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https://www.readbyqxmd.com/read/28098906/mir%C3%A2-15a%C3%A2-5p-acts-as-an-oncogene-in-renal-cell-carcinoma
#1
Lu Jin, Yifan Li, Tao He, Jia Hu, Jiaju Liu, Mingwei Chen, Zeng Zhang, Yaoting Gui, Xiangming Mao, Shangqi Yang, Yongqing Lai
miRNAs have been reported to be involved in multiple cellular processes and the tumorigenesis of various cancers. miR‑15a‑5p (also termed miR‑15a) has previously been determined to be upregulated in renal cell carcinoma (RCC) by microarray profile. However, the expression and function of miR‑15a‑5p in RCC remain to be validated. In the present study, reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) was performed to detect the expression levels of miR‑15a‑5p in RCC tissues and cells...
January 16, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28098904/identification-of-biomarkers-of-intrahepatic-cholangiocarcinoma-via-integrated-analysis-of-mrna-and-mirna-microarray-data
#2
Yaqing Chen, Dan Liu, Pengfei Liu, Yajing Chen, Huiling Yu, Quan Zhang
The present study aimed to identify potential therapeutic targets of intrahepatic cholangiocarcinoma (ICC) via integrated analysis of gene (transcript version) and microRNA (miRNA/miR) expression. The miRNA microarray dataset GSE32957 contained miRNA expression data from 16 ICC, 7 mixed type of combined hepatocellular‑cholangiocarcinoma (CHC), 2 hepatic adenoma, 3 focal nodular hyperplasia (FNH) and 5 healthy liver tissue samples, and 2 cholangiocarcinoma cell lines. In addition, the mRNA microarray dataset GSE32879 contained mRNA expression data from 16 ICC, 7 CHC, 2 hepatic adenoma, 5 FNH and 7 healthy liver tissue samples...
January 16, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28098899/analysis-of-gene-expression-profiles-of-non-small-cell-lung-cancer-at-different-stages-reveals-significantly-altered-biological-functions-and-candidate-genes
#3
Jin Wang, Jianxiang Song, Zhengya Gao, Xudong Huo, Yajun Zhang, Wencai Wang, Jianwei Qi, Shiying Zheng
We attempt to dissect the pathology of non-small cell lung cancer (NSCLC) patients at different stages and discover the novel candidate genes. Microarray data (GSE21933) were retrieved from the Gene Expression Omnibus database. The differential expression profiles of lung tumor tissues during different stages were analyzed. The significantly altered functions and pathways were assessed and the key nodes in a protein-protein interaction (PPI) network were screened out. Then, the coexpression gene pairs and tumor-related genes were assessed...
January 17, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28098893/systematic-analysis-of-microarray-datasets-to-identify-parkinson-s-disease%C3%A2-associated-pathways-and-genes
#4
Yinling Feng, Xuefeng Wang
In order to investigate commonly disturbed genes and pathways in various brain regions of patients with Parkinson's disease (PD), microarray datasets from previous studies were collected and systematically analyzed. Different normalization methods were applied to microarray datasets from different platforms. A strategy combining gene co‑expression networks and clinical information was adopted, using weighted gene co‑expression network analysis (WGCNA) to screen for commonly disturbed genes in different brain regions of patients with PD...
January 16, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28096474/junb-regulates-angiogenesis-and-neurovascular-parallel-alignment-in-mouse-embryonic-skin
#5
Yasuo Yoshitomi, Takayuki Ikeda, Hidehito Saito, Yoshino Yoshitake, Yasuhito Ishigaki, Toshihisa Hatta, Nobuo Kato, Hideto Yonekura
Blood vessels and nerve fibers are often closely arranged in parallel throughout the body. Therefore, neurovascular interactions have been suggested to be important for the development of vascular networks. However, the molecular mechanisms and genes regulating this process remain unclear. In the present study, we investigated the genes that are activated in endothelial cells (ECs) following interactions with neurons during vascular development. Microarray analyses of human primary microvascular ECs co-cultured with mouse primary dorsal root ganglion cells showed that JunB is strongly upregulated in ECs by neurovascular interactions...
January 17, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28096217/high-throughput-analysis-reveals-novel-maternal-germline-rnas-crucial-for-primordial-germ-cell-preservation-and-proper-migration
#6
Dawn A Owens, Amanda M Butler, Tristan H Aguero, Karen M Newman, Derek Van Booven, Mary Lou King
During oogenesis, hundreds of maternal RNAs are selectively localized to the animal or vegetal pole, including determinants of somatic and germline fates. Although microarray analysis has identified localized determinants, it is not comprehensive and is limited to known transcripts. Here, we utilized high-throughput RNA-sequencing analysis to comprehensively interrogate animal and vegetal pole RNAs in the fully grown Xenopus laevis oocyte. We identified 411 (198 annotated) and 27 (15 annotated) enriched mRNAs at the vegetal and animal pole, respectively...
January 15, 2017: Development
https://www.readbyqxmd.com/read/28096084/timesvector-a-vectorized-clustering-approach-to-the-analysis-of-time-series-transcriptome-data-from-multiple-phenotypes
#7
Inuk Jung, Kyuri Jo, Hyejin Kang, Hongryul Ahn, Youngjae Yu, Sun Kim
MOTIVATION: Identifying biologically meaningful gene expression patterns from time series gene expression data is important to understand the underlying biological mechanisms. To identify significantly perturbed gene sets between different phenotypes, analysis of time series transcriptome data requires consideration of time and sample dimensions. Thus, the analysis of such time series data seeks to search gene sets that exhibit similar or different expression patterns between two or more sample conditions, constituting the three-dimensional data, i...
January 17, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28095864/microrna-141-enhances-anoikis-resistance-in-metastatic-progression-of-ovarian-cancer-through-targeting-klf12-sp1-survivin-axis
#8
Celia S L Mak, Mingo M H Yung, Lynn M N Hui, Leanne L Leung, Rui Liang, Kangmei Chen, Stephanie S Liu, Yiming Qin, Thomas H Y Leung, Kai-Fai Lee, Karen K L Chan, Hextan Y S Ngan, David W Chan
BACKGROUND: Cancer metastasis is determined by the formation of the metastatic niche and the ability of cancer cells to adapt to microenvironmental stresses. Anoikis resistance is a fundamental feature of metastatic cancer cell survival during metastatic cancer progression. However, the mechanisms underlying anoikis resistance in ovarian cancer are still unclear. METHODS: Expressions of miRNA-141 and its downstream targets were evaluated by qPCR, Western blotting, Immunohistochemical (IHC) and in situ hybridization (ISH) assays...
January 17, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28095779/poly-adp-ribose-polymerase-inhibitors-activate-the-p53-signaling-pathway-in-neural-stem-progenitor-cells
#9
Akiko Okuda, Suguru Kurokawa, Masanori Takehashi, Aika Maeda, Katsuya Fukuda, Yukari Kubo, Hyuma Nogusa, Tomoka Takatani-Nakase, Shujiro Okuda, Kunihiro Ueda, Seigo Tanaka
BACKGROUND: Poly(ADP-ribose) polymerase 1 (PARP-1), which catalyzes poly(ADP-ribosyl)ation of proteins by using NAD(+) as a substrate, plays a key role in several nuclear events, including DNA repair, replication, and transcription. Recently, PARP-1 was reported to participate in the somatic cell reprogramming process. Previously, we revealed a role for PARP-1 in the induction of neural apoptosis in a cellular model of cerebral ischemia and suggested the possible use of PARP inhibitors as a new therapeutic intervention...
January 17, 2017: BMC Neuroscience
https://www.readbyqxmd.com/read/28095772/empirical-assessment-of-analysis-workflows-for-differential-expression-analysis-of-human-samples-using-rna-seq
#10
Claire R Williams, Alyssa Baccarella, Jay Z Parrish, Charles C Kim
BACKGROUND: RNA-Seq has supplanted microarrays as the preferred method of transcriptome-wide identification of differentially expressed genes. However, RNA-Seq analysis is still rapidly evolving, with a large number of tools available for each of the three major processing steps: read alignment, expression modeling, and identification of differentially expressed genes. Although some studies have benchmarked these tools against gold standard gene expression sets, few have evaluated their performance in concert with one another...
January 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28095657/characterization-of-caveola-vesicle-complexes-cvcs-protein-phist-cvc-8195-in-plasmodium-vivax
#11
Bo Wang, Feng Lu, Jin-Hee Han, Seong-Kyun Lee, Yang Cheng, Myat Htut Nyunt, Kwon-Soo Ha, Seok-Ho Hong, Won Sun Park, Eun-Taek Han
Plasmodium vivax produces numerous caveola-vesicle complex (CVC) structures beneath the membrane of infected erythrocytes. Recently, a member helical interspersed subtelomeric (PHIST) superfamily protein, PcyPHIST/CVC-8195, was identified as CVCs-associated protein in Plasmodium cynomolgi and essential for survival of this parasite. Very little information has been documented to date about PHIST/CVC-8195 protein in P. vivax. In this study, the recombinant PvPHIST/CVC-8195 N and C termini were expressed, and immunoreactivity was assessed using confirmed vivax malaria patients sera by protein microarray...
December 2016: Korean Journal of Parasitology
https://www.readbyqxmd.com/read/28095649/the-effect-of-mechanical-stress-on-the-proliferation-adipogenic-differentiation-and-gene-expression-of-human-adipose-derived-stem-cells
#12
Nora E Paul, Bernd Denecke, Bong-Sung Kim, Alice Dreser, Jürgen Bernhagen, Norbert Pallua
To allow for a better implementation of external volume expansion to clinical applications for soft tissue regeneration, it is necessary to comprehensively understand the underlying mechanisms. Since human adipose-derived stem cells (hASCs) play a crucial role in soft tissue enlargement, we investigated the impact of cyclic stretch on gene expression, proliferation rate, and adipogenic differentiation of these cells. After cyclic stretching, RNA was extracted and subjected to DNA microarray analysis and RT-qPCR...
January 17, 2017: Journal of Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/28095588/potent-effects-of-dioscin-against-pancreatic-cancer-via-mir-149-3p-mediated-inhibition-of-akt1-signaling-pathway
#13
Lingling Si, Lina Xu, Lianhong Yin, Yan Qi, Xu Han, Youwei Xu, Yanyan Zhao, Kexin Liu, Jinyong Peng
BACKGROUND AND PURPOSE: The aim of the present study was to investigate the effects and possible mechanisms of dioscin against pancreatic cancer in vitro and in vivo. EXPERIMENTAL APPROACH: In vitro actions of dioscin on ASPC-1 and PANC-1 cells, and in vivo effects to suppress the tumor growth of cell xenografts in nude mice were carried out. In addition, microRNA microarray analysis was used to find the differential expressed microRNAs caused by dioscin. Then, the mechanisms of dioscin against pancreatic cancer were carried out...
January 17, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28095459/association-of-body-mass-index-with-dna-methylation-and-gene-expression-in-blood-cells-and-relations-to-cardiometabolic-disease-a-mendelian-randomization-approach
#14
Michael M Mendelson, Riccardo E Marioni, Roby Joehanes, Chunyu Liu, Åsa K Hedman, Stella Aslibekyan, Ellen W Demerath, Weihua Guan, Degui Zhi, Chen Yao, Tianxiao Huan, Christine Willinger, Brian Chen, Paul Courchesne, Michael Multhaup, Marguerite R Irvin, Ariella Cohain, Eric E Schadt, Megan L Grove, Jan Bressler, Kari North, Johan Sundström, Stefan Gustafsson, Sonia Shah, Allan F McRae, Sarah E Harris, Jude Gibson, Paul Redmond, Janie Corley, Lee Murphy, John M Starr, Erica Kleinbrink, Leonard Lipovich, Peter M Visscher, Naomi R Wray, Ronald M Krauss, Daniele Fallin, Andrew Feinberg, Devin M Absher, Myriam Fornage, James S Pankow, Lars Lind, Caroline Fox, Erik Ingelsson, Donna K Arnett, Eric Boerwinkle, Liming Liang, Daniel Levy, Ian J Deary
BACKGROUND: The link between DNA methylation, obesity, and adiposity-related diseases in the general population remains uncertain. METHODS AND FINDINGS: We conducted an association study of body mass index (BMI) and differential methylation for over 400,000 CpGs assayed by microarray in whole-blood-derived DNA from 3,743 participants in the Framingham Heart Study and the Lothian Birth Cohorts, with independent replication in three external cohorts of 4,055 participants...
January 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28095436/arraypitope-automated-analysis-of-amino-acid-substitutions-for-peptide-microarray-based-antibody-epitope-mapping
#15
Christian Skjødt Hansen, Thomas Østerbye, Paolo Marcatili, Ole Lund, Søren Buus, Morten Nielsen
Identification of epitopes targeted by antibodies (B cell epitopes) is of critical importance for the development of many diagnostic and therapeutic tools. For clinical usage, such epitopes must be extensively characterized in order to validate specificity and to document potential cross-reactivity. B cell epitopes are typically classified as either linear epitopes, i.e. short consecutive segments from the protein sequence or conformational epitopes adapted through native protein folding. Recent advances in high-density peptide microarrays enable high-throughput, high-resolution identification and characterization of linear B cell epitopes...
2017: PloS One
https://www.readbyqxmd.com/read/28095422/high-throughput-carbon-substrate-profiling-of-mycobacterium-ulcerans-suggests-potential-environmental-reservoirs
#16
Dezemon Zingue, Amar Bouam, Muriel Militello, Michel Drancourt
BACKGROUND: Mycobacterium ulcerans is a close derivative of Mycobacterium marinum and the agent of Buruli ulcer in some tropical countries. Epidemiological and environmental studies pointed towards stagnant water ecosystems as potential sources of M. ulcerans, yet the ultimate reservoirs remain elusive. We hypothesized that carbon substrate determination may help elucidating the spectrum of potential reservoirs. METHODOLOGY/PRINCIPAL FINDINGS: In a first step, high-throughput phenotype microarray Biolog was used to profile carbon substrates in one M...
January 17, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28095394/loss-of-cul4a-expression-is-underlying-cisplatin-hypersensitivity-in-colorectal-carcinoma-cells-with-acquired-trabectedin-resistance
#17
B Englinger, M Mair, W Miklos, C Pirker, T Mohr, S van Schoonhoven, D Lötsch, W Körner, F Ferk, S Knasmüller, P Heffeter, B K Keppler, M Grusch, W Berger
BACKGROUND: Colorectal carcinoma (CRC) is the third most common cancer worldwide. Platinum-based anticancer compounds still constitute one mainstay of systemic CRC treatment despite limitations due to adverse effects and resistance development. Trabectedin has shown promising antitumor effects in CRC, however, again resistance development may occur. In this study, we aimed to develop strategies to circumvent or even exploit acquired trabectedin resistance in novel CRC treatment regimens...
January 17, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28095175/evaluation-of-the-droplet-microarray-platform-for-high-throughput-screening-of-suspension-cells
#18
Anna A Popova, Claire Depew, Katya Manuella Permana, Alexander Trubitsyn, Ravindra Peravali, Jorge Ángel González Ordiano, Markus Reischl, Pavel A Levkin
Phenotypic cell-based high-throughput screenings play a central role in drug discovery and toxicology. The main tendency in cell screenings is the increase of the throughput and decrease of reaction volume in order to accelerate the experiments, reduce the costs, and enable screenings of rare cells. Conventionally, cell-based assays are performed in microtiter plates, which exist in 96- to 1536-wells formats and cannot be further miniaturized. In addition, performing screenings of suspension cells is associated with risk of losing cell content during the staining procedures and incompatibility with high-content microscopy...
November 1, 2016: Journal of Laboratory Automation
https://www.readbyqxmd.com/read/28095111/increased-numb-protein-expression-predicts-poor-clinical-outcomes-in-esophageal-squamous-cell-carcinoma-patients
#19
Zhenguo Liu, Canqiao Luo, Weixiong Yang, Kefeng Wang, Chuang Hu, Jianyong Zou, Hua Zhu, Liwu Fu, Jing Nie, Chao Cheng
Numb is a protein whose asymmetric segregation during cell division determines cell fate and has numerous functions relevant to multiple fields of study, including developmental neurobiology and cancer biology. Little is known about the role of Numb in esophageal squamous cell carcinoma (ESCC), the predominant histological esophageal carcinoma in Asian populations. In this study, we focused on the expression and biological functions of Numb in the context of ESCC. From analysis of tissue microarrays with 212 patients, it was found that Numb was significantly upregulated in ESCC tissues compared to corresponding non-cancerous tissues...
January 17, 2017: Cancer Biology & Therapy
https://www.readbyqxmd.com/read/28094452/the-dipteran-parasitoid-exorista-bombycis-induces-pro-and-anti-oxidative-reactions-in-the-silkworm-bombyx-mori-enzymatic-and-genetic-analysis
#20
Pooja Makwana, Appukuttan Nair R Pradeep, Shambhavi P Hungund, Kangayam M Ponnuvel, Kanika Trivedy
Hymenopteran parasitoids inject various factors including polydnaviruses along with their eggs into their host insects that suppress host immunity reactions to the eggs and larvae. Less is known about the mechanisms evolved in dipteran parasitoids that suppress host immunity. Here we report that the dipteran, Exorista bombycis, parasitization leads to pro-oxidative reactions and activation of anti-oxidative enzymes in the silkworm Bombyx mori larva. We recorded increased activity of oxidase, superoxide dismutase, thioredoxin peroxidase, catalase, glutathione-S-transferase (GST), and peroxidases in the hemolymph plasma, hemocytes, and fat body collected from B...
January 17, 2017: Archives of Insect Biochemistry and Physiology
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