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Basagoudanavar SH, Hosamani M, Tamil Selvan RP, Sreenivasa BP, Sanyal A, Venkataramanan R. Host serum microRNA profiling during the early stage of foot-and-mouth disease virus infection. Arch Virol 2018; 163:2055-2063. [DOI: 10.1007/s00705-018-3824-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 03/15/2018] [Indexed: 12/29/2022]
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Csonka C, Szűcs G, Varga-Orvos Z, Bencsik P, Csont T, Zvara Á, Puskás LG, Ferdinandy P. Ischemic postconditioning alters the gene expression pattern of the ischemic heart. Exp Biol Med (Maywood) 2014; 239:141-50. [DOI: 10.1177/1535370213511017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
To profile changes in gene expression in response to ischemic postconditioning, isolated rat hearts were subjected to 30 min of regional ischemia followed by 120 min of reperfusion with or without postconditioning. At the end of reperfusion, cardiac RNA was assayed by DNA microarrays (31,000 format), verified by quantitative real-time polymerase chain reaction (QRT-PCR). Postconditioning significantly up-regulated 50 genes and down-regulated 58 different genes, including pyruvate dehydrogenase, 60 kDa heat shock protein 1, lipoprotein lipase, gamma-sarcoglycan, and phospholipase C. Gene ontology analysis revealed that most of the altered genes belong to the cellular metabolic processes cluster. Many of the genes have not previously been suspected to be involved in the mechanism of postconditioning.
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Affiliation(s)
- Csaba Csonka
- Cardiovascular Research Group, Department of Biochemistry, University of Szeged, Szeged, H-6720 Hungary
- Pharmahungary Group, Szeged, H-6723 Hungary
| | - Gergő Szűcs
- Cardiovascular Research Group, Department of Biochemistry, University of Szeged, Szeged, H-6720 Hungary
| | - Zoltán Varga-Orvos
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged, H-6726 Hungary
| | | | - Tamás Csont
- Cardiovascular Research Group, Department of Biochemistry, University of Szeged, Szeged, H-6720 Hungary
- Pharmahungary Group, Szeged, H-6723 Hungary
| | - Ágnes Zvara
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged, H-6726 Hungary
| | - László G Puskás
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged, H-6726 Hungary
| | - Péter Ferdinandy
- Pharmahungary Group, Szeged, H-6723 Hungary
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, H-1089 Hungary
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Lacroix B, Citovsky V. A mutation in negative regulator of basal resistance WRKY17 of Arabidopsis increases susceptibility to Agrobacterium-mediated genetic transformation. F1000Res 2013; 2:33. [PMID: 24358874 PMCID: PMC3799546 DOI: 10.12688/f1000research.2-33.v1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/31/2013] [Indexed: 11/20/2022] Open
Abstract
Agrobacterium is a phytopathogenic bacterium that induces crown gall disease in many plant species by transferring and integrating a segment of its own DNA (T-DNA) into its host genome. Whereas Agrobacterium usually does not trigger an extensive defense response in its host plants, it induces the expression of several defense-related genes and activates plant stress reactions. In the complex interplay between Agrobacterium and its host plant, Agrobacterium has evolved to take advantage of these plant defense pathways for its own purpose of advancement of the infection process. For example, Agrobacterium utilizes the host stress response transcriptional regulator VIP1 to facilitate nuclear import and proteasomal uncoating of its T-DNA during genetic transformation of the host cell. In Arabidopsis, the VIP1 gene expression is repressed by WRKY17, a negative regulator of basal resistance to Pseudomonas. Thus, we examined whether WRKY17 is also involved in plant susceptibility to genetic transformation by Agrobacterium. Using reverse genetics, we showed that a wrky17 mutant displays higher expression of the VIP1 gene in roots, but not in shoots. In a root infection assay, the wrky17 mutant plants were hyper-susceptible to Agrobacterium compared to wild type plants. WRKY17, therefore, may act as a positive regulator of Arabidopsis resistance to Agrobacterium. This notion is important for understanding the complex regulation of Agrobacterium-mediated genetic transformation; thus, although this paper reports a relatively small set of data that we do not plan to pursue further in our lab, we believe it might be useful for the broad community of plant pathologists and plant biotechnologists.
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Affiliation(s)
- Benoît Lacroix
- Department of Biochemistry and Cell Biology, State University of New York, New York, 11794-5215, USA
| | - Vitaly Citovsky
- Department of Biochemistry and Cell Biology, State University of New York, New York, 11794-5215, USA
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Chou HL, Yao CT, Su SL, Lee CY, Hu KY, Terng HJ, Shih YW, Chang YT, Lu YF, Chang CW, Wahlqvist ML, Wetter T, Chu CM. Gene expression profiling of breast cancer survivability by pooled cDNA microarray analysis using logistic regression, artificial neural networks and decision trees. BMC Bioinformatics 2013; 14:100. [PMID: 23506640 PMCID: PMC3614553 DOI: 10.1186/1471-2105-14-100] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 02/26/2013] [Indexed: 11/13/2022] Open
Abstract
Background Microarray technology can acquire information about thousands of genes simultaneously. We analyzed published breast cancer microarray databases to predict five-year recurrence and compared the performance of three data mining algorithms of artificial neural networks (ANN), decision trees (DT) and logistic regression (LR) and two composite models of DT-ANN and DT-LR. The collection of microarray datasets from the Gene Expression Omnibus, four breast cancer datasets were pooled for predicting five-year breast cancer relapse. After data compilation, 757 subjects, 5 clinical variables and 13,452 genetic variables were aggregated. The bootstrap method, Mann–Whitney U test and 20-fold cross-validation were performed to investigate candidate genes with 100 most-significant p-values. The predictive powers of DT, LR and ANN models were assessed using accuracy and the area under ROC curve. The associated genes were evaluated using Cox regression. Results The DT models exhibited the lowest predictive power and the poorest extrapolation when applied to the test samples. The ANN models displayed the best predictive power and showed the best extrapolation. The 21 most-associated genes, as determined by integration of each model, were analyzed using Cox regression with a 3.53-fold (95% CI: 2.24-5.58) increased risk of breast cancer five-year recurrence… Conclusions The 21 selected genes can predict breast cancer recurrence. Among these genes, CCNB1, PLK1 and TOP2A are in the cell cycle G2/M DNA damage checkpoint pathway. Oncologists can offer the genetic information for patients when understanding the gene expression profiles on breast cancer recurrence.
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Lacroix B, Citovsky V. A mutation in negative regulator of basal resistance WRKY17 of Arabidopsis increases susceptibility to Agrobacterium-mediated transient genetic transformation. F1000Res 2013. [PMID: 24358874 DOI: 10.12688/f1000research.2-33.v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Agrobacterium is a phytopathogenic bacterium that induces crown gall disease in many plant species by transferring and integrating a segment of its own DNA (T-DNA) into its host genome. Whereas Agrobacterium usually does not trigger an extensive defense response in its host plants, it induces the expression of several defense-related genes and activates plant stress reactions. In the complex interplay between Agrobacterium and its host plant, Agrobacterium has evolved to take advantage of these plant defense pathways for its own purpose of advancement of the infection process. For example, Agrobacterium utilizes the host stress response transcriptional regulator VIP1 to facilitate nuclear import and proteasomal uncoating of its T-DNA during genetic transformation of the host cell. In Arabidopsis, the VIP1 gene expression is repressed by WRKY17, a negative regulator of basal resistance to Pseudomonas. Thus, we examined whether WRKY17 is also involved in plant susceptibility to genetic transformation by Agrobacterium. Using reverse genetics, we showed that a wrky17 mutant displays higher expression of the VIP1 gene in roots, but not in shoots. In a root infection assay, the wrky17 mutant plants were hyper-susceptible to Agrobacterium compared to wild type plants. WRKY17, therefore, may act as a positive regulator of Arabidopsis resistance to Agrobacterium. This notion is important for understanding the complex regulation of Agrobacterium-mediated transient genetic transformation; thus, although this paper reports a relatively small set of data that we do not plan to pursue further in our lab, we believe it might be useful for the broad community of plant pathologists and plant biotechnologists.
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Affiliation(s)
- Benoît Lacroix
- Department of Biochemistry and Cell Biology, State University of New York, New York, 11794-5215, USA
| | - Vitaly Citovsky
- Department of Biochemistry and Cell Biology, State University of New York, New York, 11794-5215, USA
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Use of conventional and -omics based methods for health claims of dietary antioxidants: a critical overview. Br J Nutr 2009; 99 E Suppl 1:ES3-52. [PMID: 18503734 DOI: 10.1017/s0007114508965752] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This article describes the principles and limitations of methods used to investigate reactive oxygen species (ROS) protective properties of dietary constituents and is aimed at providing a better understanding of the requirements for science based health claims of antioxidant (AO) effects of foods. A number of currently used biochemical measurements aimed of determining the total antioxidant capacity and oxidised lipids and proteins are carried out under unphysiological conditions and are prone to artefact formation. Probably the most reliable approaches are measurements of isoprostanes as a parameter of lipid peroxidation and determination of oxidative DNA damage. Also the design of the experimental models has a strong impact on the reliability of AO studies: the common strategy is the identification of AO by in vitro screening with cell lines. This approach is based on the assumption that protection towards ROS is due to scavenging, but recent findings indicate that activation of transcription factors which regulate genes involved in antioxidant defence plays a key role in the mode of action of AO. These processes are not adequately represented in cell lines. Another shortcoming of in vitro experiments is that AO are metabolised in vivo and that most cell lines are lacking enzymes which catalyse these reactions. Compounds with large molecular configurations (chlorophylls, anthocyans and polyphenolics) are potent AO in vitro, but weak or no effects were observed in animal/human studies with realistic doses as they are poorly absorbed. The development of -omics approaches will improve the scientific basis for health claims. The evaluation of results from microarray and proteomics studies shows that it is not possible to establish a general signature of alterations of transcription and protein patterns by AO. However, it was shown that alterations of gene expression and protein levels caused by experimentally induced oxidative stress and ROS related diseases can be normalised by dietary AO.
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Brechenmacher L, Kim MY, Benitez M, Li M, Joshi T, Calla B, Lee MP, Libault M, Vodkin LO, Xu D, Lee SH, Clough SJ, Stacey G. Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2008; 21:631-45. [PMID: 18393623 DOI: 10.1094/mpmi-21-5-0631] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Legumes interact with nodulating bacteria that convert atmospheric nitrogen into ammonia for plant use. This nitrogen fixation takes place within root nodules that form after infection of root hairs by compatible rhizobia. Using cDNA microarrays, we monitored gene expression in soybean (Glycine max) inoculated with the nodulating bacterium Bradyrhizobium japonicum 4, 8, and 16 days after inoculation, timepoints that coincide with nodule development and the onset of nitrogen fixation. This experiment identified several thousand genes that were differentially expressed in response to B. japonicum inoculation. Expression of 27 genes was analyzed by quantitative reverse transcriptase-polymerase chain reaction, and their expression patterns mimicked the microarray results, confirming integrity of analyses. The microarray results suggest that B. japonicum reduces plant defense responses during nodule development. In addition, the data revealed a high level of regulatory complexity (transcriptional, post-transcriptional, translational, post-translational) that is likely essential for development of the symbiosis and adjustment to an altered nutritional status.
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Affiliation(s)
- Laurent Brechenmacher
- National Center for Soybean Biotechnology, Divisions of Plant Sciences and Biochemistry, University of Missouri, Columbia, MO 65211, USA
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