scholarly journals Evolutionary Approach for Relative Gene Expression Algorithms

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Marcin Czajkowski ◽  
Marek Kretowski
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Microarray Data ◽  
Experimental Validation ◽  
Solution Space ◽  
Relative Gene Expression ◽  
Relative Expression ◽  
Small Collection ◽  
Microarray Datasets ◽  
Relative Gene

A Relative Expression Analysis (RXA) uses ordering relationships in a small collection of genes and is successfully applied to classiffication using microarray data. As checking all possible subsets of genes is computationally infeasible, the RXA algorithms require feature selection and multiple restrictive assumptions. Our main contribution is a specialized evolutionary algorithm (EA) for top-scoring pairs called EvoTSP which allows finding more advanced gene relations. We managed to unify the major variants of relative expression algorithms through EA and introduce weights to the top-scoring pairs. Experimental validation of EvoTSP on public available microarray datasets showed that the proposed solution significantly outperforms in terms of accuracy other relative expression algorithms and allows exploring much larger solution space.

scholarly journals Asatone and Isoasatone A Against Spodoptera litura Fab. by Acting on Cytochrome P450 Monoxygenases and Glutathione Transferases

Molecules ◽  
2019 ◽  
Vol 24 (21) ◽  
pp. 3940
Author(s):  
Ruimei Ling ◽  
Renyue Yang ◽  
Ping Li ◽  
Xiongfei Zhang ◽  
Tunkai Shen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cytochrome P450 ◽  
Spodoptera Litura ◽  
Glutathione Transferases ◽  
Structural Deformation ◽  
Relative Gene Expression ◽  
Expression Levels ◽  
Relative Expression ◽  
Insect Activity ◽  
Relative Gene

Asatone and isoasatone A from Asarum ichangense Cheng were determined to be defensive compounds to some insects in a previous investigation. However, the anti-insect activity mechanisms to caterpillar are still unclear. The compounds asatone and isoasatone A from A. ichangense were induced by Spodoptera litura. The anti-insect activity of asatone and isoasatone A to S. litura was further tested by weight growth rate of the insect through a diet experiment. Isoasatone A showed a more significant inhibitory effect on S. litura than asatone on the second day. The concentration of asatone was higher than isoasatone A in the second instar larvae of S. litura after 12 h on the feeding test diet. Both compounds caused mid-gut structural deformation and tissue decay as determined by mid-gut histopathology of S. litura. Furthermore, some detoxification enzyme activity were measured by relative expression levels of genes using a qPCR detecting system. Asatone inhibited the gene expression of the cytochrome P450 monooxygenases (P450s) CYP6AB14. Isoasatone A inhibited the relative expression levels of CYP321B1, CYP321A7, CYP6B47, CYP6AB14, and CYP9A39. Asatone increased the relative gene expression of the glutathione transferases (GSTs) SIGSTe1 and SIGSTo1, in contrast, isoasatone A decreased the relative gene expression of SIGSTe1 by about 33 fold. Neither compound showed an effect on acetylcholinesterase SIAce1 and SIAce2. The mechanism of anti-insect activity by both compounds could be explained by the inhibition of enzymes P450s and GSTs. The results provide new insights into the function of unique secondary metabolites asatone and isoasatone A in genus Asarum, and a new understanding of why A. ichangense is largely free of insect pests.

scholarly journals Expression of the Arginine Deiminase Pathway Genes in Lactobacillus sakei Is Strain Dependent and Is Affected by the Environmental pH

2012 ◽  
Vol 78 (14) ◽  
pp. 4874-4883 ◽  
Author(s):  
T. Rimaux ◽  
A. Rivière ◽  
K. Illeghems ◽  
S. Weckx ◽  
L. De Vuyst ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arginine Deiminase ◽  
Expression Level ◽  
Exponential Growth Phase ◽  
Lactobacillus Sakei ◽  
Relative Gene Expression ◽  
Content Type ◽  
Relative Expression ◽  
Relative Expression Level ◽  
Relative Gene

ABSTRACTThe adaptation ofLactobacillus sakeito a meat environment is reflected in its metabolic potential. For instance, the ability to utilize arginine through the arginine deiminase (ADI) pathway, resulting in additional ATP, represents a competitive benefit. InL. sakeiCTC 494, thearcoperon (arcABCTDR) shows the same gene order and organization as that inL. sakei23K, the genome sequence of which is known. However, differences in relative gene expression were found, and these seemed to be optimal in different growth phases, namely, the highest relative gene expression level was in the end exponential growth phase in the case ofL. sakeiCTC 494 and in the mid-exponential growth phase ofL. sakei23K. Also, the environmental pH influenced the relative expression level of thearcoperon, as shown forL. sakeiCTC 494, with the highest relative expression level occurring at the optimal pH for growth (pH 6.0). Deviations from this optimal pH (pH 5.0 and pH 7.0) resulted in an overall decline of the relative expression level of all genes of thearcoperon. Furthermore, a differential relative expression of the individual genes of thearcoperon was found, with the highest relative gene expression occurring for the first two genes of thearcoperon (arcAandarcB). Finally, it was shown that someL. sakeistrains were able to convert agmatine into putrescine, suggesting an operational agmatine deiminase pathway in these strains, a metabolic trait that is undesirable in meat fermentations. This study shows that this metabolic trait is most probably encoded by a previously erroneously annotated second putativearcoperon.

scholarly journals Embryo-to-embryo variability in RNAi knockdown efficiency of dKDM5/lid in Drosophila melanogaster

2021 ◽  
Author(s):  
Ashley Albright ◽  
Michael Eisen
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Relative Gene Expression ◽  
Relative Expression ◽  
Individual Control ◽  
Knock Down ◽  
Qrt Pcr ◽  
Relative Gene

AbstractWe used the maternal-Gal4 shRNA system to knock down expression of dKDM5/lid in Drosophila melanogaster embryos, and analyzed the efficacy of the knockdown by qRT-PCR. Although average relative expression of lid was significantly lower in knockdown conditions compared to the driver-only control, we observed a wide and overlapping range of relative gene expression between individual control and knockdown embryos.

scholarly journals Influence of Angiopoietin Treatment with Hypoxia and Normoxia on Human Intervertebral Disc Progenitor Cell’s Proliferation, Metabolic Activity, and Phenotype

2021 ◽  
Vol 11 (15) ◽  
pp. 7144
Author(s):  
Muriel C. Bischof ◽  
Sonja Häckel ◽  
Andrea Oberli ◽  
Andreas S. Croft ◽  
Katharina A. C. Oswald ◽  
...  
Keyword(s):  
Gene Expression ◽  
Intervertebral Disc ◽  
Metabolic Activity ◽  
Cell Metabolism ◽  
Trauma Patients ◽  
Low Back ◽  
Relative Gene Expression ◽  
Progenitor Cell Population ◽  
Ivd Degeneration ◽  
Relative Gene

Increasing evidence implicates intervertebral disc (IVD) degeneration as a major contributor to low back pain. In addition to a series of pathogenic processes, degenerated IVDs become vascularized in contrast to healthy IVDs. In this context, angiopoietin (Ang) plays a crucial role and is involved in cytokine recruitment, and anabolic and catabolic reactions within the extracellular matrix (ECM). Over the last decade, a progenitor cell population has been described in the nucleus pulposus (NP) of the IVD to be positive for the Tie2 marker (also known as Ang-1 receptor). In this study, we investigated the influence of Ang-1 and Ang-2 on human NP cell (Tie2+, Tie2- or mixed) populations isolated from trauma patients during 7 days in normoxia (21% O2) or hypoxia (≤ 5% O2). At the end of the process, the proliferation and metabolic activity of the NP cells were analyzed. Additionally, the relative gene expression of NP-related markers was evaluated. NP cells showed a higher proliferation depending on the Ang treatment. Moreover, the study revealed higher NP cell metabolism when cultured in hypoxia. Additionally, the relative gene expression followed, with an increase linked to the oxygen level and Ang concentration. Our study comparing different NP cell populations may be the start of new approaches for the treatment of IVD degeneration.

Sources and levels of zinc affect relative gene expression related to protein metabolism in broilers

2019 ◽  
Author(s):  
D.L. Silva ◽  
B.R. Carvalho ◽  
H.C. Ferreira Júnior ◽  
H.C. Oliveira ◽  
C.R. Ferreira ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Metabolism ◽  
Relative Gene Expression ◽  
Relative Gene

scholarly journals Elevated Lipocalin-2 Can Indicate the Vascular Inflammation in Patients with Ischemic Stroke

2019 ◽  
Author(s):  
Rajnics P ◽  
◽  
Kellner A ◽  
Nagy F ◽  
Alföldi V ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ischemic Stroke ◽  
Gene Expression Level ◽  
Expression Level ◽  
Neutrophil Granulocytes ◽  
Lipocalin 2 ◽  
Relative Gene Expression ◽  
Thrombotic Risk ◽  
Relative Gene ◽  
Relative Gene Expression Level

Purpose: Elevated level of Lipocalin-2 (LCN2), a new acute phase adipokine, was described after ischemic stroke. A number of researchers feel as though that LCN2 originated from the infiltrating neutrophils and other cells in brain after stroke. Others measured elevated LCN2 expression in arteriosclerotic plaque. Therefore we have investigated LCN2 relative gene expression level of blood neutrophil granulocytes in patients with ischemic stroke to assess if elevated LCN2 is the cause or consequence of ischemic stroke. Methods: Laboratory and anamnestic data were collected, which could have a role in development of thrombo-embolic events in patients with ischemic stroke. RNA based method was used to evaluate the relative gene expression level of LCN2. We calculated Odds Ratio (OR) and Confidence Interval (CI) for the association between LCN2 and ischemic stroke. Results: 34 samples were available for evaluation. The LCN 2 relative gene expression level was decreased in 12 cases. In this group, 91% of patients have Atrial Fibrillation (AF) at the time of hospitalisation. The mean LCN2 relative gene expression value was 64.25% (ranges: 34%-115%) in patients with AF. It was significantly lower than in patients with normal sinus rhythm (409.2%; ranges: 127%-1127%; p=0.0003). The elevated LCN2 relative gene expression level significantly (p=0.012) increases the risk of stroke (OR: 12.6) independently from other factors. Conclusions: High LCN2 expression level seems to have strong positive predictive value on ischemic stroke, and may be useful in thrombotic risk stratification of plaque vulnerability in these patients.

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