scholarly journals Distinct Biphasic mRNA Changes in Response to Asian Soybean Rust Infection

2007 ◽  
Vol 20 (8) ◽  
pp. 887-899 ◽  
Author(s):  
Martijn van de Mortel ◽  
Justin C. Recknor ◽  
Michelle A. Graham ◽  
Dan Nettleton ◽  
Jaime D. Dittman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Expression Profiles ◽  
Fungal Growth ◽  
Initial Response ◽  
Soybean Rust ◽  
Specific Response ◽  
Susceptible Genotype ◽  
Rust Infection ◽  
Asian Soybean Rust

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi, is now established in all major soybean-producing countries. Currently, there is little information about the molecular basis of ASR–soybean interactions, which will be needed to assist future efforts to develop effective resistance. Toward this end, abundance changes of soybean mRNAs were measured over a 7-day ASR infection time course in mock-inoculated and infected leaves of a soybean accession (PI230970) carrying the Rpp2 resistance gene and a susceptible genotype (Embrapa-48). The expression profiles of differentially expressed genes (ASR-infected compared with the mock-inoculated control) revealed a biphasic response to ASR in each genotype. Within the first 12 h after inoculation (hai), which corresponds to fungal germination and penetration of the epidermal cells, differential gene expression changes were evident in both genotypes. mRNA expression of these genes mostly returned to levels found in mock-inoculated plants by 24 hai. In the susceptible genotype, gene expression remained unaffected by rust infection until 96 hai, a time period when rapid fungal growth began. In contrast, gene expression in the resistant genotype diverged from the mock-inoculated control earlier, at 72 h, demonstrating that Rpp2-mediated defenses were initiated prior to this time. These data suggest that ASR initially induces a non-specific response that is transient or is suppressed when early steps in colonization are completed in both soybean genotypes. The race-specific resistance phenotype of Rpp2 is manifested in massive gene expression changes after the initial response prior to the onset of rapid fungal growth that occurs in the susceptible genotype.

scholarly journals Bayesian approach for predicting responses to therapy from high-dimensional time-course gene expression profiles

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Arika Fukushima ◽  
Masahiro Sugimoto ◽  
Satoru Hiwa ◽  
Tomoyuki Hiroyasu
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Response To Therapy ◽  
Hcv Infection ◽  
Entire Treatment Period ◽  
Time Points ◽  
Time Course Data ◽  
Conventional Methods

Abstract Background Historical and updated information provided by time-course data collected during an entire treatment period proves to be more useful than information provided by single-point data. Accurate predictions made using time-course data on multiple biomarkers that indicate a patient’s response to therapy contribute positively to the decision-making process associated with designing effective treatment programs for various diseases. Therefore, the development of prediction methods incorporating time-course data on multiple markers is necessary. Results We proposed new methods that may be used for prediction and gene selection via time-course gene expression profiles. Our prediction method consolidated multiple probabilities calculated using gene expression profiles collected over a series of time points to predict therapy response. Using two data sets collected from patients with hepatitis C virus (HCV) infection and multiple sclerosis (MS), we performed numerical experiments that predicted response to therapy and evaluated their accuracies. Our methods were more accurate than conventional methods and successfully selected genes, the functions of which were associated with the pathology of HCV infection and MS. Conclusions The proposed method accurately predicted response to therapy using data at multiple time points. It showed higher accuracies at early time points compared to those of conventional methods. Furthermore, this method successfully selected genes that were directly associated with diseases.

scholarly journals Transcriptome analyses and virus induced gene silencing identify genes in the Rpp4-mediated Asian soybean rust resistance pathway

2013 ◽  
Vol 40 (10) ◽  
pp. 1029 ◽  
Author(s):  
Aguida M. A. P. Morales ◽  
Jamie A. O'Rourke ◽  
Martijn van de Mortel ◽  
Katherine T. Scheider ◽  
Timothy J. Bancroft ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Gene Silencing ◽  
Differentially Expressed ◽  
Soybean Rust ◽  
Phakopsora Pachyrhizi ◽  
R Gene ◽  
Virus Induced Gene Silencing ◽  
Asian Soybean Rust ◽  
Defence Responses

Rpp4 (Resistance to Phakopsora pachyrhizi 4) confers resistance to Phakopsora pachyrhizi Sydow, the causal agent of Asian soybean rust (ASR). By combining expression profiling and virus induced gene silencing (VIGS), we are developing a genetic framework for Rpp4-mediated resistance. We measured gene expression in mock-inoculated and P. pachyrhizi-infected leaves of resistant soybean accession PI459025B (Rpp4) and the susceptible cultivar (Williams 82) across a 12-day time course. Unexpectedly, two biphasic responses were identified. In the incompatible reaction, genes induced at 12 h after infection (hai) were not differentially expressed at 24 hai, but were induced at 72 hai. In contrast, genes repressed at 12 hai were not differentially expressed from 24 to 144 hai, but were repressed 216 hai and later. To differentiate between basal and resistance-gene (R-gene) mediated defence responses, we compared gene expression in Rpp4-silenced and empty vector-treated PI459025B plants 14 days after infection (dai) with P. pachyrhizi. This identified genes, including transcription factors, whose differential expression is dependent upon Rpp4. To identify differentially expressed genes conserved across multiple P. pachyrhizi resistance pathways, Rpp4 expression datasets were compared with microarray data previously generated for Rpp2 and Rpp3-mediated defence responses. Fourteen transcription factors common to all resistant and susceptible responses were identified, as well as fourteen transcription factors unique to R-gene-mediated resistance responses. These genes are targets for future P. pachyrhizi resistance research.

scholarly journals Effects of Collagen–Glycosaminoglycan Mesh on Gene Expression as Determined by Using Principal Component Analysis-Based Unsupervised Feature Extraction

Polymers ◽  
2021 ◽  
Vol 13 (23) ◽  
pp. 4117
Author(s):  
Y-h. Taguchi ◽  
Turki Turki
Keyword(s):  
Gene Expression ◽  
Principal Component Analysis ◽  
Feature Extraction ◽  
Cell Lines ◽  
Time Course ◽  
Expression Profiles ◽  
Principal Component ◽  
Component Analysis ◽  
Altered Expression ◽  
Unsupervised Feature Extraction

The development of the medical applications for substances or materials that contact cells is important. Hence, it is necessary to elucidate how substances that surround cells affect gene expression during incubation. In the current study, we compared the gene expression profiles of cell lines that were in contact with collagen–glycosaminoglycan mesh and control cells. Principal component analysis-based unsupervised feature extraction was applied to identify genes with altered expression during incubation in the treated cell lines but not in the controls. The identified genes were enriched in various biological terms. Our method also outperformed a conventional methodology, namely, gene selection based on linear regression with time course.

scholarly journals Molecular mapping of quantitative trait loci for agronomical traits in soybean under Asian soybean rust infection

2018 ◽  
Vol 18 (4) ◽  
pp. 390-398 ◽  
Author(s):  
João Vitor Maldonado dos Santos ◽  
Naoki Yamanaka ◽  
Francismar Corrêa Marcelino-Guimarães ◽  
José Francisco Ferraz de Toledo ◽  
Carlos Alberto Arrabal Arias ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Molecular Mapping ◽  
Soybean Rust ◽  
Rust Infection ◽  
Asian Soybean Rust ◽  
Trait Loci ◽  
Agronomical Traits

scholarly journals Prediction of Pharmacological and Xenobiotic Responses to Drugs Based on Time Course Gene Expression Profiles

PLoS ONE ◽  
2009 ◽  
Vol 4 (12) ◽  
pp. e8126 ◽  
Author(s):  
Tao Huang ◽  
WeiRen Cui ◽  
LeLe Hu ◽  
KaiYan Feng ◽  
Yi-Xue Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Expression Profiles ◽  
Gene Expression Profiles

scholarly journals Estrogen regulation in human breast cancer cells of new downstream gene targets involved in estrogen metabolism, cell proliferation and cell transformation

2004 ◽  
Vol 32 (2) ◽  
pp. 397-414 ◽  
Author(s):  
JA Vendrell ◽  
F Magnino ◽  
E Danis ◽  
MJ Duchesne ◽  
S Pinloche ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Cell Proliferation ◽  
Time Course ◽  
Cell Transformation ◽  
Expression Profiles ◽  
Estrogen Metabolism ◽  
Breast Carcinoma Cell Line ◽  
Human Breast ◽  
Estrogen Regulation

We explored, by cDNA mini-arrays, gene expression measurements of MVLN, a human breast carcinoma cell line derived from MCF-7, after 4 days of exposure to 17beta-estradiol (E(2)) treatment, in order to extend our understanding of the mechanism of the pharmacological action of estrogens. We focused on 22 genes involved in estrogen metabolism, cell proliferation regulation and cell transformation. The specificity of the E(2) response was reinforced by comparison with 4-hydroxytamoxifen (OH-Tam), ICI 182,780 and E(2)+OH-Tam expression profiles. Real-time quantitative PCR (RTQ-PCR) confirmed the variation of expression of known (TFF1, AREG, IRS1, IGFBP4, PCNA, ERBB2, CTSD, MYC) as well as novel (DLEU2, CCNA2, UGT1A1, ABCC3, ABCC5, TACC1, EFNA1, NOV, CSTA, MMP15, ZNF217) genes. The temporal response of these gene expression regulations was then investigated after 6 and 18 h of E(2) treatment and this allowed the identification of different time-course patterns. Cycloheximide treatment studies indicated first that estrogen affected the transcript levels of ABCC3 and ABCC5 through dissimilar pathways, and secondly that protein synthesis was needed for modulation of the expression of the CCNA2 and TACC1 genes by estrogens. Western blot analysis performed on TFF1, IRS1, IGFBP4, amphiregulin, PCNA, cyclin A2, TACC1 and ABCC5 proteins confirmed the mini-array and RTQ-PCR data, even for genes harboring low variations of mRNA expression. Our findings should enhance the understanding of changes induced by E(2) on the transcriptional program of human E(2)-responsive cells and permit the identification of new potential diagnostic/prognostic tools for the monitoring of estrogen-related disease conditions such as breast cancer.

scholarly journals Infectomic Analysis of Gene Expression Profiles of Human Brain Microvascular Endothelial Cells Infected withCryptococcus neoformans

2008 ◽  
Vol 2008 ◽  
pp. 1-7 ◽  
Author(s):  
Ambrose Jong ◽  
Chun-Hua Wu ◽  
Wensheng Zhou ◽  
Han-Min Chen ◽  
Sheng-He Huang
Keyword(s):  
Gene Expression ◽  
Endothelial Cells ◽  
Human Brain ◽  
Time Course ◽  
Expression Profiles ◽  
Host Cells ◽  
Microvascular Endothelial Cells ◽  
Brain Microvascular Endothelial Cells ◽  
Microvascular Endothelial ◽  
Time Point

In order to dissect the pathogenesis ofCryptococcus neoformansmeningoencephalitis, a genomic survey of the changes in gene expression of human brain microvascular endothelial cells infected byC.neoformanswas carried out in a time-course study. Principal component analysis (PCA) revealed sigificant fluctuations in the expression levels of different groups of genes during the pathogen-host interaction. Self-organizing map (SOM) analysis revealed that most genes were up- or downregulated 2 folds or more at least at one time point during the pathogen-host engagement. The microarray data were validated by Western blot analysis of a group of genes, includingβ-actin, Bcl-x, CD47, Bax, Bad, and Bcl-2. Hierarchical cluster profile showed that 61 out of 66 listed interferon genes were changed at least at one time point. Similarly, the active responses in expression of MHC genes were detected at all stages of the interaction. Taken together, our infectomic approaches suggest that the host cells significantly change the gene profiles and also actively participate in immunoregulations of the central nervous system (CNS) duringC.neoformansinfection.

Gene expression profiling of normal and malignant CD34-derived megakaryocytic cells

Blood ◽  
2004 ◽  
Vol 104 (10) ◽  
pp. 3126-3135 ◽  
Author(s):  
Elena Tenedini ◽  
Maria Elena Fagioli ◽  
Nicola Vianelli ◽  
Pier Luigi Tazzari ◽  
Francesca Ricci ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Mitochondrial Permeability Transition ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Annexin V ◽  
Permeability Transition Pore ◽  
Permeability Transition ◽  
Course Evaluation ◽  
Oligonucleotide Microarray Analysis

Abstract Gene expression profiles of bone marrow (BM) CD34-derived megakaryocytic cells (MKs) were compared in patients with essential thrombocythemia (ET) and healthy subjects using oligonucleotide microarray analysis to identify differentially expressed genes and disease-specific transcripts. We found that proapoptotic genes such as BAX, BNIP3, and BNIP3L were down-regulated in ET MKs together with genes that are components of the mitochondrial permeability transition pore complex, a system with a pivotal role in apoptosis. Conversely, antiapoptotic genes such as IGF1-R and CFLAR were up-regulated in the malignant cells, as was the SDF1 gene, which favors cell survival. On the basis of the array results, we characterized apoptosis of normal and ET MKs by time-course evaluation of annexin-V and sub-G1 peak DNA stainings of immature and mature MKs after culture in serum-free medium with an optimal thrombopoietin concentration, and annexin-V–positive MKs only, with decreasing thrombopoietin concentrations. ET MKs were more resistant to apoptosis than their normal counterparts. We conclude that imbalance between proliferation and apoptosis seems to be an important step in malignant ET megakaryocytopoiesis.

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