keyword
MENU ▼
Read by QxMD icon Read
search

ChIP assay

keyword
https://www.readbyqxmd.com/read/28527901/photonic-ring-resonance-is-a-versatile-platform-for-performing-multiplex-immunoassays-in-real-time
#1
Sasi Mudumba, Sophia de Alba, Randy Romero, Carli Cherwien, Alice Wu, Jue Wang, Martin A Gleeson, Muzammil Iqbal, Rufus W Burlingame
Photonic ring resonance is a property of light where in certain circumstances specific wavelengths are trapped in a ring resonator. Sensors based on silicon photonic ring resonators function by detecting the interaction between light circulating inside the sensor and matter deposited on the sensor surface. Binding of biological material results in a localized change in refractive index on the sensor surface, which affects the circulating optical field extending beyond the sensor boundary. That is, the resonant wavelength will change when the refractive index of the medium around the ring resonator changes...
May 17, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28526484/regulation-of-cacybp-sip-expression-by-nfat1-transcription-factor
#2
Beata Kądziołka, Wiesława Leśniak, Anna Filipek
In this work we have shown that NFAT1 transcription factor is involved in the regulation of CacyBP/SIP expression. We have demonstrated, by applying Western blot, RT-PCR and luciferase assay that the level of CacyBP/SIP increases upon NFAT1 overexpression. Moreover, inhibition or stimulation of NFAT transcriptional activity exerts a corresponding effect on the expression of CacyBP/SIP gene. Furthermore, EMSA and chromatin immunoprecipitation (ChIP) assay have shown that NFAT1 binds to its specific binding sites within the CacyBP/SIP gene...
May 11, 2017: Immunobiology
https://www.readbyqxmd.com/read/28525851/a-fully-integrated-distance-readout-elisa-chip-for-point-of-care-testing-with-sample-in-answer-out-capability
#3
Dan Liu, Xingrui Li, Junkai Zhou, Shibo Liu, Tian Tian, Yanling Song, Zhi Zhu, Leiji Zhou, Tianhai Ji, Chaoyong Yang
Enzyme-linked immunosorbent assay (ELISA) is a popular laboratory technique for detection of disease-specific protein biomarkers with high specificity and sensitivity. However, ELISA requires labor-intensive and time-consuming procedures with skilled operators and spectroscopic instrumentation. Simplification of the procedures and miniaturization of the devices are crucial for ELISA-based point-of-care (POC) testing in resource-limited settings. Here, we present a fully integrated, instrument-free, low-cost and portable POC platform which integrates the process of ELISA and the distance readout into a single microfluidic chip...
May 4, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28522256/sporadic-early-onset-diffuse-gastric-cancers-have-high-frequency-of-somatic-cdh1-alterations-but-low-frequency-of-somatic-rhoa-mutations-compared-with-late-onset-cancers
#4
Soo Young Cho, Jun Won Park, Yang Liu, Young Soo Park, Ju Hee Kim, Hanna Yang, Hyejin Um, Woo Ri Ko, Byung Il Lee, Sun Young Kwon, Seung Wan Ryu, Chae Hwa Kwon, Do Youn Park, Jae-Hyuk Lee, Sang Il Lee, Kyu Sang Song, Hoon Hur, Sang-Uk Han, Heekyung Chang, Su-Jin Kim, Byung-Sik Kim, Jeong-Hwan Yook, Moon-Won Yoo, Beom-Su Kim, In-Seob Lee, Myeong-Cherl Kook, Nina Thiessen, An He, Chip Stewart, Andrew Dunford, Jaegil Kim, Juliann Shih, Gordon Saksena, Andrew D Cherniack, Steven Schumacher, Amaro-Taylor Weiner, Mara Rosenberg, Gad Getz, Eun Gyeong Yang, Min Hee Ryu, Adam J Bass, Hark Kyun Kim
BACKGROUND & AIMS: Early-onset gastric cancer, which develops in younger patients than most gastric cancers, is usually detected at advanced stages, has diffuse histologic features, and occurs more frequently in women. We investigated somatic genomic alterations associated with the unique characteristics of sporadic diffuse gastric cancers (DGCs) from younger patients. METHODS: We conducted whole exome and RNA sequence analyses of 80 resected DGC samples from patients 45 years old or younger in Korea...
May 15, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28520400/femtomole-scale-high-throughput-screening-of-protein-ligands-with-droplet-based-thermal-shift-assay
#5
Wen-Wen Liu, Ying Zhu, Qun Fang
There is a great demand to measure protein-ligand interactions in rapid and low cost way. Here we developed a microfluidic droplet-based thermal shift assay (dTSA) system for high throughput screening of small-molecule protein ligands. The system is composed of a nanoliter droplet array chip, a microfluidic droplet robot, and a real-time fluorescence detection system. Total 324 assays could be performed in parallel in a single chip with an 18 × 18 droplet array. The consumption of dTSA for each protein or ligand sample was only 5 nL (femtomole scale), which is significantly reduced by over 3 orders of magnitude compared with those in 96 or 384-well plate-based systems...
May 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28520392/gold-nanostar-enhanced-surface-plasmon-resonance-detection-of-an-antibiotic-at-attomolar-concentrations-via-an-aptamer-antibody-sandwich-assay
#6
Suhee Kim, Hye Jin Lee
A new sandwich assay for tetracycline (TC) involving a DNA aptamer and antibody pair is demonstrated in conjunction with gold nanostar (GNS) enhanced surface plasmon resonance (SPR) to achieve detection in the low attomolar range. GNS particles were covalently functionalized with the antibody probe (antiTC) and integrated into a surface sandwich assay in conjunction with a SPR gold chip modified with the TC-specific aptamer. After it was demonstrated that both affinity probes can bind simultaneously to TC, optimization of the assay was performed using either antiTC only or GNS-antiTC conjugates to interact with aptamer/TC complexes present on the chip surface...
May 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28515787/a-computational-approach-for-the-functional-classification-of-the-epigenome
#7
Francesco Gandolfi, Anna Tramontano
BACKGROUND: In the last decade, advanced functional genomics approaches and deep sequencing have allowed large-scale mapping of histone modifications and other epigenetic marks, highlighting functional relationships between chromatin organization and genome function. Here, we propose a novel approach to explore functional interactions between different epigenetic modifications and extract combinatorial profiles that can be used to annotate the chromatin in a finite number of functional classes...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28513702/stretchable-impedance-sensor-for-mammalian-cell-proliferation-measurements
#8
Xudong Zhang, William Wang, Fang Li, Ioana Voiculescu
This paper presents the fabrication and testing of a novel stretchable electric cell-substrate impedance sensing (ECIS) lab on a chip device. This is the first time that ECIS electrodes were fabricated on a stretchable polydimethylsiloxane (PDMS) substrate and ECIS measurements were performed on mammalian cells exposed to cyclic strain. The stretchable ECIS biosensors simulate in vitro the dynamic environment of organisms, such as pulsation, bending and stretching, which enables investigations on cell behavior that undergoes mechanical stimuli in biological tissue...
May 17, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28510366/hmga2-plays-an-important-role-in-cr-vi-induced-autophagy
#9
Fan Yang, Lian Zhao, Dan Mei, Liping Jiang, Chengyan Geng, Qiujuan Li, Xiaofeng Yao, Yong Liu, Ying Kong, Jun Cao
Cr (VI) is mutagenic and carcinogenic, but the mechanism is unclear. In this study, the involvement of high mobility group A2 (HMGA2) in Cr (VI)-induced autophagy was investigated. Cr (VI) treatment induced formation of autophagosomes, increased expression of LC3II, Atg12-Atg5, Atg4, Atg10, HMGA1 and HMGA2 proteins, and decreased the expression of p62 in A549 cells. Silencing of HMGA2 gene by siRNA blocked Cr (VI)-induced formation of autophagosomes, expression of LC3II, Atg12-Atg5, Atg10 and reduction of p62...
May 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28505562/ultra-fast-electronic-detection-of-antimicrobial-resistance-genes-using-isothermal-amplification-and-thin-film-transistor-sensors
#10
Chunxiao Hu, Sumit Kalsi, Ioannis Zeimpekis, Kai Sun, Peter Ashburn, Carrie Turner, J Mark Sutton, Hywel Morgan
A low cost thin-film transistor (TFT) nanoribbon (NR) sensor has been developed for rapid real-time detection of DNA amplification using an isothermal Recombinase Polymerase Amplification (RPA) method. The semiconductor chip measures DNA amplification through a pH change, rather than via fluorescence. The utility of the method was demonstrated by amplifying CTX-M and NDM, two genes that confer bacterial resistance to cephalosporins and carbapenems, respectively. It is shown that this approach provides extremely fast and sensitive detection...
May 9, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28505247/single-cell-regulome-data-analysis-by-scrat
#11
Zhicheng Ji, Weiqiang Zhou, Hongkai Ji
Summary: Emerging single-cell technologies (e.g., single-cell ATAC-seq, DNase-seq or ChIP-seq) have made it possible to assay regulome of individual cells. Single-cell regulome data are highly sparse and discrete. Analyzing such data is challenging. User-friendly software tools are still lacking. We present SCRAT, a Single-Cell Regulome Analysis Toolbox with a graphical user interface, for studying cell heterogeneity using single-cell regulome data. SCRAT can be used to conveniently summarize regulatory activities according to different features (e...
May 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28500307/alox5-exhibits-anti-tumor-and-drug-sensitizing-effects-in-mll-rearranged-leukemia
#12
Yungui Wang, Jennifer R Skibbe, Chao Hu, Lei Dong, Kyle Ferchen, Rui Su, Chenying Li, Hao Huang, Hengyou Weng, Huilin Huang, Xi Qin, Jie Jin, Jianjun Chen, Xi Jiang
MLL-rearranged acute myeloid leukemia (AML) remains a fatal disease with a high rate of relapse and therapeutic failure due to chemotherapy resistance. In analysis of our Affymetrix microarray profiling and chromatin immunoprecipitation (ChIP) assays, we found that ALOX5 is especially down-regulated in MLL-rearranged AML, via transcription repression mediated by Polycomb repressive complex 2 (PRC2). Colony forming/replating and bone marrow transplantation (BMT) assays showed that Alox5 exhibited a moderate anti-tumor effect both in vitro and in vivo...
May 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28500268/a-rice-nac-transcription-factor-promotes-leaf-senescence-via-aba-biosynthesis
#13
Chanjuan Mao, Songchong Lu, Bo Lv, Bin Zhang, Jiabin Shen, Jianmei He, Liqiong Luo, Dandan Xi, Xu Chen, Feng Ming
It has been well known that ABA induced leaf senescence and premature leaf senescence negatively affects the yield of rice. However, the molecular mechanism underlying this relationship, especially the upstream transcriptional network that modulates ABA level during leaf senescence, remains largely unknown. Here, we demonstrate a rice NAC transcription factor, OsNAC2, participated in ABA-induced leaf senescence. Overexpression of OsNAC2 dramatically accelerated leaf senescence, whereas its knockdown lines showed a delay in leaf senescence...
May 12, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28499864/role-of-hepatitis-b-core-protein-in-hbv-transcription-and-recruitment-of-histone-acetyltransferases-to-cccdna-minichromosome
#14
Chun Kong Chong, Ching Yan Serene Cheng, Sin Yi Jasmine Tsoi, Fung-Yu Huang, Fen Liu, Wai-Kay Seto, Ching-Lung Lai, Man-Fung Yuen, Danny Ka-Ho Wong
The hepatitis B core protein (HBc) has been suggested to interact with covalently closed circular DNA (cccDNA) and regulate hepatitis B virus (HBV) transcription. However, direct evidence is lacking. We aimed to identify the specific HBc region(s) responsible for transcription regulation and its interaction with cccDNA. Seventeen mutants with mutations at the four arginine-rich clusters of the HBc carboxyl-terminal domain (CTD) were created. The effect of HBc mutations on the levels of HBV DNA, RNA, and hepatitis B surface antigen (HBsAg) were measured...
May 10, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28499349/epimetheus-a-multi-profile-normalizer-for-epigenomic-sequencing-data
#15
Mohamed-Ashick M Saleem, Marco-Antonio Mendoza-Parra, Pierre-Etienne Cholley, Matthias Blum, Hinrich Gronemeyer
BACKGROUND: Exponentially increasing numbers of NGS-based epigenomic datasets in public repositories like GEO constitute an enormous source of information that is invaluable for integrative and comparative studies of gene regulatory mechanisms. One of today's challenges for such studies is to identify functionally informative local and global patterns of chromatin states in order to describe the regulatory impact of the epigenome in normal cell physiology and in case of pathological aberrations...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28496150/long-non-coding-rna-particle-bridges-histone-and-dna-methylation
#16
Valerie Bríd O'Leary, Sarah Hain, Doris Maugg, Jan Smida, Omid Azimzadeh, Soile Tapio, Saak Victor Ovsepian, Michael John Atkinson
PARTICLE (Gene PARTICL- 'Promoter of MAT2A-Antisense RadiaTion Induced Circulating LncRNA) expression is transiently elevated following low dose irradiation typically encountered in the workplace and from natural sources. This long non-coding RNA recruits epigenetic silencers for cis-acting repression of its neighbouring Methionine adenosyltransferase 2A gene. It now emerges that PARTICLE operates as a trans-acting mediator of DNA and histone lysine methylation. Chromatin immunoprecipitation sequencing (ChIP-seq) and immunological evidence established elevated PARTICLE expression linked to increased histone 3 lysine 27 trimethylation...
May 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28495269/identification-of-novel-regulatory-gre-binding-elements-in-the-porcine-ip3r1-gene-promoter-and-their-transcriptional-activation-under-glucocorticoid-stimulation
#17
Jin Chai, Qi Xiong, Dan Wang, Xuebing Wan, Hongdan Niu, Hong Xiang, Huanan Li, Hongshuai Wang, Rong Zheng, Jian Peng, Siwen Jiang
Inositol 1,4,5-trisphosphate receptor 1 (IP3R1) is a type of ligand-gated calcium channel that is expressed predominantly in mammalian skeletal muscle, where it acts as a key regulator of calcium homeostasis. In meat, calcium disequilibrium is accompanied by the deterioration of meat quality. Here we show that serum cortisol concentration was higher and the IP3R1 gene expression level increased markedly in pigs exposed to high stress. In porcine primary muscle cells, dexamethasone (DEX, a synthetic glucocorticoid) increased the protein levels of porcine IP3R1 and GRα, and cell apoptosis, and the specific GRα inhibitor RU486 attenuated these effects...
May 8, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28493959/novel-genetic-locus-at-mhc-region-for-esophageal-squamous-cell-carcinoma-in-chinese-populations
#18
Peng Zhang, Xin-Min Li, Xue-Ke Zhao, Xin Song, Ling Yuan, Fang-Fang Shen, Zong-Min Fan, Li-Dong Wang
BACKGROUND: Our previous genome-wide association study (GWAS) identified three independent single nucleotide polymorphisms (SNPs) in human major histocompatibility complex (MHC) region showing association with esophageal squamous cell carcinoma (ESCC). In this study, we increased GWAS sample size on MHC region and performed validation in an independent ESCC cases and normal controls with aim to find additional loci at MHC region showing association with an increased risk to ESCC. METHODS: The 1,077 ESCC cases and 1,733 controls were genotyped using Illumina Human 610-Quad Bead Chip, and 451 cases and 374 controls were genotyped using Illumina Human 660W-Quad Bead Chip...
2017: PloS One
https://www.readbyqxmd.com/read/28490809/hepatic-estrogen-receptor-%C3%AE-is-critical-for-regulation-of-gluconeogenesis-and-lipid-metabolism-in-males
#19
Shuiqing Qiu, Juliana Torrens Vazquez, Erin Boulger, Haiyun Liu, Ping Xue, Mehboob Ali Hussain, Andrew Wolfe
Impaired estrogens action is associated with features of the metabolic syndrome in animal models and humans. We sought to determine whether disruption of hepatic estrogens action in adult male mice could recapitulate aspects of the metabolic syndrome to understand the mechanistic basis for the phenotype. We found 17β-estradiol (E2) inhibited hepatic gluconeogenic genes such as phosphoenolpyruvate carboxykinase 1 (Pck-1) and glucose 6-phosphatase (G6Pase) and this effect was absent in mice lacking liver estrogen receptor α (Esr1) (LERKO mice)...
May 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28490592/epstein-barr-virus-rta-mediated-accumulation-of-dna-methylation-interferes-with-ctcf-binding-in-both-host-and-viral-genomes
#20
Yen-Ju Chen, Yu-Lian Chen, Yao Chang, Chung-Chun Wu, Ying-Chieh Ko, Sai Wah Tsao, Jen-Yang Chen, Su-Fang Lin
Rta, an Epstein-Barr virus (EBV) immediate-early protein, reactivates viral lytic replication that is closely associated with tumorigenesis. In previous studies, we demonstrated that in epithelial cells Rta efficiently induced cellular senescence, which is an irreversible G1 arrest likely to provide a favorable environment for productive replications of EBV and Kaposi's sarcoma-associated herpesvirus (KSHV). To restrict progression of the cell cycle, Rta simultaneously upregulates CDK inhibitors and downregulates MYC, CCND1 and JUN, among others...
May 10, 2017: Journal of Virology
keyword
keyword
99484
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"