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Age-Specific Gene Expression Profiles of Rhesus Monkey Ovaries Detected by microarray Analysis

BIOMED RESEARCH INTERNATIONAL 2015年第0期2015卷 625192-625192页

作者： Wei, Hengxi Liu, Xiangjie Yuan, Jihong Li, Li Zhang, Dongdong Guo, Xinzheng Liu, Lin Zhang, Shouquan South China Agr Univ Guangdong Prov Key Lab Agroanim Genom & Mol Breed Natl Engn Res Ctr Breeding Swine Ind Coll Anim Sci Guangzhou 510642 Guangdong Peoples R China Nankai Univ Dept Cell Biol & Genet Coll Life Sci State Key Lab Med Chem Biol Tianjin 300071 Peoples R China

The biological function of human ovaries declines with age. To identify the potential molecular changes in ovarian aging, we performed genome-wide gene expression analysis by microarray of ovaries from young, middle-aged, and old rhesus monkeys. microarray data was validated by quantitative real-time PCR. Results showed that a total of 503 (60 upregulated, 443 downregulated) and 84 (downregulated) genes were differentially expressed in old ovaries compared to young and middle-aged groups, respectively. No difference in gene expression was found between middle-aged and young groups. Differentially expressed genes were mainly enriched in cell and organelle, cellular and physiological process, binding, and catalytic activity. These genes were primarily associated with KEGG pathways of cell cycle, DNA replication and repair, oocyte meiosis and maturation, MAPK, TGF-beta, and p53 signaling pathway. Genes upregulated were involved in aging, defense response, oxidation reduction, and negative regulation of cellular process;genes downregulated have functions in reproduction, cell cycle, DNA and RNA process, macromolecular complex assembly, and positive regulation of macromolecule metabolic process. These findings show that monkey ovary undergoes substantial change in global transcription with age. Gene expression profiles are useful in understanding the mechanisms underlying ovarian aging and age-associated infertility in primates.

关键词： GENE expression RHESUS monkey OVARIES microarray technology POLYMERASE chain reaction DOWN-regulation (Biology) CELL cycle MACROMOLECULES

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mRMR-ABC: A Hybrid Gene Selection Algorithm for Cancer Classification Using microarray Gene Expression Profiling

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BIOMED RESEARCH INTERNATIONAL 2015年第0期2015卷 604910-604910页

作者： Alshamlan, Hala Badr, Ghada Alohali, Yousef King Saud Univ Coll Comp & Informat Sci POB 22452 Riyadh 11495 Saudi Arabia City Sci & Technol IRI Alexandria Egypt

An artificial bee colony (ABC) is a relatively recent swarm intelligence optimization approach. In this paper, we propose the first attempt at applying ABC algorithm in analyzing a microarray gene expression profile. In addition, we propose an innovative feature selection algorithm, minimum redundancy maximum relevance (mRMR), and combine it with an ABC algorithm, mRMR-ABC, to select informative genes from microarray profile. The new approach is based on a support vector machine (SVM) algorithm to measure the classification accuracy for selected genes. We evaluate the performance of the proposed mRMR-ABC algorithm by conducting extensive experiments on six binary and multiclass gene expression microarray datasets. Furthermore, we compare our proposed mRMR-ABC algorithm with previously known techniques. We reimplemented two of these techniques for the sake of a fair comparison using the same parameters. These two techniques are mRMR when combined with a genetic algorithm (mRMR-GA) and mRMR when combined with a particle swarm optimization algorithm (mRMR-PSO). The experimental results prove that the proposed mRMR-ABC algorithm achieves accurate classification performance using small number of predictive genes when tested using both datasets and compared to previously suggested methods. This shows that mRMR-ABC is a promising approach for solving gene selection and cancer classification problems.

关键词： TUMOR classification ALGORITHMS ANIMAL experimentation GENE expression GENES FINANCING of research microarray technology TUMOR genetics

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Development of a Planar Waveguide microarray for the Monitoring and Early Detection of Five Harmful Algal Toxins in Water and Cultures

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ENVIRONMENTAL SCIENCE & technology 2014年第22期48卷 13340-13349页

作者： McNamee, Sara E. Elliott, Christopher T. Greer, Brett Lochhead, Michael Campbell, Katrina Queens Univ Belfast Sch Biol Sci Inst Global Food Secur Belfast BT9 5AG Antrim North Ireland MBio Diagnost Inc Boulder CO 80303 USA

A novel multiplex microarray has been developed for the detection of five groups of harmful algal and cyanobacterial toxins found in marine, brackish, and freshwater environments including domoic acid (DA), okadaic acid (OA, and analogues), saxitoxin (STX, and analogues), cylindrospermopsin (CYN) and microcystins (MC, and analogues). The sensitivity and specificity were determined and feasibility to be used as a screening tool investigated. Results for algal/cyanobacterial cultures (n = 12) and seawater samples (n = 33) were compared to conventional analytical methods, such as high performance liquid chromatography (HPLC) and liquid chromatography tandem mass spectrometry (LC-MS/MS). Detection limits for the 15 min assay were 0.37, 0.44, 0.05, 0.08, and 0.40 ng/mL for DA, OA, STX, CYN, and MC, respectively. The correlation of data obtained from the microarray compared to conventional analysis for the 12 cultures was r(2) = 0.83. Analysis of seawater samples showed that 82, 82, 70, 82, and 12% of samples were positive (>IC20) compared to 67, 55, 36, 0, and 0% for DA, OA, STX, CYN, and MC, respectively, for conventional analytical methods. The discrepancies in results can be attributed to the enhanced sensitivity and cross-reactivity profiles of the antibodies in the MBio microarray. The feasibility of the microarray as a rapid, easy to use, and highly sensitive screening tool has been illustrated for the five-plex detection of biotoxins. The research demonstrates an early warning screening assay to support national monitoring agencies by providing a faster and more accurate means of identifying and quantifying harmful toxins in water samples.

关键词： PLANAR waveguides microarray technology ALGAL toxins SENSITIVITY & specificity (Statistics) LIQUID chromatography-mass spectrometry DOMOIC acid SAXITOXIN MICROCYSTINS

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Současné metody analýzy genomu a jejich využití v hledání genetických příčin nemocí

Současné metody analýzy genomu a jejich využití v hled...

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作者： Stránecký, Viktor Charles University of Prague

The study of rare genetic diseases presents unique opportunity to uncover the genetic and molecular basis of human traits and greatly helped to the identification of genes, to the elucidation of their function and to the characterization of metabolic pathways and cellular processes. Over the past decades, linkage analysis has been appropriate approach to search for the genes causing Mendelian diseases and contributed to the identification of many genes, but the genetic cause of many diseases remains unknown. New methods of studying the human genome, microarray technology and massively parallel sequencing (next generation sequencing), represent a way to efficiently identify the cause of genetically determined diseases, based on direct observation of mutations in the genome of affected individuals. These techniques replaced the traditional method of disease gene identification represented by linkage analysis and sequencing of candidate genes and have become the standard approach to elucidate the molecular basis of diseases. In this work, i describe the the results achieved by using these methods - identification of the genes underlying mucopolysacharidosis type IIIC, isolated defect of ATP synthase, Rotor syndrome, autosomal dominat ANCL and GAPO syndrome.

关键词： rare diseases genetic mapping microarray technology exome sequencing neuronal ceroid lipofuscinosis Rotor syndrome isolated defect of ATP synthase GAPO syndrome

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A quantitative liposome microarray to systematically characterize protein-lipid interactions

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NATURE METHODS 2014年第1期11卷 47-+页

作者： Saliba, Antoine-Emmanuel Vonkova, Ivana Ceschia, Stefano Findlay, Greg M. Maeda, Kenji Tischer, Christian Deghou, Samy van Noort, Vera Bork, Peer Pawson, Tony Ellenberg, Jan Gavin, Anne-Claude European Mol Biol Lab Struct & Computat Biol Unit Heidelberg Germany Mt Sinai Hosp Samuel Lunenfeld Res Inst Toronto ON M5G 1X5 Canada European Mol Biol Lab Adv Light Microscopy Facil Heidelberg Germany European Mol Biol Lab Cell Biol & Biophys Unit Heidelberg Germany

Lipids have a role in virtually all biological processes, acting as structural elements, scaffolds and signaling molecules, but they are still largely under-represented in known biological networks. Here we describe a liposome microarray-based assay (LiMA), a method that measures protein recruitment to membranes in a quantitative, automated, multiplexed and high-throughput manner.

关键词： LIPOSOMES PROTEIN-lipid interactions CELLULAR signal transduction MEMBRANE proteins INTERMOLECULAR interactions microarray technology

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Efficacy of a novel PCR- and microarray-based method in diagnosis of a prosthetic joint infection

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ACTA ORTHOPAEDICA 2014年第2期85卷 165-170页

作者： Metso, Leena Maki, Minna Tissari, Paivi Remes, Ville Piiparinen, Pasi Kirveskari, Juha Tarkka, Eveliina Anttila, Veli-Jukka Vaara, Martti Huotari, Kaisa Helsinki Univ Cent Hosp Dept Orthoped Peijas Hosp Helsinki Finland Mobidiag Ltd Biomedicum 2 Helsinki Finland Helsinki Univ Hosp Lab Div Clin Microbiol Helsinki Finland Helsinki Univ Cent Hosp Div Infect Dis Dept Med Helsinki Finland

Background and purpose - Polymerase chain reaction (PCR) methods enable detection and species identification of many pathogens. We assessed the efficacy of a new PCR and microarray- based platform for detection of bacteria in prosthetic joint infections (PJIs). Methods - This prospective study involved 61 suspected PJIs in hip and knee prostheses and 20 negative controls. 142 samples were analyzed by Prove-it Bone and Joint assay. The laboratory staff conducting the Prove-it analysis were not aware of the results of microbiological culture and clinical findings. The results of the analysis were compared with diagnosis of PJIs defined according to the Musculoskeletal Infection Society (MSIS) criteria and with the results of microbiological culture. Results - 38 of 61 suspected PJIs met the definition of PJI according to the MSIS criteria. Of the 38 patients, the PCR detected bacteria in 31 whereas bacterial culture was positive in 28 patients. 15 of the PJI patients were undergoing antimicrobial treatment as the samples for analysis were obtained. When antimicrobial treatment had lasted 4 days or more, PCR detected bacteria in 6 of the 9 patients, but positive cultures were noted in only 2 of the 9 patients. All PCR results for the controls were negative. Of the 61 suspected PJIs, there were false-positive PCR results in 6 cases. Interpretation - The Prove-it assay was helpful in PJI diagnostics during ongoing antimicrobial treatment. Without preceding treatment with antimicrobials, PCR and microarray-based assay did not appear to give any additional information over culture.

关键词： INFECTION DIAGNOSIS POLYMERASE chain reaction -- Methodology BACTERIA BIOLOGICAL assay CONFIDENCE intervals FISHER exact test JOINTS (Anatomy) LONGITUDINAL method PROSTHESIS PREDICTIVE tests EQUIPMENT & supplies -- Maintenance & repair microarray technology DESCRIPTIVE statistics

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Absolute quantification of protein copy number using a single-molecule-sensitive microarray

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ANALYST 2014年第13期139卷 3235-3244页

作者： Burgin, Edward Salehi-Reyhani, Ali Barclay, Michael Brown, Aidan Kaplinsky, Joseph Novakova, Miroslava Neil, Mark A. A. Ces, Oscar Willison, Keith R. Klug, David R. Univ London Imperial Coll Sci Technol & Med Inst Chem Biol Single Cell Prote Project London SW7 2AZ England Univ London Imperial Coll Sci Technol & Med Inst Chem Biol London SW7 2AZ England Univ London Imperial Coll Sci Technol & Med Dept Chem London SW7 2AZ England Univ London Imperial Coll Sci Technol & Med Dept Phys London SW7 2AZ England

We report the use of a microfluidic microarray incorporating single molecule detection for the absolute quantification of protein copy number in solution. In this paper we demonstrate protocols which enable calibration free detection for two protein detection assays. An EGFP protein assay has a limit of detection of <30 EGFP proteins in a microfluidic analysis chamber (limited by non-specific background binding), with a measured limit of linearity of approximately 6 x 10(6) molecules of analyte in the analysis chamber and a dynamic range of >5 orders of magnitude in protein concentration. An antibody sandwich assay was used to detect unlabelled human tumour suppressor protein p53 with a limit of detection of approximately 21 p53 proteins and a dynamic range of >3 orders of magnitude. We show that these protocols can be used to calibrate data retrospectively to determine the absolute protein copy number at the single cell level in two human cancer cell lines.

关键词： PREDICATE calculus microarray technology SINGLE molecules CANCER cells MOLECULES

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MMAD: microarray microdissection with analysis of differences is a computational tool for deconvoluting cell type-specific contributions from tissue samples

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BIOINFORMATICS 2014年第5期30卷 682-689页

作者： Liebner, David A. Huang, Kun Parvin, Jeffrey D. Ohio State Univ Dept Internal Med Div Med Oncol Columbus OH 43210 USA Ohio State Univ Dept Biomed Informat Columbus OH 43210 USA Ohio State Univ Ctr Comprehens Canc Columbus OH 43210 USA

Background: One of the significant obstacles in the development of clinically relevant microarray-derived biomarkers and classifiers is tissue heterogeneity. Physical cell separation techniques, such as cell sorting and laser-capture microdissection, can enrich samples for cell types of interest, but are costly, labor intensive and can limit investigation of important interactions between different cell types. Results: We developed a new computational approach, called microarray microdissection with analysis of differences (MMAD), which performs microdissection in silico. Notably, MMAD (i) allows for simultaneous estimation of cell fractions and gene expression profiles of contributing cell types, (ii) adjusts for microarray normalization bias, (iii) uses the corrected Akaike information criterion during model optimization to minimize overfitting and (iv) provides mechanisms for comparing gene expression and cell fractions between samples in different classes. Computational microdissection of simulated and experimental tissue mixture datasets showed tight correlations between predicted and measured gene expression of pure tissues as well as tight correlations between reported and estimated cell fraction for each of the individual cell types. In simulation studies, MMAD showed superior ability to detect differentially expressed genes in mixed tissue samples when compared with standard metrics, including both significance analysis of microarrays and cell type-specific significance analysis of microarrays. Conclusions: We have developed a new computational tool called MMAD, which is capable of performing robust tissue microdissection in silico, and which can improve the detection of differentially expressed genes. MMAD software as implemented in MATLAB is publically available for download at http://***/projects/mmad/.

关键词： microarray technology BIOCHEMICAL markers RESEARCH HETEROGENEITY CELL separation MICRODISSECTION

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DNA microarray Analysis of Labial Salivary Glands in IgG4-Related Disease

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ARTHRITIS & RHEUMATOLOGY 2014年第10期66卷 2892-2899页

作者： Tsuboi, Hiroto Nakai, Yuji Iizuka, Mana Asashima, Hiromitsu Hagiya, Chihiro Tsuzuki, Sayaka Hirota, Tomoya Miki, Haruka Hagiwara, Shinya Kondo, Yuya Tanaka, Akihiko Moriyama, Masafumi Matsumoto, Isao Nakamura, Seiji Yoshihara, Toshio Abe, Keiko Sumida, Takayuki Univ Tsukuba Tsukuba Ibaraki 3058575 Japan Univ Tokyo Tokyo Japan Kyushu Univ Fukuoka 812 Japan Tokyo Womens Med Univ Tokyo Japan

ObjectiveTo compare gene expression in labial salivary glands (LSGs) from patients with IgG4-related disease with that in LSGs from patients with Sjogren's syndrome (SS). MethodsGene expression was analyzed by DNA microarray in LSG samples from 5 patients with IgG4-related disease, 5 SS patients, and 3 healthy controls. Genes differentially expressed in IgG4-related disease and SS were identified, and gene annotation enrichment analysis of these differentially expressed genes was performed using Gene Ontology (GO) annotation. Validation of the results was performed by quantitative polymerase chain reaction (PCR) using LSG samples from 9 patients with IgG4-related disease, 10 SS patients, and 4 controls. ResultsGene expression patterns in patients with IgG4-related disease, SS patients, and healthy controls were quite different from each other in hierarchical clustering as well as in principal components analysis. In IgG4-related disease compared with SS, a total of 1,771 probe sets (corresponding to 1,321 genes) were identified as up-regulated, and 1,785 probe sets (corresponding to 1,320 genes) were identified as down-regulated (false discovery rate of <5%). GO term analysis indicated that the up-regulated set of differentially expressed genes in IgG4-related disease encoded proteins that function in cell proliferation, extracellular matrix organization, and organ development. PCR validated significantly higher expression of lactotransferrin in patients with IgG4-related disease than in SS patients (P < 0.05) and significantly higher expression of CCL18 in patients with IgG4-related disease than in SS patients and controls (P < 0.05). ConclusionThe results clearly showed that the gene expression pattern in LSGs from patients with IgG4-related disease is different from that in LSGs from SS patients.

关键词： AUTOIMMUNE disease diagnosis SJOGREN'S syndrome diagnosis ACADEMIC medical centers DIFFERENTIAL diagnosis GENE expression IMMUNOGLOBULINS POLYMERASE chain reaction FINANCING of research SALIVARY gland diseases STATISTICS DATA analysis microarray technology

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Dynamical Regulation Analysis Identifies Molecular Mechanisms of Fuzheng-Huayu Formula against Hepatitis B-Caused Liver Cirrhosis

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EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2015年第1期2015卷 1-9页

作者： Chen, Qi-Long Lu, Yi-Yu Peng, Jing-Hua Dong, Shu Wei, Bin Song, Ya-Nan Zhou, Qian-Mei Zhang, Hui Liu, Ping Su, Shi-Bing Shanghai Univ TCM Res Ctr TCM Complex Syst Shanghai 201203 Peoples R China Shanghai Univ TCM Shuguang Hosp Inst Liver Dis Shanghai 201203 Peoples R China Shanghai Univ TCM Shanghai 201203 Peoples R China

Fuzheng-Huayu (FZHY) tablet was formulated based on Chinese medicine theory in treating liver fibrosis. A clinical trial has indicated that FZHY can against hepatitis B-caused liver cirrhosis (HBC), but the underlying mechanism of FZHY efficacy is unclear. Here, we report that miRNA expression levels are remarkably changed when FZHY formula was used in HBC patient's treatment as a paradigm of trials. Then, we functionally characterize the significant impact of potential kernel miRNAs by miRNA-target network analysis. Enrichment analysis show that the FZHY formula dramatically effecting the molecular regulated module in HBC. Thus, we infer that FZHY plays a critical function in HBC treatment process and directly regulated many important pathways, including but not limited to cell cycle, p53 signaling pathway, and TGF-beta signaling pathway, suggesting a new strategy for investigating the molecular mechanism of FZHY treatment.

关键词： CHINESE medicine BIOCHEMICAL markers CLINICAL trials CLUSTER analysis (Statistics) GENE expression HEPATITIS B HERBAL medicine CIRRHOSIS of the liver MATHEMATICAL statistics PLACEBOS (Medicine) RNA STATISTICS T-test (Statistics) PARAMETERS (Statistics) CONTROL groups (Research) microarray technology DISEASE complications THERAPEUTIC use

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