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Yan J, Zhao C, Ma Y, Yang W. Three-dimensional protein microarrays fabricated on reactive microsphere modified COC substrates. J Mater Chem B 2021; 10:293-301. [PMID: 34913463 DOI: 10.1039/d1tb02238e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Fabrication of three-dimensional (3D) surface structures for the high density immobilization of biomolecules is an effective way to prepare highly sensitive biochips. In this work, a strategy to attach polymeric microspheres on a cyclic olefin copolymer (COC) substrate for the preparation of a 3D protein chip was developed. The COC surface was firstly functionalized by the photograft technique with epoxy groups, which were subsequently converted to amine groups. Then monodisperse poly(styrene-alt-maleic anhydride) (PSM) copolymer microspheres were prepared by self-stabilized precipitation polymerization and deposited as a single layer on a modified COC surface to form a 3D surface texture. The surface roughness of the COC support undergoes a significant increase from 1.4 nm to 37.1 nm after deposition of PSM microspheres with a size of 460 nm, and the modified COC still maintains a transmittance of more than 63% at the fluorescence excitation wavelengths (555 nm and 647 nm). The immobilization efficiency of immunoglobulin G (IgG) on the 3D surface reached 75.6% and the immobilization density was calculated to be 0.255 μg cm-2, at a probe protein concentration of 200 μg mL-1. The 3D protein microarray can be rapidly blocked by gaseous ethylenediamine within 10 minutes due to the high reactivity of anhydride groups in PSM microspheres. Immunoassay results show that the 3D protein microarray achieved specific identification of the target protein with a linear detection range from 6.25 ng mL-1 to 250 ng mL-1 (R2 > 0.99) and a limit of detection of 8.87 ng mL-1. This strategy offers a novel way to develop high performance polymer-based 3D protein chips.
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Affiliation(s)
- Jian Yan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.,Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Changwen Zhao
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.,Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China. .,Key Laboratory of Biomedical Materials of Natural Macromolecules, Ministry of Education, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuhong Ma
- Key Laboratory of Carbon Fiber and Functional Polymers, Ministry of Education, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wantai Yang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.,Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China. .,Key Laboratory of Biomedical Materials of Natural Macromolecules, Ministry of Education, Beijing University of Chemical Technology, Beijing 100029, China
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2
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Ochmann SE, Vietz C, Trofymchuk K, Acuna GP, Lalkens B, Tinnefeld P. Optical Nanoantenna for Single Molecule-Based Detection of Zika Virus Nucleic Acids without Molecular Multiplication. Anal Chem 2017; 89:13000-13007. [DOI: 10.1021/acs.analchem.7b04082] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Sarah E. Ochmann
- Institute
for Physical and Theoretical Chemistry, and Braunschweig Integrated
Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology
(LENA), Braunschweig University of Technology, Rebenring 56, 38106 Braunschweig, Germany
| | - Carolin Vietz
- Institute
for Physical and Theoretical Chemistry, and Braunschweig Integrated
Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology
(LENA), Braunschweig University of Technology, Rebenring 56, 38106 Braunschweig, Germany
| | - Kateryna Trofymchuk
- Institute
for Physical and Theoretical Chemistry, and Braunschweig Integrated
Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology
(LENA), Braunschweig University of Technology, Rebenring 56, 38106 Braunschweig, Germany
| | - Guillermo P. Acuna
- Institute
for Physical and Theoretical Chemistry, and Braunschweig Integrated
Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology
(LENA), Braunschweig University of Technology, Rebenring 56, 38106 Braunschweig, Germany
| | - Birka Lalkens
- Institute
for Physical and Theoretical Chemistry, and Braunschweig Integrated
Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology
(LENA), Braunschweig University of Technology, Rebenring 56, 38106 Braunschweig, Germany
| | - Philip Tinnefeld
- Institute
for Physical and Theoretical Chemistry, and Braunschweig Integrated
Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology
(LENA), Braunschweig University of Technology, Rebenring 56, 38106 Braunschweig, Germany
- Department
of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universitaet Muenchen, Butenandtstrasse 5-13, 81377 Muenchen, Germany
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Ceccaroli C, Pulliero A, Geretto M, Izzotti A. Molecular fingerprints of environmental carcinogens in human cancer. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2015; 33:188-228. [PMID: 26023758 DOI: 10.1080/10590501.2015.1030491] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Identification of specific molecular changes (fingerprints) is important to identify cancer etiology. Exploitable biomarkers are related to DNA, epigenetics, and proteins. DNA adducts are the turning point between environmental exposures and biological damage. DNA mutational fingerprints are induced by carcinogens in tumor suppressor and oncogenes. In an epigenetic domain, methylation changes occurs in specific genes for arsenic, benzene, chromium, and cigarette smoke. Alteration of specific microRNA has been reported for environmental carcinogens. Benzo(a)pyrene, cadmium, coal, and wood dust hits specific heat-shock proteins and metalloproteases. The multiple analysis of these biomarkers provides information on the carcinogenic mechanisms activated by exposure to environmental carcinogens.
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Affiliation(s)
- C Ceccaroli
- a Department of Health Sciences, University of Genoa , Italy
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4
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Wu YJ, Wu YJ, Luo X, Shen XL, Zhao DG. Identification of differentially expressed genes that potentially confer pest resistance in transgenic ChIFN-γ tobacco. Gene 2014; 543:181-9. [PMID: 24747016 DOI: 10.1016/j.gene.2014.04.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 04/04/2014] [Accepted: 04/15/2014] [Indexed: 11/30/2022]
Abstract
Chicken interferon-γ (ChIFN-γ) is both an inhibitor of viral replication and a regulator of numerous immunological functions. However, since little is known about the mechanisms underlying the insect-resistance of transgenic ChIFN-γ, a transgenic ChIFN-γ tobacco line was employed in the present study to explore this mechanism. A cDNA microarray (with 43,760 unigenes) was used to analyze the gene expression profiles of transgenic and wild-type (WT) tobacco leaves at two different growth stages. Compared with the WT, 1529 and 405 expressed sequence tags were significantly up- or downregulated on days 119 and 147, respectively. The differentially expressed genes (DEGs) are involved in metabolic regulation, cell division and differentiation, material synthesis and transport, signal transduction, and protein synthesis and degradation. Candidate genes that may increase cell density, thicken cell walls, promote secondary metabolite synthesis, and mediate plant hormone-induced resistance responses were used to identify the ChIFN-γ-mediated insect-resistance mechanisms. The insect-resistance of transgenic ChIFN-γ tobacco possibly involves unknown signaling pathways, which may directly or indirectly affect DEG expression-mediating genes. The degree of pest resistance increased as the plants grew. Three genes likely to be related to jasmonic acid- or salicylic acid-dependent plant defense responses, including CAF 1, Cop 8/CSN, and HD, are implicated in the insect-resistance of the transgenic plants. The mechanism of transgenic ChIFN-γ tobacco resistance also involves RPS20 and other genes that induce microRNA-based gene regulation. The ChIFN-γ-mediated DGEs contribute to insect-resistance in transgenic ChIFN-γ tobacco, which provides new insight into the role of ChIFN-γ.
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Affiliation(s)
- Yong-Jun Wu
- Guizhou Key Laboratory of Agro-Bioengineering, College of Life Sciences, South Campus of Guizhou University, Guiyang 550025, PR China.
| | - Yu-Jun Wu
- Guizhou Key Laboratory of Agro-Bioengineering, College of Life Sciences, South Campus of Guizhou University, Guiyang 550025, PR China
| | - Xi Luo
- Guizhou Key Laboratory of Agro-Bioengineering, College of Life Sciences, South Campus of Guizhou University, Guiyang 550025, PR China
| | - Xi-Long Shen
- Guizhou Key Laboratory of Agro-Bioengineering, College of Life Sciences, South Campus of Guizhou University, Guiyang 550025, PR China
| | - De-Gang Zhao
- Guizhou Key Laboratory of Agro-Bioengineering, College of Life Sciences, South Campus of Guizhou University, Guiyang 550025, PR China
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Rao AN, Grainger DW. BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE. Biomater Sci 2014; 2:436-471. [PMID: 24765522 PMCID: PMC3992954 DOI: 10.1039/c3bm60181a] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools.
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Affiliation(s)
- Archana N. Rao
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112 USA
| | - David W. Grainger
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112 USA
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112 USA
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Carthew P, Fletcher S, White A, Harries H, Weber K. Transcriptomic and histopathology changes in rat lung after intratracheal instillation of polymers. Inhal Toxicol 2014; 18:227-45. [PMID: 22397320 DOI: 10.1080/08958370500444304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The lung toxicity of inhalable polymer materials is normally carried out by evaluation of the histopathology responses of rat lungs to repeat, nose-only, exposures of an inhalable aerosol of material in a 13-wk subchronic repeat dose toxicity study. The introduction of transcriptomics into toxicology has allowed the comparison of histopathological responses in target organs, after exposure, with the "signature" of gene expression ( Waters et al., 2003 ), characteristic of the pathology processes known to be involved in the response to inhaled particulates. The transcriptomic and histopathological changes have been examined in a dose response study of the rat lung to intratracheally administered acrylate polymer solutions at time points equivalent to those used in a 13-wk inhalation study with an additional 13-wk recovery period. The doses administered in the intratracheal study were equivalent to the total doses achieved in a comparable 13-wk inhalation study. The changes in gene expression were found to be dose dependent, as was the histopathology. The changes in regulation of the genes expressed were also consistent with the histopathological responses, such as acute and chronic inflammation, commonly observed with inhalation exposure of the rat lungs to polymers. Functional classification of the genes affected highlight changes in inflammatory and immune response combined with macrophage recruitment, as well as cell adhesion and matrix formation. This would suggest a degree of tissue remodeling and is consistent with the histopathology observed. With further confirmation of the consistency of this response, the use of a transcriptomic approach in toxicology may be valuable in defining "signature" markers for the acute and chronic inflammation induced by polymers, or other inhalables, deposited in the lung. Osteopontin, in particular, a gene implicated in granuloma formation during chronic tissue damage, was significantly upregulated at high levels of exposure to polymer.
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Affiliation(s)
- Philip Carthew
- SEAC Toxicology, Unilever Research, Sharnbrook, Bedfordshire, United Kingdom
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7
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Lin SR, Huang MY, Chang MS. A high-performance gene chip platform for detecting genetic markers from circulating tumor cells. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.gmbhs.2013.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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8
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Virok DP, Kis Z, Szegedi V, Juhász G, Zvara A, Müller G, Lévay G, Hársing LG, Rajkó R, Penke B, Janka Z, Janáky T, Puskás LG. Functional changes in transcriptomes of the prefrontal cortex and hippocampus in a mouse model of anxiety. Pharmacol Rep 2011; 63:348-61. [PMID: 21602590 DOI: 10.1016/s1734-1140(11)70501-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 10/06/2010] [Indexed: 12/13/2022]
Abstract
Anxiety is a multi-etiology disorder influenced by both genetic background and environment. To study the impact of a genetic predisposition, we developed a novel mouse model of anxiety using a combination of crossbreeding and behavioral selection. Comparison of the transcriptomes from the prefrontal cortex and hippocampus of anxious and control mice revealed that the numbers of significantly up- and down-regulated genes were modest, comprising approximately 2% of the tested genes. Functional analysis of the significantly altered gene sets showed that functional groups such as nervous system development, behavior, glial cell differentiation and synaptic transmission were significantly enriched among the up-regulated genes, whereas functional groups such as potassium ion transport, Wnt signaling and neuropeptidergic signaling were significantly enriched among the down-regulated genes. Many of the identified genes and functional groups have been previously linked to the molecular biology of anxiety, while several others, such as transthyretin, vasoactive intestinal polypeptide and various potassium ion channels, are novel or not as well described in this context. Supporting the gene expression data, we also found increased excitability in the hippocampi of anxious mice, which can be a phenotypic result of decreased potassium channel density. Our transcriptome screen showed that the initiation and/or effect of anxiety involve multiple pathways and cellular processes. The identified novel genes and pathways could be involved in the molecular pathogenesis of anxiety and provide potential targets for further drug development.
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Affiliation(s)
- Dezso P Virok
- Institute for Plant Genomics, Human Biotechnology and Bioenergy (BAY-GEN), 6726 Szeged Derkovits fasor 2., Hungary.
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9
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Lee HY, Ahn YT, Park SH, Ahn YM, Shim JJ, Lee JH, Lee JS, Surh YJ, Huh CS, Kim DH. Evaluation of Anti-Colitic Effect of Chung-Jang-Hwan (C-mix) in Mice. Biomol Ther (Seoul) 2011. [DOI: 10.4062/biomolther.2011.19.1.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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10
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A new method for the evaluation of vaccine safety based on comprehensive gene expression analysis. J Biomed Biotechnol 2010; 2010:361841. [PMID: 20617152 PMCID: PMC2896671 DOI: 10.1155/2010/361841] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 04/02/2010] [Indexed: 01/03/2023] Open
Abstract
For the past 50 years, quality control and safety tests have been used to evaluate vaccine safety. However, conventional animal safety tests need to be improved in several aspects. For example, the number of test animals used needs to be reduced and the test period shortened. It is, therefore, necessary to develop a new vaccine evaluation system. In this review, we show that gene expression patterns are well correlated to biological responses in vaccinated rats. Our findings and methods using experimental biology and genome science provide an important means of assessment for vaccine toxicity.
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11
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Lee H, Ahn YT, Lee JH, Huh CS, Kim DH. Evaluation of Anti-colitic Effect of Lactic Acid Bacteria in Mice by cDNA Microarray Analysis. Inflammation 2009; 32:379-86. [DOI: 10.1007/s10753-009-9146-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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12
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The enzyme-amplified amperometric DNA sensor using an electrodeposited polymer redox mediator. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s11426-009-0084-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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13
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van Leeuwen DM, Gottschalk RWH, Schoeters G, van Larebeke NA, Nelen V, Baeyens WF, Kleinjans JCS, van Delft JHM. Transcriptome analysis in peripheral blood of humans exposed to environmental carcinogens: a promising new biomarker in environmental health studies. ENVIRONMENTAL HEALTH PERSPECTIVES 2008; 116:1519-25. [PMID: 19057705 PMCID: PMC2592272 DOI: 10.1289/ehp.11401] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Accepted: 06/23/2008] [Indexed: 05/04/2023]
Abstract
BACKGROUND Human carcinogenesis is known to be initiated and/or promoted by exposure to chemicals that occur in the environment. Molecular cancer epidemiology is used to identify human environmental cancer risks by applying a range of effect biomarkers, which tend to be nonspecific and do not generate insights into underlying modes of action. Toxicogenomic technologies may improve on this by providing the opportunity to identify molecular biomarkers consisting of altered gene expression profiles. OBJECTIVES The aim of the present study was to monitor the expression of selected genes in a random sample of adults in Flanders selected from specific regions with (presumably) different environmental burdens. Furthermore, associations of gene expression with blood and urinary measures of biomarkers of exposure, early phenotypic effects, and tumor markers were investigated. RESULTS Individual gene expression of cytochrome p450 1B1, activating transcription factor 4, mitogen-activated protein kinase 14, superoxide dismutase 2 (Mn), chemokine (C-X-C motif) lig-and 1 (melanoma growth stimulating activity, alpha), diacylglycerol O-acyltransferase homolog 2 (mouse), tigger transposable element derived 3, and PTEN-induced putative kinase1 were measured by means of quantitative polymerase chain reaction in peripheral blood cells of 398 individuals. After correction for the confounding effect of tobacco smoking, inhabitants of the Olen region showed the highest differences in gene expression levels compared with inhabitants from the Gent and fruit cultivation regions. Importantly, we observed multiple significant correlations of particular gene expressions with blood and urinary measures of various environmental carcinogens. CONCLUSIONS Considering the observed significant differences between gene expression levels in inhabitants of various regions in Flanders and the associations of gene expression with blood or urinary measures of environmental carcinogens, we conclude that gene expression profiling appears promising as a tool for biological monitoring in relation to environmental exposures in humans.
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Affiliation(s)
- Danitsja M van Leeuwen
- Department of Health Risk Analysis and Toxicology, Maastricht University, Maastricht, the Netherlands.
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Zhang L, Sun H, Li D, Song S, Fan C, Wang S. A Conjugated Polymer-Based Electrochemical DNA Sensor: Design and Application of a Multi-Functional and Water-Soluble Conjugated Polymer. Macromol Rapid Commun 2008. [DOI: 10.1002/marc.200800260] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Li D, Yan Y, Wieckowska A, Willner I. Amplified electrochemical detection of DNA through the aggregation of Au nanoparticles on electrodes and the incorporation of methylene blue into the DNA-crosslinked structure. Chem Commun (Camb) 2008:3544-6. [PMID: 18080539 DOI: 10.1039/b704731b] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The amplified electrochemical sensing of DNA is accomplished by the analyte-induced aggregation of nucleic acid-functionalized Au nanoparticles, deposition of the aggregates on a thiolated monolayer-functionalized electrode, and the voltammetric analysis of the redox-active methylene blue intercalated in the nucleic acid duplexes associated with the aggregates.
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Affiliation(s)
- Di Li
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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16
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Ding Y, Xu L, Jovanovic BD, Helenowski IB, Kelly DL, Catalona WJ, Yang XJ, Pins M, Bergan RC. The methodology used to measure differential gene expression affects the outcome. J Biomol Tech 2007; 18:321-330. [PMID: 18166675 PMCID: PMC2392989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Confirmation of gene expression by a second methodology is critical in order to detect false-positive findings associated with microarrays. However, the impact of methodology upon the measurement of gene expression has not been rigorously evaluated. In the current study, we compared differential gene expression between PC3 and PC3-M human prostate cancer cell lines using three separate methods: microarray, quantitative RT/PCR (qRT/PCR), and Northern blotting. The PC3 to PC3-M ratio of gene expression was determined for each of 24 different genes evaluated, by each of the three methods. Comparison of gene expression ratios between Northern and microarray, Northern and qRT/PCR, and microarray and qRT/PCR, gave correlation coefficients (r) of 0.72, 0.39, and 0.63, respectively. In each instance, one to two outlier genes were apparent. Their exclusion from analysis gave r values of 0.79, 0.72, and 0.83, respectively. These findings demonstrate that the assessment of differential gene expression is dependent upon the methodology used in each situation where outcome between different methodologies was compared, the presence of a relatively limited number of outlier genes precludes high overall correlation between the methods. Validation of gene expression by different methods should be performed whenever possible.
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Affiliation(s)
- Yongzeng Ding
- Division of Hematology/Oncology, Department of Medicine
| | - Li Xu
- Division of Hematology/Oncology, Department of Medicine
| | | | | | - David L. Kelly
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE
| | | | - Ximing J. Yang
- Pathology, Northwestern University Medical School and the Robert H. Lurie Cancer Center of Northwestern University, Chicago, IL
| | - Michael Pins
- Pathology, Northwestern University Medical School and the Robert H. Lurie Cancer Center of Northwestern University, Chicago, IL
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Global gene expression analysis of the mouse colonic mucosa treated with azoxymethane and dextran sodium sulfate. BMC Cancer 2007; 7:84. [PMID: 17506908 PMCID: PMC1890554 DOI: 10.1186/1471-2407-7-84] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Accepted: 05/17/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chronic inflammation is well known to be a risk factor for colon cancer. Previously we established a novel mouse model of inflammation-related colon carcinogenesis, which is useful to examine the involvement of inflammation in colon carcinogenesis. To shed light on the alterations in global gene expression in the background of inflammation-related colon cancer and gain further insights into the molecular mechanisms underlying inflammation-related colon carcinogenesis, we conducted a comprehensive DNA microarray analysis using our model. METHODS Male ICR mice were given a single ip injection of azoxymethane (AOM, 10 mg/kg body weight), followed by the addition of 2% (w/v) dextran sodium sulfate (DSS) to their drinking water for 7 days, starting 1 week after the AOM injection. We performed DNA microarray analysis (Affymetrix GeneChip) on non-tumorous mucosa obtained from mice that received AOM/DSS, AOM alone, and DSS alone, and untreated mice at wks 5 and 10. RESULTS Markedly up-regulated genes in the colonic mucosa given AOM/DSS at wk 5 or 10 included Wnt inhibitory factor 1 (Wif1, 48.5-fold increase at wk 5 and 5.7-fold increase at wk 10) and plasminogen activator, tissue (Plat, 48.5-fold increase at wk 5), myelocytomatosis oncogene (Myc, 3.0-fold increase at wk 5), and phospholipase A2, group IIA (platelets, synovial fluid) (Plscr2, 8.0-fold increase at wk 10). The notable down-regulated genes in the colonic mucosa of mice treated with AOM/DSS were the peroxisome proliferator activated receptor binding protein (Pparbp, 0.06-fold decrease at wk 10) and the transforming growth factor, beta 3 (Tgfb3, 0.14-fold decrease at wk 10). The inflammation-related gene, peroxisome proliferator activated receptor gamma (Ppargamma 0.38-fold decrease at wk 5), was also down-regulated in the colonic mucosa of mice that received AOM/DSS. CONCLUSION This is the first report describing global gene expression analysis of an AOM/DSS-induced mouse colon carcinogenesis model, and our findings provide new insights into the mechanisms of inflammation-related colon carcinogenesis and the establishment of novel therapies and preventative strategies against carcinogenesis.
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19
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Zhang H, Su YA, Hu P, Yang J, Zheng B, Wu P, Peng J, Tang Y, Zhang L. Signature patterns revealed by microarray analyses of mice infected with influenza virus A and Streptococcus pneumoniae. Microbes Infect 2006; 8:2172-85. [PMID: 16797204 PMCID: PMC7110625 DOI: 10.1016/j.micinf.2006.04.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2006] [Revised: 03/31/2006] [Accepted: 04/10/2006] [Indexed: 01/07/2023]
Abstract
We used cDNA microarrays to identify differentially expressed genes in mice in response to infections with influenza virus A/PR/8/34 (H1N1) and Streptococcus pneumoniae. Expression microarray analysis showed up-regulation and down-regulation of many genes involved in the defense, inflammatory response and intracellular signaling pathways including chemokine, apoptosis, MAPK, Notch, Jak-STAT, T-cell receptor and complement and coagulation cascades. We have revealed signature patterns of gene expression in mice infected with two different classes of pathogens: influenza virus A and S. pneumoniae. Quantitative real-time RT-PCR results confirmed microarray results for most of the genes tested. These studies document clear differences in gene expression profiles between mice infected with influenza virus A and S. pneumoniae. Identification of genes that are differentially expressed after respiratory infections can provide insights into the mechanisms by which the host interacts with different pathogens, useful information about stage of diseases and selection of suitable targets for early diagnosis and treatments. The advantage of this novel approach is that the detection of pathogens is based on the differences in host gene expression profiles in response to different pathogens instead of detecting pathogens directly.
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Affiliation(s)
- Hong Zhang
- Z-BioMed Inc., 15725 Crabbs Branch Way, Rockville, MD 20855, USA.
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20
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Zhu B, Xu F, Baba Y. An evaluation of linear RNA amplification in cDNA microarray gene expression analysis. Mol Genet Metab 2006; 87:71-9. [PMID: 16214384 DOI: 10.1016/j.ymgme.2005.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2005] [Revised: 08/12/2005] [Accepted: 08/15/2005] [Indexed: 11/16/2022]
Abstract
DNA microarray is becoming a common tool across a broad range of disciplines, particularly in the basic and clinical biomedical sciences. However, the limitation of this technology is the requirement for relatively large amount of RNA for labeling and hybridization. T7-based linear amplification technique can overcome this limitation and enables consumption of very low amount of samples. In this study, we utilized a low RNA input fluorescent linear amplification kit from Agilent to amplify 0.2mug total RNA and compared the gene expression profiles generated from amplified aRNA and total RNA. Our results demonstrated that nanograms total RNA can be amplified reproducibly with this protocol and can generate gene expression profiles comparable with unamplified total RNA. Furthermore, quantitative real-time PCR measurements of a set of 10 genes showed good correlation with amplified aRNA arrays.
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Affiliation(s)
- Bingmei Zhu
- Department of Molecular and Pharmaceutical Biotechnology, Graduate School of Pharmaceutical Sciences, The University of Tokushima, CREST, JST, The 21st Century COE Program, Shomachi-1, Tokushima 770-8505, Japan.
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21
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Crimi M, O'Hearn SF, Wallace DC, Comi GP. Molecular research technologies in mitochondrial diseases: The microarray approach. IUBMB Life 2005; 57:811-8. [PMID: 16393784 DOI: 10.1080/15216540500460269] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mitochondria are ubiquitous in eukaryotic cells where they generate much of the cellular energy by the process of oxidative phosphorylation (OXPHOS). The approximately 1500 genes of the mitochondrial genome are distributed between the cytoplasmic, maternally-inherited, mitochondrial DNA (mtDNA) which encodes 37 genes and the nuclear DNA (nDNA) which encompasses the remaining mitochondrial genes. The interplay between the mtDNA and nDNA encoded mitochondrial genes and their role in mitochondrial disorders is still largely unclear. One approach for elucidating the pathophysiology of mitochondrial diseases has been to look at changes in the expression of mtDNA and nDNA-encoded genes in response to specific mitochondrial genetic defects. Initial studies of gene expression changes in response to mtDNA defect employed blot technologies to analyze changes in the expression of individual genes one at a time. While Southern/Northern blot experiments confirmed the importance of nDNA-mtDNA interactions in the pathophysiology of mitochondrial myopathy, the methodology used limited the number of genes that could be analyzed from each patient. This barrier has been overcome, in part by the advent of DNA microarray technology. In DNA microarrays gene sequences or oligonucleotides homologous to gene sequences are arrayed on a solid support. The RNA from the subject is then isolated, the mRNA converted to cDNA and the cDNA labeled with a fluorescent probe. The labeled cDNA is hybridized on the microarray and the fluorescence bound to each array is then quantified. Recently, these technologies have been applied to mitochondrial disease patient tissues and the presence of coordinate changes in mitochondrial gene expression confirmed.
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Affiliation(s)
- Marco Crimi
- Center for Molecular and Mitochondrial Medicine and Genetics, Department of Biological Chemistry, University of California, Irvine, California 92697-3940, USA.
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22
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Zhu B, Ping G, Shinohara Y, Zhang Y, Baba Y. Comparison of gene expression measurements from cDNA and 60-mer oligonucleotide microarrays. Genomics 2005; 85:657-65. [PMID: 15885493 DOI: 10.1016/j.ygeno.2005.02.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2004] [Revised: 01/26/2005] [Accepted: 02/17/2005] [Indexed: 01/31/2023]
Abstract
As the data generated by microarray technology continue to amass, it is necessary to compare and combine gene expression data from different platforms. To evaluate the performance of cDNA and long oligonucleotide (60-mer) arrays, we generated gene expression profiles for two cancer cell lines and compared the data between the two platforms. All 6182 unique genes represented on both platforms were included in the analysis. A limited correlation (r = 0.4708) was obtained and the difference in measurement of low-expression genes was considered to contribute to the limited correlation. Further restriction of the data set to differentially expressed genes detected in cDNA microarrays (1205 genes) and oligonucleotide arrays (1325 genes) showed modest correlations of 0.7076 and 0.6441 between the two platforms. Quantitative real-time PCR measurements of a set of 10 genes showed better correlation with oligonucleotide arrays. Our results demonstrate that there is substantial variation in the data generated from cDNA and 60-mer oligonucleotide arrays. Although general agreement was observed in measurements of differentially expressed genes, we suggest that data from different platforms could not be directly amassed.
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Affiliation(s)
- Bingmei Zhu
- Department of Molecular and Pharmaceutical Biotechnology, Graduate School of Pharmaceutical Sciences, University of Tokushima, Shomachi-1, Tokushima 770-8505, Japan.
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Shostak S. The emergence of toxicogenomics: a case study of molecularization. SOCIAL STUDIES OF SCIENCE 2005; 35:367-403. [PMID: 16060075 DOI: 10.1177/0306312705049882] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
This paper described the efforts of scientists at the National Institute of Environmental Health Sciences (NIEHS) and their allies in the National Toxicology Program to molecularize toxicology by fostering the emergence of a new discipline: toxicogenomics. I demonstrate that the molecularization of toxicology at the NIEHS began in a process of 'co-construction'. However, the subsequent emergence of the discipline of toxicogenomics has required the deliberate development of communication across the myriad disciplines necessary to produce toxicogenomic knowledge; articulation of emergent forms, standards, and practices with extant ones; management of the tensions generated by grounding toxicogenomics in traditional toxicological standards and work practices even it transforms those standards and practices; and identification and stabilization of roles for toxicogenomic knowledge in markets and service sites, such as environmental health risk assessment and regulation. This paper describes the technological, institutional, and inter-sectoral strategies that scientists have pursued in order to meet these challenges. In so doing, this analysis offers a vista into both the means and meanings of molecularization.
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Dill K, Montgomery DD, Ghindilis AL, Schwarzkopf KR. Immunoassays and sequence-specific DNA detection on a microchip using enzyme amplified electrochemical detection. ACTA ACUST UNITED AC 2005; 59:181-7. [PMID: 15163529 DOI: 10.1016/j.jbbm.2004.01.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2003] [Revised: 01/21/2004] [Accepted: 01/23/2004] [Indexed: 10/26/2022]
Abstract
A CMOS fabricated silicon microchip was used as a platform for immunoassays and DNA synthesis and hybridization. The chip is covered with a biofriendly matrix wherein the chemistries occur. The active silicon chip has over 1000 active electrodes that can be individually addressed for both synthesis of DNA and protein attachment to a membrane on the chip surface. Additionally, the active chip can be further used for the detection of various analytes at the chip surface via digital read out resulting from the redox enzymes on the captured oligonucleotide or antibody.
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Affiliation(s)
- Kilian Dill
- CombiMatrix Corporation, 6500 Harbour Heights Parkway, Suite 301, Mukilteo, WA 98275, USA.
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25
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Da Lee R, Rhee GS, An SM, Kim SS, Kwack SJ, Seok JH, Chae SY, Park CH, Yoon HJ, Cho DH, Kim HS, Park KL. Differential gene profiles in developing embryo and fetus after in utero exposure to ethanol. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2004; 67:2073-2084. [PMID: 15513904 DOI: 10.1080/15287390490515001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Alcohol consumption during pregnancy results in morphological abnormalities in the fetuses of humans and experimental animals, and is referred to as fetal alcohol syndrome (FAS). However, the molecular mechanism underlying FAS has not been completely elucidated. The aim of the present study was to investigate the potential molecular mechanisms of ethanol-induced FAS in the developing embryo and fetus. cDNA microarray analysis was used to screen for altered gene profiles. Ethanol at a teratogenic dosage (3.8 g/kg, twice a day) was administered intraperitoneally to pregnant C57Bl/6J mice from gestation day (GD) 6 to 8. Morphologic observations showed excessive malformations of the craniofacial regions (reduction of the face, the absence of eyes, nose, jaw, and mandible, underdevelopment of vibrissae areas, cleft lip, and palate) in ethanol-exposed embryos (GD 10) and fetusus (GD 15). cDNA microarray analysis showed alterations in several gene profiles, including the "palate, lung, and nasal epithelium clone (plunc), "neurofilament, " and "pale ear. " Of these genes, the expressions of plunc were confirmed by reverse-transcription polymerase chain reaction (RT-PCR) and whole-mount in situ hybridization. The plunc was highly expressed in the craniofacial region, specifically in upper airways and nasopharyngeal epithelium. RT-PCR analysis revealed that normal plunc mRNA expression levels were present in GD 15 fetuses, but not in GD 10 embryos. Interestingly, ethanol significantly downregulated the plunc expression in GD 15 fetuses. Our results suggest that ethanol-induced FAS is due in part to the downregulation of plunc expression in the fetus, and this gene may be a candidate biological marker for FAS.
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Affiliation(s)
- Rhee Da Lee
- Department of Toxicology, National Institute of Toxicological Research, Korea Food and Drug Administration, Seoul, Korea
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Gu W, Bertone AL. Generation and performance of an equine-specific large-scale gene expression microarray. Am J Vet Res 2004; 65:1664-73. [PMID: 15631031 DOI: 10.2460/ajvr.2004.65.1664] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To create high-quality sequence data for the generation of an equine gene expression microarray and evaluate array performance by use of lipopolysaccharide (LPS) exposure of synoviocytes. SAMPLE POPULATION Public nucleotide sequence database from Equus caballus and synoviocytes from clinically normal adult horses. PROCEDURE Computer procurement of equine gene sequences, probe design, and manufacture of an oligomicroarray were performed. Array performance was evaluated by use of patterns for equine synoviocytes in response to LPS. RESULTS Starting with 18,924 equine gene sequences, 3,098 equine 3' sequences were annotated and met the inclusion criteria for an expression microarray. An equine oligonucleotide expression microarray was created by use of 68,266 of the 25-oligomer probes to uniquely identify each gene. Most genes in the array (68%) were expressed in equine synoviocytes. Repeatability of the array was high (r, > 0.99), and LPS upregulated (> 5-fold change) 84 genes, many of which were inflammatory mediators, and downregulated (> 5-fold change) 14 genes. An initial pattern of gene expression for effects of LPS on synoviocytes consisted of 102 genes. CONCLUSIONS AND CLINICAL RELEVANCE Use of a computer algorithm to curate an equine sequence database generated high-quality annotated species-specific gene sequences and probe sets for a gene expression oligomicroarray, which was used to document changes in gene expression associated with LPS exposure of equine synoviocytes. The equine public database was expanded from 290 annotated genes to > 3,000 provisionally annotated genes. Similar curation and annotation of public databases could be used to create other species-specific microarrays.
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Affiliation(s)
- Weisong Gu
- Comparative Orthopedic Molecular Medicine Research Laboratories, Department of Veterinary Clinical Science, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
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Abstract
Toxicogenomics combines transcript, protein and metabolite profiling with conventional toxicology to investigate the interaction between genes and environmental stress in disease causation. The patterns of altered molecular expression that are caused by specific exposures or disease outcomes have revealed how several toxicants act and cause disease. Despite these success stories, the field faces noteworthy challenges in discriminating the molecular basis of toxicity. We argue that toxicology is gradually evolving into a systems toxicology that will eventually allow us to describe all the toxicological interactions that occur within a living system under stress and use our knowledge of toxicogenomic responses in one species to predict the modes-of-action of similar agents in other species.
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Affiliation(s)
- Michael D Waters
- National Center for Toxicogenomics, National Institute of Environmental Health Sciences, PO Box 12233, MD F1-05, 111 Alexander Drive, Research Triangle Park, North Carolina 27709-2233, USA.
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Abstract
Mounting evidence points to dietary habits as an important determinant of cancer risk and tumor behavior. Although the linkages with diet are intriguing, the literature is also laden with inconsistencies. The reasons for these inconsistencies are likely multi-factorial, but probably reflect variations in the ability of bioactive constituents to reach or affect critical molecular targets. Fluctuations in the foods consumed not only influence the intake of particular bioactive components, but may alter metabolism and potentially influence the sites of action of both essential and nonessential nutrients. Genetic polymorphisms are increasingly recognized as another factor that can alter the response to dietary components (nutritional transcriptomic effect) by influencing the absorption, metabolism, or sites of action. Likewise, variation in DNA methylation patterns and other epigenetic events that influence overall gene expression can be influenced by dietary intakes. Furthermore, variation in the ability of food components to increase or depress gene expression (nutrigenomic effect) may account for some of the observed inconsistencies in the response to dietary change. Because a host of food components are recognized to influence phosphorylation and other posttranslational events, it is also likely that these and other proteomic modifications account for at least part of the response and variation that is reported in the literature. Collectively, it is clear that bioactive food components can influence a number of key molecular events that are involved in health and disease resistance. As the era of molecular nutrition unfolds, a greater understanding of how these foods and components influence cancer will surely arise. Such information will be critical in the development of effective tailored strategies for reducing cancer burden. Just as important, however, is that as this information unfolds it is utilized within a responsible bioethical framework.
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Affiliation(s)
- J A Milner
- Nutritional Sciences Research Group, Division of Cancer Prevention, National Cancer Institute, NIH/DHHS, Rockville, MD 20852, USA.
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Wintzer M, Mladinic M, Lazarevic D, Casseler C, Cattaneo A, Nicholls J. Strategies for identifying genes that play a role in spinal cord regeneration. J Anat 2004; 204:3-11. [PMID: 14690473 PMCID: PMC1571237 DOI: 10.1111/j.1469-7580.2004.00258.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A search for genes that promote or block CNS regeneration requires numerous approaches; for example, tests can be made on individual candidate molecules. Here, however, we describe methods for comprehensive identification of genes up- and down-regulated in neurons that can and cannot regenerate after injury. One problem concerns identification of low-abundance genes out of the 30,000 or so genes expressed by neurons. Another difficulty is knowing whether a single gene or multiple genes are necessary. When microchips and subtractive differential display are used to identify genes turned on or off, the numbers are still too great to test which molecules are actually important for regeneration. Candidates are genes coding for trophic, inhibitory, receptor and extracellular matrix molecules, as well as unknown genes. A preparation useful for narrowing the search is the neonatal opossum. The spinal cord and optic nerve can regenerate after injury at 9 days but cannot at 12 days after birth. This narrow window allows genes responsible for the turning off of regeneration to be identified. As a next step, sites at which they are expressed (forebrain, midbrain, spinal cord, neurons or glia, intracellular or extracellular) must be determined. An essential step is to characterize proteins, their levels of expression, and their importance for regeneration. Comprehensive searches for molecular mechanisms represent a lengthy series of experiments that could help in devising strategies for repairing injured spinal cord.
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Abstract
The remarkable speed with which biotechnology has become critical to the practice of life sciences owes much to a series of technological revolutions. Microarray is the latest invention in this ongoing technological revolution. This technology holds the promise to revolutionize the future of biology and medicine unlike any other technology that preceded it. Development of microarray technology has significantly changed the way questions about diseases and/or biological phenomena are addressed. This is because microarrays facilitate monitoring the expression of thousands of genes or proteins in a single experiment. This enormous power of microarrays has enabled scientists to monitor thousands of genes and their products in a given living organism in one experiment, and to understand how these genes function in an orchestrated manner. Obtaining such a global view of life at the molecular level was impossible using conventional molecular biological techniques. However, despite all the progress made in developing this technology, microarray is yet to reach a point where all data are obtained, analyzed, and shared in a standardized fashion. The present article is a brief overview of microarray technologies and their applications with an emphasis on DNA microarray.
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Affiliation(s)
- Supratim Choudhuri
- Division of Biotechnology and GRAS Notice Review, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, MD 20740, USA.
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Shrader EA, Henry TR, Greeley MS, Bradley BP. Proteomics in zebrafish exposed to endocrine disrupting chemicals. ECOTOXICOLOGY (LONDON, ENGLAND) 2003; 12:485-488. [PMID: 14680328 DOI: 10.1023/b:ectx.0000003034.69538.eb] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Embryonic zebrafish were examined for changes in protein expression following exposure to sublethal concentrations of 17beta-estradiol (E2) and the estrogen mimic 4-nonylphenol (4-NP). Protein Expression Signatures were derived from embryo homogenates by two-dimensional electrophoresis and digital imaging. In both experiments approximately 30% of the proteins sampled were specific to either E2 or 4-NP and about 33% were common to the control, 4-NP and E2. However, of the proteins induced by either E2 or 4-NP, 28% were common to both chemicals at 1 ppm but only 7% were common to both at 0.1 ppm. While there are many proteins that respond specifically to each chemical, relatively few are common to the two chemicals suggesting that the response pathways of the two chemicals are distinct.
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Affiliation(s)
- E A Shrader
- University of Maryland (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA
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32
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Miracle AL, Toth GP, Lattier DL. The path from molecular indicators of exposure to describing dynamic biological systems in an aquatic organism: microarrays and the fathead minnow. ECOTOXICOLOGY (LONDON, ENGLAND) 2003; 12:457-462. [PMID: 14680324 DOI: 10.1023/b:ectx.0000003030.67752.04] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The extent to which humans and wildlife are exposed to toxicants is an important focus of environmental research. This work has been directed toward the development of molecular indicators diagnostic for exposure to various stressors in freshwater fish. Research includes the discovery of genes, indicative of environmental exposure, in the Agency's long-established aquatic toxicological organism, the fathead minnow (Pimephales promelas). Novel cDNAs and coding sequences will be used in DNA microarray analyses for pattern identification of stressor-specific, differentially up- and down-regulated genes. The methods currently used to discover genes in this organism, for which few annotated nucleic acid sequences exist, are cDNA subtraction libraries, differential display, exploiting PCR primers for known genes of other members of the family Cyprinidae and use of degenerate PCR primers designed from regions of moderate protein homology. Single or multiple genes noted as being differentially expressed in microarray analyses will then be used in separate studies to measure bioavailable stressors in the laboratory and field. These analyses will be accomplished by quantitative RT-PCR. Moving from analysis of single gene exposures to the global state of the transcriptome offers possibilities that those genes identified by DNA microarray analyses might be critical components of dynamic biological systems and networks, wherein chemical stressors exert toxic effects through various modes of action. Additionally, the ability to discriminate bioavailability of stressors in complex environmental mixtures, and correlation with adverse effects downstream from these early molecular events, presents challenging new ground to be broken in the area of risk assessment.
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Affiliation(s)
- Ann L Miracle
- Molecular Ecology Research Branch, Ecological Exposure Research Division, National Exposure Research Laboratory, Office of Research and Development, United States Environmental Protection Agency, 26 W Martin Luther King Dr., Cincinnati, OH 45268, USA
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Ko SY, Lin SC, Chang KW, Liu CJ, Chang SS, Lu SY, Liu TY. Modulation of KGF-1 gene expression in oral fibroblasts by ripe areca nut extract. J Oral Pathol Med 2003; 32:399-407. [PMID: 12846786 DOI: 10.1034/j.1600-0714.2003.00133.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND Areca chewing is a common habit of Asians, leading to a high propensity for a variety of oral diseases in this population. This research aimed to study the expression level of genes in oral fibroblast cell lines in response to exposure to ripe areca nut extract (rANE). METHODS Fifteen oral fibroblast cell lines obtained from individuals aged 20-77 years were established. Treatment of a cell line with 40 micro g/ml rANE for 24 h was performed to achieve RNA for cDNA microarray analysis. RESULTS Among some 320 genes exhibiting detectable expression levels, 14 were up-regulated and 26 were down-regulated more than 2.5-fold. Semi-quantitative RT-PCR analysis suggested that up-regulation of IL-6 expression and down-regulation of PDGFR, APP-1 and KGF-1 expressions in multiple cell lines assayed, were compatible with the results of the microarray analysis. Using quantitative real-time RT-PCR analysis, a remarkable down-regulation of KGF-1 expression in response to 40 microg/ml rANE, ranging 1.5-ninefold as compared to controls, was found in 60% (9/15) of the cell lines. CONCLUSION This study established a novel toxicogenomic database for rANE. The down-regulation of KGF-1 expression in oral fibroblast cell lines potentially impairs the proliferation of overlying keratinocytes, which could partially explain the frequent epithelial atrophy observed in chronic areca chewers in vivo.
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Affiliation(s)
- Shun-Yao Ko
- Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan
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34
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Amin RP, Hamadeh HK, Bushel PR, Bennett L, Afshari CA, Paules RS. Genomic interrogation of mechanism(s) underlying cellular responses to toxicants. Toxicology 2002; 181-182:555-63. [PMID: 12505366 DOI: 10.1016/s0300-483x(02)00481-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Assessment of the impact of xenobiotic exposure on human health and disease progression is complex. Knowledge of mode(s) of action, including mechanism(s) contributing to toxicity and disease progression, is valuable for evaluating compounds. Toxicogenomics, the subdiscipline which merges genomics with toxicology, holds the promise to contributing significantly toward the goal of elucidating mechanism(s) by studying genome-wide effects of xenobiotics. Global gene expression profiling, revolutionized by microarray technology and a crucial aspect of a toxicogenomic study, allows measuring transcriptional modulation of thousands of genes following exposure to a xenobiotic. We use our results from previous studies on compounds representing two different classes of xenobiotics (barbiturate and peroxisome proliferator) to discuss the application of computational approaches for analyzing microarray data to elucidate mechanism(s) underlying cellular responses to toxicants. In particular, our laboratory demonstrated that chemical-specific patterns of gene expression can be revealed using cDNA microarrays. Transcript profiling provides discrimination between classes of toxicants, as well as, genome-wide insight into mechanism(s) of toxicity and disease progression. Ultimately, the expectation is that novel approaches for predicting xenobiotic toxicity in humans will emerge from such information.
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Affiliation(s)
- Rupesh P Amin
- National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Mail Drop F1-05, Research Triangle Park, NC 27709, USA
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35
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Crump D, Werry K, Veldhoen N, Van Aggelen G, Helbing CC. Exposure to the herbicide acetochlor alters thyroid hormone-dependent gene expression and metamorphosis in Xenopus Laevis. ENVIRONMENTAL HEALTH PERSPECTIVES 2002; 110:1199-205. [PMID: 12460798 PMCID: PMC1241106 DOI: 10.1289/ehp.021101199] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A growing number of substances released into the environment disrupt normal endocrine mechanisms in a wide range of vertebrates. Little is known about the effects and identities of endocrine-disrupting chemicals (EDCs) that target thyroid hormone (TH) action, particularly at the cellular level. Frog tadpole metamorphosis depends completely on TH, which has led to the suggestion of a metamorphosis-based assay for screening potential EDCs. A major mechanism of TH action is the alteration of gene expression via hormone-bound nuclear receptors. To assess the gene expression profiles in the frog model, we designed a novel multispecies frog cDNA microarray. Recently, the preemergent herbicide acetochlor was shown to accelerate 3,5,3 -triiodothyronine (T3)-induced forelimb emergence and increase mRNA expression of thyroid hormone ss receptors in ranid tadpoles. Here we show that T3-induced metamorphosis of Xenopus laevis, a species commonly used in the laboratory, is accelerated upon acute exposure to an environmentally relevant level of acetochlor. The morphologic changes observed are preceded by alterations in gene expression profiles detected in the tadpole tail, and the nature of these profiles suggest a novel mechanism of action for acetochlor.
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Affiliation(s)
- Doug Crump
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
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36
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Marciano PG, Eberwine JH, Ragupathi R, Saatman KE, Meaney DF, McIntosh TK. Expression profiling following traumatic brain injury: a review. Neurochem Res 2002; 27:1147-55. [PMID: 12462413 DOI: 10.1023/a:1020973308941] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Traumatic brain injury (TBI) elicits a complex sequence of putative autodestructive and neuroprotective cellular cascades. It is hypothesized that the genomic responses of cells in the injured brain serve as the basis for these cascades. Traditional methods for analyzing differential gene expression following brain trauma demonstrate that immediate early genes, cytokines, transcription factors, and neurotrophic factors can all participate in the brain's active and directed response to injury, and may do so concurrently. It is this complexity and multiplicity of interrelated molecular mechanisms that has demanded new methods for comprehensive and parallel evaluation of putative as well as novel gene targets. Recent advances in DNA microarray technology have enabled the simultaneous evaluation of thousands of genes and the subsequent generation of massive amounts of biological data relevant to CNS injury. This emerging technology can serve to further current knowledge regarding recognized molecular cascades as well as to identify novel molecular mechanisms that occur throughout the post-traumatic period. The elucidation of the complex alterations in gene expression underlying the pathological sequelae following TBI is of central importance in the design of future therapeutic agents.
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Affiliation(s)
- Paolo G Marciano
- Department of Neuroscience, University of Pennsylvania, Philadelphia, USA
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37
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Liu Y, Rauch CB, Stevens RL, Lenigk R, Yang J, Rhine DB, Grodzinski P. DNA amplification and hybridization assays in integrated plastic monolithic devices. Anal Chem 2002; 74:3063-70. [PMID: 12141665 DOI: 10.1021/ac020094q] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PCR amplification, DNA hybridization, and a hybridization wash have been integrated in a disposable monolithic DNA device, containing all of the necessary fluidic channels and reservoirs. These integrated devices were fabricated in polycarbonate plastic material by CO2 laser machining and were assembled using a combination of thermal bonding and adhesive tape bonding. Pluronics polymer phase change valves were implemented in the devices to fulfill the valving requirements. Pluronics polymer material is PCR compatible, and 30% Pluronics polymer valves provide enough holding pressure to ensure a successful PCR amplification. By reducing the temperature locally, to approximately 5 degrees C, Pluronics valves were liquefied and easily opened. A hybridization channel was made functional by oligonucleotide deposition, using Motorola proprietary surface attachment chemistry. Reagent transport on the device was provided by syringe pumps, which were docked onto the device. Peltier thermal electrical devices powered the heating and cooling functionality of the device. Asymmetrical PCR amplification and subsequent hybridization detection of both Escherichia coli K-12 MG1655 and Enterococcus faecalis DNAE genes have been successfully demonstrated in these disposable monolithic devices.
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Affiliation(s)
- Yingjie Liu
- Physical Sciences Research Laboratories, Motorola, Inc., Tempe, Arzona 85284, USA
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38
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Affiliation(s)
- Nigel J Walker
- Environmental Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
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39
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Tennant RW. The National Center for Toxicogenomics: using new technologies to inform mechanistic toxicology. ENVIRONMENTAL HEALTH PERSPECTIVES 2002; 110:A8-10. [PMID: 11781174 PMCID: PMC1240702 DOI: 10.1289/ehp.110-a8] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
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40
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2002. [PMCID: PMC2447253 DOI: 10.1002/cfg.117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
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Eddy SF, Storey KB. Dynamic Use of cDNA Arrays: Heterologous Probing for Gene Discovery and Exploration of Organismal Adaptation to Environmental Stress. CELL AND MOLECULAR RESPONSE TO STRESS 2002. [DOI: 10.1016/s1568-1254(02)80024-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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