A combination of kernel methods and genetic programming for gene expression pattern classification

Abstract Background Free radicals generated in the biological system bring about modifications in biological molecules causing damage to their structure and function. Identifying the damage caused by ROS and RNS is important to predict the pathway of apoptosis due to stress in PC12 cells. The first defense mechanisms against them are antioxidants which act in various pathways through important cellular organelles like the mitochondria and endoplasmic reticulum. Specific biomarkers like Gadd153 which is a marker for endoplasmic reticulum stress, Nrf2 which responds to the redox changes and translocates the antioxidant response elements, and Btg2 which is an antioxidant regulator have not been addressed in different stress conditions previously in PC12 cells. Therefore, the study was conducted to analyze the gene expression pattern (SOD, Catalase, Btg2, Gadd153, and Nrf2) and the protein expression pattern (iNOS and MnSOD) of the antioxidant stress markers in differential stress-induced PC12 cells. Peroxynitrite (1 μM), rotenone (1 μM), H2O2(100 mM), and high glucose (33 mM) were used to induce oxidative and nitrosative stress in PC12 cells. Results The results obtained suggested that rotenone-induced PC12 cells showed a significant increase in the expression of catalase, Btg2, and Gadd153 compared to the control. Peroxynitrite-induced PC12 cells showed higher expression of Btg2 compared to the control. H2O2 and high glucose showed lesser expression compared to the control in all stress marker genes. In contrast, the Nrf2 gene expression is downregulated in all the stress-induced PC12 cells compared to the control. Further, MnSOD and iNOS protein expression studies suggest that PC12 cells exhibit a selective downregulation. Lower protein expression of MnSOD and iNOS may be resulted due to the mitochondrial dysfunction in peroxynitrite-, high glucose-, and H2O2-treated cells, whereas rotenone-induced cells showed lower expression, which could be the result of a dysfunction of the endoplasmic reticulum. Conclusion Different stress inducers like rotenone, peroxynitrite, H2O2, and high glucose increase the NO and ROS. Btg2 and Gadd153 genes were upregulated in the stress-induced cells, whereas the Nrf2 was significantly downregulated in differential stress-induced PC12 cells. Further, antioxidant marker genes were differentially expressed with different stress inducers.

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CNS gene expression pattern associated with spontaneous experimental autoimmune encephalomyelitis

Journal of Neuroscience Research ◽

10.1002/jnr.10689 ◽

2003 ◽

Vol 73 (5) ◽

pp. 667-678 ◽

Cited By ~ 19

Author(s):

Agata Matejuk ◽

Corwyn Hopke ◽

Jami Dwyer ◽

Sandhya Subramanian ◽

Richard E. Jones ◽

...

Keyword(s):

Gene Expression ◽

Experimental Autoimmune Encephalomyelitis ◽

Expression Pattern ◽

Gene Expression Pattern ◽

Autoimmune Encephalomyelitis ◽

Experimental Autoimmune

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Why publish Gene Expression Pattern papers in Brain Research?

Molecular Brain Research ◽

10.1016/s0169-328x(03)00480-7 ◽

2003 ◽

Vol 119 (2) ◽

pp. v

Keyword(s):

Gene Expression ◽

Expression Pattern ◽

Brain Research ◽

Gene Expression Pattern ◽

Publish Gene Expression

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Verticillium wilt resistant and susceptible olive cultivars express a very different basal set of genes in roots

BMC Genomics ◽

10.1186/s12864-021-07545-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Jorge A. Ramírez-Tejero ◽

Jaime Jiménez-Ruiz ◽

Alicia Serrano ◽

Angjelina Belaj ◽

Lorenzo León ◽

...

Keyword(s):

Gene Expression ◽

Expression Pattern ◽

Growth And Development ◽

Expression Patterns ◽

Gene Expression Pattern ◽

Expression Level ◽

Resistant Cultivars ◽

Pathogen Invasion ◽

Wide Range ◽

Olive Cultivars

Abstract Background Olive orchards are threatened by a wide range of pathogens. Of these, Verticillium dahliae has been in the spotlight for its high incidence, the difficulty to control it and the few cultivars that has increased tolerance to the pathogen. Disease resistance not only depends on detection of pathogen invasion and induction of responses by the plant, but also on barriers to avoid the invasion and active resistance mechanisms constitutively expressed in the absence of the pathogen. In a previous work we found that two healthy non-infected plants from cultivars that differ in V. dahliae resistance such as ‘Frantoio’ (resistant) and ‘Picual’ (susceptible) had a different root morphology and gene expression pattern. In this work, we have addressed the issue of basal differences in the roots between Resistant and Susceptible cultivars. Results The gene expression pattern of roots from 29 olive cultivars with different degree of resistance/susceptibility to V. dahliae was analyzed by RNA-Seq. However, only the Highly Resistant and Extremely Susceptible cultivars showed significant differences in gene expression among various groups of cultivars. A set of 421 genes showing an inverse differential expression level between the Highly Resistant to Extremely Susceptible cultivars was found and analyzed. The main differences involved higher expression of a series of transcription factors and genes involved in processes of molecules importation to nucleus, plant defense genes and lower expression of root growth and development genes in Highly Resistant cultivars, while a reverse pattern in Moderately Susceptible and more pronounced in Extremely Susceptible cultivars were observed. Conclusion According to the different gene expression patterns, it seems that the roots of the Extremely Susceptible cultivars focus more on growth and development, while some other functions, such as defense against pathogens, have a higher expression level in roots of Highly Resistant cultivars. Therefore, it seems that there are constitutive differences in the roots between Resistant and Susceptible cultivars, and that susceptible roots seem to provide a more suitable environment for the pathogen than the resistant ones.

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