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https://www.readbyqxmd.com/read/28334916/mocap-large-scale-inference-of-transcription-factor-binding-sites-from-chromatin-accessibility
#1
Xi Chen, Bowen Yu, Nicholas Carriero, Claudio Silva, Richard Bonneau
Differential binding of transcription factors (TFs) at cis-regulatory loci drives the differentiation and function of diverse cellular lineages. Understanding the regulatory interactions that underlie cell fate decisions requires characterizing TF binding sites (TFBS) across multiple cell types and conditions. Techniques, e.g. ChIP-Seq can reveal genome-wide patterns of TF binding, but typically requires laborious and costly experiments for each TF-cell-type (TFCT) condition of interest. Chromosomal accessibility assays can connect accessible chromatin in one cell type to many TFs through sequence motif mapping...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334623/rapid-on-chip-apoptosis-assay-on-human-carcinoma-cells-based-on-annexin-v-quantum-dot-probes
#2
Helena Montón, Mariana Medina-Sánchez, Joan Antoni Soler, Andrzej Chałupniak, Carme Nogués, Arben Merkoçi
Despite all the efforts made over years to study the cancer expression and the metastasis event, there is not a clear understanding of its origins and effective treatment. Therefore, more specialized and rapid techniques are required for studying cell behaviour under different drug-based treatments. Here we present a quantum dot signalling-based cell assay carried out in a segmental microfluidic device that allows studying the effect of anti-cancer drugs in cultured cell lines by monitoring phosphatidylserine translocation that occurs in early apoptosis...
March 18, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28334197/ppar%C3%AE-regulates-tumor-cell-proliferation-and-senescence-via-a-novel-target-gene-carnitine-palmitoyltransferase-1c
#3
Yixin Chen, Yongtao Wang, Yaoyao Huang, Hang Zeng, Bingfang Hu, Lihuan Guan, Huizhen Zhang, Ai-Ming Yu, Caroline H Johnson, Frank J Gonzalez, Min Huang, Huichang Bi
Carnitine palmitoyltransferase 1C (CPT1C), an enzyme located in the outer mitochondria membrane, has a crucial role in fatty acid transport and oxidation. It is also involved in cell proliferation and is a potential driver for cancer cell senescence. However, its upstream regulatory mechanism is unknown. Peroxisome proliferator activated receptor α (PPARα) is a ligand-activated transcription factor that regulates lipid metabolism and tumor progression. The current study aimed to elucidate whether and how PPARα regulates CPT1C and then affects cancer cell proliferation and senescence...
March 3, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28334049/mmp1-expression-is-activated-by-slug-and-enhances-multi-drug-resistance-mdr-in-breast-cancer
#4
Ching-Ju Shen, Yu-Ling Kuo, Chien-Chung Chen, Ming-Jenn Chen, Ya-Min Cheng
High matrix metalloproteinase 1 (MMP1) expression is associated with enhanced breast cancer growth and metastasis and also might predict poor prognosis. In this study, we further investigated the functional role of MMP1 and how it is upregulated in multi-drug resistant (MDR) breast cancer cells. By retrieving microarray data in GEO datasets and the survival data in the Kaplan Meier plotter, we observed that MMP1 is significantly upregulated in MCF-7/ADR cells compared to the parental MCF-7 cells, while high MMP1 expression is associated with worse overall survival (OS) and recurrence free survival (RFS) in breast cancer patients after systematic therapy...
2017: PloS One
https://www.readbyqxmd.com/read/28333959/fnc-efficiently-inhibits-mantle-cell-lymphoma-growth
#5
Yan Zhang, Rong Zhang, Xixi Ding, Bangan Peng, Ning Wang, Fang Ma, Youmei Peng, Qingduan Wang, Junbiao Chang
FNC, 2'-deoxy-2'-β-fluoro-4'-azidocytidine, is a novel cytidine analogue, that has shown strong antiproliferative activity in human lymphoma, lung adenocarcinoma and acute myeloid leukemia. In this study, we investigated the effects of FNC on mantle cell lymphoma (MCL) and the underlying mechanisms. In in vitro experiments, cell viability was detected by the CCK8 assay, and cell cycle progression and apoptosis were assessed by flow cytometry, and the expression of relative apoptosis proteins were detected by Western Blot...
2017: PloS One
https://www.readbyqxmd.com/read/28327666/hypoxia-induces-h19-expression-through-direct-and-indirect-hif-1%C3%AE-activity-promoting-oncogenic-effects-in-glioblastoma
#6
Weining Wu, Qi Hu, Er Nie, Tianfu Yu, Youzhi Wu, Tongle Zhi, Kuan Jiang, Feng Shen, Yingyi Wang, Junxia Zhang, Yongping You
H19 expression is elevated in many human tumors including glioblastomas, suggesting an oncogenic role for the long noncoding RNA; yet the upregulation of H19 in glioblastomas remains unclear. Here we report that hypoxia significantly stimulated H19 expression in glioblastoma cell lines, which was related to hypoxia-inducible factors 1α (Hif-1α). Hif-1α promoted H19 expression in U87 and U251 cells. Meanwhile PTEN is an advantageous factor to affect H19 expression, through attenuating Hif-1α stability. Hif-1α also positively correlates with H19 in human glioblastoma samples depending on PTEN status...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327356/type-2-inositol-trisphosphate-receptor-gene-expression-in-hepatocytes-is-regulated-by-cyclic-amp
#7
Emma Kruglov, M Ananthanarayanan, Pedro Sousa, Jittima Weerachayaphorn, Mateus T Guerra, Michael H Nathanson
The type 2 inositol 1,4,5-trisphosphate receptor (IP3R2) is the principal intracellular Ca(2+) release channel in hepatocytes, and so is important for bile secretion and other functions. IP3R2 activity is regulated in part by post-translational modifications but little is known about transcriptional regulation of its expression. We found that both IP3R2 mRNA and protein levels in liver were increased during fasting. Treatment of hepatocytes with forskolin or 8-CPT-cAMP also increased IP3R2, and this was reduced by actinomycin D...
March 18, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28327155/vasohibin-2-reduces-chemosensitivity-to-gemcitabine-in-pancreatic-cancer-cells-via-jun-proto-oncogene-dependent-transactivation-of-ribonucleotide-reductase-regulatory-subunit-m2
#8
Min Tu, Haifeng Li, Nan Lv, Chunhua Xi, Zipeng Lu, Jishu Wei, Jianmin Chen, Feng Guo, Kuirong Jiang, Guoxin Song, Wentao Gao, Yi Miao
BACKGROUND: Vasohibin 2 (VASH2) has previously been identified as an agiogenenic factor and a cancer related protein. Here we investigated the association of VASH2 expression and chemoresistance in pancreatic cancer. METHODS: Immunohistochemical staining for VASH2 was performed on 102 human pancreatic cancer samples. Pancreatic cancer cell line models exhibiting overexpression or knockdown of VASH2 were generated. Gene expression analyses were carried out to determine genes differentially regulated by VASH2...
March 21, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28327132/simultaneous-analysis-of-mirna-mrna-in-human-meningiomas-by-integrating-transcriptome-a-relationship-between-ptx3-and-mir-29c
#9
Altay Burak Dalan, Sukru Gulluoglu, Emre Can Tuysuz, Aysegul Kuskucu, Cumhur Kaan Yaltirik, Oguz Ozturk, Ugur Ture, Omer Faruk Bayrak
BACKGROUND: Although meningioma is a common disease, there is a lack of understanding of the underlying molecular mechanisms behind its initiation and progression. We used combined miRNA-mRNA transcriptome analysis to discover dysregulated genes and networks in meningiomas. METHODS: Fourteen fresh-frozen meningioma samples and one human meningeal cell line were analyzed by using miRNA and whole transcriptome microarray chips. Data was filtered and analyzed. Candidate miRNAs and mRNAs were selected for validation in fifty-eight patient samples...
March 21, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28324065/neurod-factors-discriminate-mineralocorticoid-from-glucocorticoid-receptor-dna-binding-in-the-male-rat-brain
#10
Lisa T C M van Weert, Jacobus C Buurstede, Ahmed Mahfouz, Pamela S M Braakhuis, J Annelies E Polman, Hetty C M Sips, Benno Roozendaal, Judit Balog, E Ronald de Kloet, Nicole A Datson, Onno C Meijer
In the limbic brain, mineralocorticoid receptors (MRs) and glucocorticoid receptors (GRs) both function as receptors for the naturally occurring glucocorticoids (corticosterone/cortisol), but mediate distinct effects on cellular physiology via transcriptional mechanisms. The transcriptional basis for specificity of these MR- versus GR-mediated effects is unknown. To address this conundrum we have identified the extent of MR/GR DNA binding selectivity in the rat hippocampus using chromatin immunoprecipitation followed by sequencing (ChIP-seq)...
January 24, 2017: Endocrinology
https://www.readbyqxmd.com/read/28322799/novel-method-for-measurement-of-heparin-anticoagulant-activity-using-spr
#11
Jing Zhao, Xinyue Liu, Anju Malhotra, Quanhong Li, Fuming Zhang, Robert J Linhardt
A novel method has been developed for the easy measurement of heparin's anticoagulant activity using surface plasmon resonance. The anticoagulant activity of target heparin was evaluated by measuring the competitive antithrombin III binding of analyte heparin in the solution phase and USP heparin immobilized on chip surface. Heparins, obtained from different animal sources, and low molecular weight heparins were analyzed. The results were reproducible and correlated well with the results of chromogenic assays (correlation coefficient r = 0...
March 18, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28322517/materials-for-microfluidic-immunoassays-a-review
#12
REVIEW
Lei Mou, Xingyu Jiang
Conventional immunoassays suffer from at least one of these following limitations: long processing time, high costs, poor user-friendliness, technical complexity, poor sensitivity and specificity. Microfluidics, a technology characterized by the engineered manipulation of fluids in channels with characteristic lengthscale of tens of micrometers, has shown considerable promise for improving immunoassays that could overcome these limitations in medical diagnostics and biology research. The combination of microfluidics and immunoassay can detect biomarkers with faster assay time, reduced volumes of reagents, lower power requirements, and higher levels of integration and automation compared to traditional approaches...
March 21, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28322300/noncanonical-nf-%C3%AE%C2%BAb-mediates-the-suppressive-effect-of-neutrophil-elastase-on-il-8-cxcl8-by-inducing-nkrf-in-human-airway-smooth-muscle
#13
Shu-Chuan Ho, Sheng-Ming Wu, Po-Hao Feng, Wen-Te Liu, Kuan-Yuan Chen, Hsiao-Chi Chuang, Yao-Fei Chan, Lu-Wei Kuo, Kang-Yun Lee
Neutrophil elastase (NE) suppresses IL-8/CXCL8 in human airway smooth muscle cells (hASM) while stimulating its production in respiratory epithelial cells. This differential effect is mediated by the selective induction of NKRF and dysregulation in chronic inflammatory diseases. We hypothesized that the differential activation of NF-κB subunits confer the opposite effect of NKRF on IL-8/CXCL8 in primary hASM and A549 cells stimulated with NE. The events occurring at the promoters of NKRF and IL-8/CXCL8 were observed by ChIP assays, and the functional role of RelB was confirmed by knockdown and overexpression...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28320521/differential-mirna-expression-analysis-during-late-stage-terminal-hindgut-development-in-fetal-rats
#14
Shuguang Jin, Junxiang Wang, Hong Chen, Bo Xiang
BACKGROUND: Terminal hindgut deformity is the leading digestive tract malformation, however, the etiology and pathogenesis remained unknown. To date, gene expression abnormalities were considered the primary cause of these diseases. miRNAs have been found to play an important role in regulating the expression of genes. METHODS: A total of 24 pregnant rats were randomly divided into two groups. The experimental group (n=12) received 1% ethylenethiourea (125mg/kg) by gavage on gestational day 11, while the control group (n=12) received the same volume of distilled water...
March 12, 2017: Journal of Pediatric Surgery
https://www.readbyqxmd.com/read/28319902/ultra-high-sensitivity-of-the-non-immunological-affinity-of-graphene-oxide-peptide-based-surface-plasmon-resonance-biosensors-to-detect-human-chorionic-gonadotropin
#15
Nan-Fu Chiu, Chia-Tzu Kuo, Ting-Li Lin, Chia-Chen Chang, Chen-Yu Chen
Specific peptide aptamers can be used in place of expensive antibody proteins, and they are gaining increasing importance as sensing probes due to their potential in the development of non-immunological assays with high sensitivity, affinity and specificity for human chorionic gonadotropin (hCG) protein. We combined graphene oxide (GO) sheets with a specific peptide aptamer to create a novel, simple and label-free tool to detect abnormalities at an early stage of pregnancy, a GO-peptide-based surface plasmon resonance (SPR) biosensor...
March 7, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28319898/immunodetection-of-salivary-biomarkers-by-an-optical-microfluidic-biosensor-with-polyethylenimine-modified-polythiophene-c70-organic-photodetectors
#16
Tao Dong, Nuno Miguel Matos Pires
This work reports a novel optical microfluidic biosensor with highly sensitive organic photodetectors (OPDs) for absorbance-based detection of salivary protein biomarkers at the point of care. The compact and miniaturized biosensor has comprised OPDs made of polythiophene-C70 bulk heterojunction for the photoactive layer; whilst a calcium-free cathode interfacial layer, made of linear polyethylenimine, was incorporated to the photodetectors to enhance the low cost. The OPDs realized onto a glass chip were aligned to antibody-functionalized chambers of a poly(methyl methacrylate) microfluidic chip, in where immunogold-silver assays were conducted...
March 6, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28317863/dynamic-monitoring-of-membrane-nanotubes-formation-induced-by-vaccinia-virus-on-a-high-throughput-microfluidic-chip
#17
Min Xiao, Na Xu, Cheng Wang, Dai-Wen Pang, Zhi-Ling Zhang
Membrane nanotubes (MNTs) are physical connections for intercellular communication and induced by various viruses. However, the formation of vaccinia virus (VACV)-induced MNTs has never been studied. In this report, VACV-induced MNTs formation process was monitored on a microfluidic chip equipped with a series of side chambers, which protected MNTs from fluidic shear stress. MNTs were formed between susceptible cells and be facilitated by VACV infection through three patterns. The formed MNTs varied with cell migration and virus concentration...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28317836/microscale-symmetrical-electroporator-array-as-a-versatile-molecular-delivery-system
#18
Mengxing Ouyang, Winfield Hill, Jung Hyun Lee, Soojung Claire Hur
Successful developments of new therapeutic strategies often rely on the ability to deliver exogenous molecules into cytosol. We have developed a versatile on-chip vortex-assisted electroporation system, engineered to conduct sequential intracellular delivery of multiple molecules into various cell types at low voltage in a dosage-controlled manner. Micro-patterned planar electrodes permit substantial reduction in operational voltages and seamless integration with an existing microfluidic technology. Equipped with real-time process visualization functionality, the system enables on-chip optimization of electroporation parameters for cells with varying properties...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28300261/quantifying-3d-chemotaxis-in-microfluidic-based-chips-with-step-gradients-of-collagen-hydrogel-concentrations
#19
C Del Amo, C Borau, N Movilla, Jesús Asín, J M García-Aznar
Cell migration is an essential process involved in crucial stages of tissue formation, regeneration or immune function as well as in pathological processes including tumor development or metastasis. During the last few years, the effect of gradients of soluble molecules on cell migration has been widely studied, and complex systems have been used to analyze cell behavior under simultaneous mechano-chemical stimuli. Most of these chemotactic assays have, however, focused on specific substrates in 2D. The aim of the present work is to develop a novel microfluidic-based chip that allows the long-term chemoattractant effect of growth factors (GFs) on 3D cell migration to be studied, while also providing the possibility to analyze the influence of the interface generated between different adjacent hydrogels...
March 16, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28300215/chromatin-modification-contributes-to-the-expression-divergence-of-three-tags2-homoeologs-in-hexaploid-wheat
#20
Wei Zhang, Xiaoli Fan, Yingjie Gao, Lei Liu, Lijing Sun, Qiannan Su, Jie Han, Na Zhang, Fa Cui, Jun Ji, Yiping Tong, Junming Li
Plastic glutamine synthetase (GS2) is responsible for ammonium assimilation. The reason that TaGS2 homoeologs in hexaploid wheat experience different selection pressures in the breeding process remains unclear. TaGS2 were minimally expressed in roots but predominantly expressed in leaves, and TaGS2-B had higher expression than TaGS2-A and TaGS2-D. ChIP assays revealed that the activation of TaGS2-B expression in leaves was correlated with increased H3K4 trimethylation. The transcriptional silencing of TaGS2 in roots was correlated with greater cytosine methylation and less H3K4 trimethylation...
March 16, 2017: Scientific Reports
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