine or appropriate drugs for large-scale public health interventions are yet available. Accurate diagnosis is essential for the early identification and follow up of vector-borne cases and to prevent transmission of the disease by way of blood transfusions and organ transplantation. Diagnosis is routinely performed using serological methods, some of which require the production of parasite lysates, parasite antigenic fractions or purified recombinant antigens...
October 9, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28991232/the-extracellular-matrix-protein-mindin-attenuates-colon-cancer-progression-by-blocking-angiogenesis-via-egr-1-mediated-regulation
#18
L-F Wang, Y-S Liu, B Yang, P Li, X-S Cheng, C-X Xiao, J-J Liu, S Li, J-L Ren, B Guleng
Mindin, a secreted, highly conserved extracellular matrix (ECM) protein, exerts a broad spectrum of effects on the innate immune system. However, its function in colorectal cancer (CRC) progression is not well established, and its upstream regulation mechanisms remain unclear. Contrary to previous reports, this study used two different enzyme-linked immunosorbent assay (ELISA) kits to show that the serum level of mindin was significantly decreased in CRC patients and that this decreased level is more significantly associated with the early stages of the disease...
October 9, 2017: Oncogene
https://www.readbyqxmd.com/read/28988979/irx3-promotes-the-browning-of-white-adipocytes-and-its-rare-variants-are-associated-with-human-obesity-risk
#19
Yaoyu Zou, Peng Lu, Juan Shi, Wen Liu, Minglan Yang, Shaoqian Zhao, Na Chen, Maopei Chen, Yingkai Sun, Aibo Gao, Qingbo Chen, Zhiguo Zhang, Qinyun Ma, Tinglu Ning, Xiayang Ying, Jiabin Jin, Xiaxing Deng, Baiyong Shen, Yifei Zhang, Bo Yuan, Sophie Kauderer, Simin Liu, Jie Hong, Ruixin Liu, Guang Ning, Weiqing Wang, Weiqiong Gu, Jiqiu Wang
BACKGROUND: IRX3 was recently reported as the effector of the FTO variants. We aimed to test IRX3's roles in the browning program and to evaluate the association between the genetic variants in IRX3 and human obesity. METHODS: IRX3 expression was examined in beige adipocytes in human and mouse models, and further validated in induced beige adipocytes. The browning capacity of primary preadipocytes was assessed with IRX3 knockdown. Luciferase reporter analysis and ChIP assay were applied to investigate IRX3's effects on UCP1 transcriptional activity...
September 13, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28986581/nucleosome-stability-measured-in-situ-by-automated-quantitative-imaging
#20
László Imre, Zoltán Simándi, Attila Horváth, György Fenyőfalvi, Péter Nánási, Erfaneh Firouzi Niaki, Éva Hegedüs, Zsolt Bacsó, Urbain Weyemi, Rebekka Mauser, Juan Ausio, Albert Jeltsch, William Bonner, László Nagy, Hiroshi Kimura, Gábor Szabó
Current approaches have limitations in providing insight into the functional properties of particular nucleosomes in their native molecular environment. Here we describe a simple and powerful method involving elution of histones using intercalators or salt, to assess stability features dependent on DNA superhelicity and relying mainly on electrostatic interactions, respectively, and measurement of the fraction of histones remaining chromatin-bound in the individual nuclei using histone type- or posttranslational modification- (PTM-) specific antibodies and automated, quantitative imaging...
October 6, 2017: Scientific Reports
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