Read by QxMD icon Read

Use of microarray

Qiyu Liu, Chong Lu, Wanjun Dai, Ke Li, Jing Xu, Yunke Huang, Guiling Li, Yu Kang, Anil K Sood, Congjian Xu
In order to elucidate the mechanisms underlying the biobehavioral factors responsible for cervical cancer from the perspective of lncRNAs. Tumor samples were obtained from patients with stage Ib-IIb squamous cervical cancer, which were divided into high- and low-risk groups according to biobehavioral risk factors. A lncRNA + mRNA microarray was performed, and the results were validated using qRT-PCR. Gene ontology (GO), pathway, and lncRNA-mRNA co-expression analysis were performed to predict the potential functions of the differentially expressed transcripts...
2018: Bioscience Trends
Rebecca R Payton, Louisa A Rispoli, Kimberly A Nagle, Cedric Gondro, Arnold M Saxton, Brynn H Voy, J Lannett Edwards
Hyperthermia during estrus has direct consequences on the maturing oocyte that carries over to the resultant embryo to compromise its ability to continue in development. Because early embryonic development is reliant upon maternal transcripts and other ooplasmic components, we examined impact of heat stress on bovine oocyte transcripts using microarray. Oocytes were matured at 38.5ºC for 24 h or 41.0ºC for the first 12 h of in vitro maturation; 38.5ºC thereafter. Transcriptome profile was performed on total (adenylated + deadenylated) RNA and polyadenylated mRNA populations...
March 18, 2018: Journal of Reproduction and Development
Zhou Zhou, Ming-Jiang Xu, Yan Cai, Wei Wang, Joy X Jiang, Zoltan V Varga, Dechun Feng, Pal Pacher, George Kunos, Natalie J Torok, Bin Gao
Background & Aims: Hepatic infiltration of neutrophils is a hallmark of steatohepatitis; however, the role of neutrophils in the progression of steatohepatitis remains unknown. Methods: A clinically relevant mouse model of steatohepatitis induced by high-fat diet (HFD) plus binge ethanol feeding was used. Liver fibrosis was examined. In vitro cell culture was used to analyze the interaction of hepatic stellate cells (HSCs) and neutrophils. Results: HFD plus one binge ethanol (HFD+1B) feeding induced significant hepatic neutrophil infiltration, liver injury, and fibrosis...
March 2018: Cellular and Molecular Gastroenterology and Hepatology
Haiting Cheng, Can Cui, Shousi Lu, Binbin Xia, Xiaorong Li, Pinxiang Xu, Ming Xue
Hypoxia preconditioning is an effective strategy of intrinsic cell protection. An acute repetitive hypoxic mice model was developed. High-throughput microarray analysis was performed to explore the integrative alterations of gene expression in repetitive hypoxic mice. Data obtained was analyzed via multiple bioinformatics approaches to identify the hub genes, pathways and biological processes related to hypoxia preconditioning. The current study, for the first time, provides insights into the gene expression profiles in repetitive hypoxic mice...
February 23, 2018: Oncotarget
Jiaming Huang, Tianyu Liu, Chunliang Shang, Yunhe Zhao, Wei Wang, Yanchun Liang, Luyan Guo, Shuzhong Yao
Long non-coding RNAs (lncRNAs) have been acknowledged to serve a significant role in cancer biology and abnormal expression in tumors is frequently observed. However, their mechanisms in cervical cancer remain unclear. With a genome-wide analysis of lncRNA expression in cervical cancer tissues, the present study aimed to identify lncRNA targets for the further study of cervical cancer. To elucidate the specific role of lncRNAs in the pathogenesis of this type of cancer, 6 cervical cancer samples paired with normal cervical tissues were obtained...
April 2018: Oncology Letters
Dong Leng, Ran Miao, Xiaoxi Huang, Ying Wang
Octamer-binding protein 2 (Oct2) binds to the ATGCAAAT octamer on the IgH enhancer and stimulates IgH expression in human multiple myeloma (MM). Cysteine-rich secreted protein 3 (CRISP3) possesses the ATGCAAAT sequence and thus is activated by Oct2 in mouse B cells, suggesting that CRISP3 may be activated in and be a potential biomarker for MM. The present study involved a meta-analysis of the gene expression profiling data of human MM peripheral blood. Significantly expressed genes were analyzed on merged super array microarray data and selected sample data with significantly expressed genes were additionally analyzed by principal component analysis and Bayesian probit regression...
April 2018: Oncology Letters
Liang Wei, Qi Wang, Yanfei Zhang, Cheng Yang, Hongxin Guan, Jianxin Jiang, Zhiyang Sun
Intracranial aneurysm (IA) is a localized dilation of the blood vessel. The present study was designed to explore the mechanisms of rupture of IA. GSE13353 (including 11 ruptured and 8 unruptured IA samples) and GSE15629 (including 8 ruptured and 6 unruptured IA samples) were downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) identified using limma and MetaDE packages were merged, and a protein-protein interaction (PPI) network analysis was performed using Cytoscape software...
April 2018: Oncology Letters
Choon Sen Seah, Shahreen Kasim, Mohd Farhan Md Fudzee, Jeffrey Mark Law Tze Ping, Mohd Saberi Mohamad, Rd Rohmat Saedudin, Mohd Arfian Ismail
Microarray technology has become one of the elementary tools for researchers to study the genome of organisms. As the complexity and heterogeneity of cancer is being increasingly appreciated through genomic analysis, cancerous classification is an emerging important trend. Significant directed random walk is proposed as one of the cancerous classification approach which have higher sensitivity of risk gene prediction and higher accuracy of cancer classification. In this paper, the methodology and material used for the experiment are presented...
December 2017: Saudi Journal of Biological Sciences
Racha El-Hajj Ghaoui, Luke St Heaps, Dorothy Hung, Sumanth Nagabushan, Catherine Harris, Oksana Mirochnik, Praveen Sharma, Stewart J Kellie, Dale C Wright
Acute promyelocytic leukaemia with PML-RARA fusion is usually associated with the t(15;17)(q24.1;q21.1) translocation but may also arise from complex or cryptic rearrangements. The fusion usually resides on chromosome 15 but occasionally on others. We describe a cryptic PML-RARA fusion within a novel chromosome 17 rearrangement. We performed interphase fluorescence in situ hybridisation (FISH) using a dual-fusion PML-RARA probe, followed by reverse transcriptase-polymerase chain reaction (RT-PCR) for PML-RARA, karyotyping, and metaphase FISH using RARA break-apart, locus-specific, and subtelomere probes for chromosome 17...
March 17, 2018: Cytogenetic and Genome Research
Shinako Masuda, Katsuhisa Matsuura, Tatsuya Shimizu
Fibroblasts not only play key roles under physiological and pathological conditions in various tissues and organs including the heart but also are indispensable for fabricating bioengineered cardiac tissues and their functions through cell-cell interactions. Because tissue functions and cells surrounding fibroblasts in vivo are different among tissues, the properties of fibroblasts might be different according to their tissue origin. Understanding the molecular mechanisms of fibroblasts may lead to fabrication of bioengineered tissues close to biological tissues...
March 2, 2018: Biomaterials
Soon-Sen Leow, Alice Luu, Swechhya Shrestha, K C Hayes, Ravigadevi Sambanthamurthi
Palm fruit juice (PFJ) containing oil palm phenolics is obtained as a by-product from oil palm (Elaeis guineensis) fruit milling. It contains shikimic acid, soluble fibre and various phenolic acids including p-hydroxybenzoic acid and three caffeoylshikimic acid isomers. PFJ has also demonstrated beneficial health properties in various biological models. Increasing concentrations of PFJ and different PFJ fractions were used to assess growth dynamics and possible anti-ageing properties in fruit flies (Drosophila melanogaster) genotype w1118 ...
March 14, 2018: Experimental Gerontology
Chun-Fu Hong, Ying-Chen Chen, Wei-Chun Chen, Keng-Chang Tu, Meng-Hsiun Tsai, Yung-Kuan Chan, Shyr Shen Yu
A microarray analysis generally contains expression data of thousands of genes, but most of them are irrelevant to the disease of interest, making analyzing the genes concerning specific diseases complicated. Therefore, filtering out a few essential genes as well as their regulatory networks is critical, and a disease can be easily diagnosed just depending on the expression profiles of a few critical genes. In this study, a target gene screening (TGS) system, which is a microarray-based information system that integrates F-statistics, pattern recognition matching, a two-layer K-means classifier, a Parameter Detection Genetic Algorithm (PDGA), a genetic-based gene selector (GBG selector) and the association rule, was developed to screen out a small subset of genes that can discriminate malignant stages of cancers...
March 14, 2018: Journal of Biomedical Informatics
Lucy M Hinder, Benjamin J Murdock, Meeyoung Park, Diane E Bender, Phillipe D O'Brien, Amy E Rumora, Junguk Hur, Eva L Feldman
Diabetic peripheral neuropathy is the most common complication of diabetes and a source of considerable morbidity. Numerous molecular pathways are linked to neuropathic progression, but it is unclear whether these pathways are altered throughout the course of disease. Moreover, the methods by which these molecular pathways are analyzed can produce significantly different results; as such it is often unclear whether previously published pathways are viable targets for novel therapeutic approaches. In the current study we examine changes in gene expression patterns in the sciatic nerve (SCN) and dorsal root ganglia (DRG) of db/db diabetic mice at 8, 16, and 24 weeks of age using microarray analysis...
March 14, 2018: Experimental Neurology
Gregor Jezernik, Uroš Potočnik
Fatty acids and their derivatives play an important role in inflammation. Diet and genetics influence fatty acid profiles. Abnormalities of fatty acid profiles have been observed in inflammatory bowel diseases (IBD), a group of complex diseases defined by chronic gastrointestinal inflammation. IBD associated fatty acid profile abnormalities were observed independently of nutritional status or disease activity, suggesting a common genetic background. However, no study so far has attempted to look for overlap between IBD loci and fatty acid associated loci or investigate the genetics of fatty acid profiles in IBD...
March 2018: Prostaglandins, Leukotrienes, and Essential Fatty Acids
Jeong-Oh Kim, Jung-Young Shin, Min Young Kim, Kyoung Hwa Son, Chan Kwon Jung, Tae-Jung Kim, Su Young Kim, Jae Kil Park, Sook Whan Sung, Sang Ju Bae, Hyun Jung Min, Jin-Hyoung Kang
BACKGROUND: We screened resected tumor tissues from patients with lung cancer for EGFR mutations, ALK rearrangements, and rearranged during transfection (RET) gene variants (including RET rearrangements and the Kinesin Family Member 5B (KIF5B)-RET fusion gene) using various methods including reverse transcription polymerase chain reaction (RT-PCR), transcript assays, fluorescence in situ hybridization (FISH), and immunohistochemistry (IHC). We also examined the protein expression of associated downstream signaling molecules to assess the effect of these variants on patient outcome...
March 2018: Surgical Oncology
Konrad Sachse, Kh Shamsur Rahman, Christiane Schnee, Elke Müller, Madlen Peisker, Thomas Schumacher, Evelyn Schubert, Anke Ruettger, Bernhard Kaltenboeck, Ralf Ehricht
Serological analysis of Chlamydia (C.) spp. infections is still mainly based on micro-immunofluorescence and ELISA. To overcome the limitations of conventional serology, we have designed a novel microarray carrying 52 synthetic peptides representing B-cell epitopes from immunodominant proteins of all 11 chlamydial species. The new assay has been validated using monospecific mouse hyperimmune sera. Subsequently, serum samples from cattle, sheep and humans with a known history of chlamydial infection were examined...
March 16, 2018: Scientific Reports
Yimin Wang, Fang Ye, Chanyan Huang, Faling Xue, Yingyuan Li, Shaowei Gao, Zeting Qiu, Si Li, Qinchang Chen, Huaqiang Zhou, Yiyan Song, Wenqi Huang, Wulin Tan, Zhongxing Wang
BACKGROUND: Neuropathic pain is one of the common complications after spinal cord injury (SCI), affecting patients' life quality. The molecular mechanism for neuropathic pain after SCI is still unclear. We aimed to discover potential genes and MicroRNAs(miRNAs) related to neuropathic pain by bioinformatics method. METHODS: Microarray data of GSE69901 were obtained from Gene Expression Omnibus (GEO) database. Peripheral blood samples from patients with or without neuropathic pain after spinal cord injury (SCI) were collected...
March 15, 2018: Clinical Journal of Pain
Maria J Gonzalez-Moa, Bieke Van Dorst, Ole Lagatie, Ann Verheyen, Lieven Stuyver, Marco A Biamonte
Three O. volvulus immunogenic peptide sequences recently discovered by peptide microarray were adapted to a lateral flow assay (LFA). The LFA employs gold nanoshells as novel high-contrast reporter nanoparticles and detects a serological response against the 3 peptides, found in OvOC9384, OvOC198, and OvOC5528, respectively. When tested on 118 sera from O. volvulus infected patients and 208 control sera, the LFA was 90, 63, and 98% sensitive for each peptide, respectively, and 99-100% specific vs. samples from healthy volunteers...
March 16, 2018: ACS Infectious Diseases
Nailia R Khasbiullina, Nadezhda V Shilova, Maxim E Navakouski, Alexey Yu Nokel, Yuri A Knirel, Ola Blixt, Nicolai V Bovin
Innate immunity natural Abs (NAbs) execute a number of functions, including protection and surveillance. Despite active research, the stimuli that induce the formation of NAbs are still described only hypothetically. Here, we compared repertoires of anti-glycan Abs in the peripheral blood of mice that received per os various bacteria. The repertoires of Abs of mice primed in this way were compared using a microarray that included about 350 glycans, as well as 150 bacterial polysaccharides. Sterile mice did not possess anti-glycan Abs...
January 1, 2018: Innate Immunity
Quan Zhou, Li Hong, Jing Wang
PURPOSE: The aim of this study was to elucidate the molecular mechanisms and to identify the key genes and pathways for pelvic organ prolapse (POP) using bioinformatics analysis. METHODS: The microarray data for GSE53868 included 12 POP and 12 non-POP anterior vaginal wall samples. Differentially expressed genes (DEGs) were identified by GEO2R online tool. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the DAVID database, and a DEG-associated protein-protein interaction (PPI) network was constructed using STRING and visualized in Cytoscape...
March 15, 2018: Archives of Gynecology and Obstetrics
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"