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

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.

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

Austin Journal of Cerebrovascular Disease & Stroke ◽

10.26420/austinjcerebrovascdisstroke.2019.1081 ◽

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

Molecules ◽

10.3390/molecules24213940 ◽

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.

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A152 INVESTIGATING THE ROLE OF NOVEL NUDT15 VARIANT IN AZATHIOPRINE-RELATED MYELOTOXICITY

Journal of the Canadian Association of Gastroenterology ◽

10.1093/jcag/gwab002.150 ◽

2021 ◽

Vol 4 (Supplement_1) ◽

pp. 155-157

Author(s):

Q Wang ◽

A Wilson

Keyword(s):

Gene Expression ◽

Gene Expression Level ◽

Expression Level ◽

Lower Amount ◽

Relative Gene Expression ◽

Rt Pcr ◽

Its Gene ◽

The Impact ◽

Relative Gene ◽

Relative Gene Expression Level

Abstract Background Azathioprine (AZA), an immunosuppressant, has classically been used to treat patients with inflammatory bowel disease (IBD). AZA inhibits purine synthesis, and its metabolism occurs via a pathway involving thiopurine methyltransferase (TPMT). While standard TPMT genetic screening is conducted for IBD patients initiating AZA treatment to minimize adverse drug effects (ADE), a majority of patients experiencing ADE have wildtype TPMT. Another gene, NUDT15, has been found to be associated with AZA-related myelotoxicity Aims In this study we report two novel variants in NUDT15 and aim to evaluate the impact of NUDT15 variation on its gene expression. We hypothesize that the mutations found within novel NUDT15 variant are detrimental either to the gene’s expression levels or its translation process, resulting in a lower amount of NUDT15 product present and hence translating to AZA-related myelotoxicity observed clinically. Methods IBD patients experiencing AZA-related myelotoxicity were recruited for this study. Patients were then genotyped and the NUDT15 variants were replicated through site-directed mutagenesis. The NUDT15 variants were subsequently transformed into mammalian cell lines then E. coli cells. DNA products were isolated, and transcription levels were assessed through RT-PCR. Results Patient cohort consisted of 27 AZA-exposed IBD patients who developed myelotoxicity despite their TPMT wildtype genotype. Two novel NUDT15 variants were found. The mutation in one of the variants was placed in 3’ UTR, and hence further research was not pursued. Further analysis was conducted for the variant with mutation in coding region. RT-PCR was conducted to assess and compare gene transcription levels between wildtype and variant NUDT15. Wildtype NUDT15 had a relative gene expression level of 0.8x107, whereas variant NUDT15’s relative gene expression level was at 1.1x107. The two groups were not significantly different in terms of gene expression. Conclusions Contrary to our initial hypothesis, it appears that the mutation in the start codon for variant NUDT15 gene does not significantly impact its gene expression as compared to the wildtype gene. We are currently pursuing protein expression analysis studies to assess for translational deficits possibly present in the novel NUDT15 variant. Funding Agencies SRTP - Schulich School of Medicine

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The Spatial Distribution Characteristics of Typical Pathogens and Nitrogen and Phosphorus in the Sediments of Shahe Reservoir and their Relationships

10.21203/rs.3.rs-477678/v1 ◽

2021 ◽

Author(s):

Wen Sun ◽

Ke Yang ◽

Risheng Li ◽

Tianqing Chen ◽

Longfei Xia ◽

...

Keyword(s):

Gene Expression ◽

Vertical Distribution ◽

Pathogenic Bacteria ◽

Horizontal Distribution ◽

Gene Expression Level ◽

Expression Level ◽

Relative Gene Expression ◽

E Coli ◽

Relative Gene ◽

Relative Gene Expression Level

Abstract Using samples collected in Shahe Reservoir in the upper North Canal in China, this research analyzes the structure of a microorganism group in sediment and the gene expression levels of two typical pathogenic bacteria (Escherichia coli and Enterococcus), and their relationship with environmental factors including total nitrogen (TN) and total phosphorus (TP). The study of samples collected from the surface (0–20 cm) and sediment cores shows that the absolute gene expression level of E. coli in in horizontal distribution in the sediment is higher than the relative gene expression level in the downstream of the reservoir and contaminated area. In vertical distribution, the absolute gene expression level of the two pathogenic bacteria in the sediment tends to decrease with increasing depth, although the relative gene expression level has its highest value at 10–30 cm depth. The relative gene expression level of the two pathogenic bacteria is much greater in the sediment of Shahe Reservoir with the structure of horizontal groups including Clortridium sensu stricto, unclassified Anaeroineaceae, and Povalibacter, while Anaeroineaceae is much more abundant in the group structure of the vertical distribution. Pearson correlation analysis suggests positive correlation in horizontal distribution for E. coli and TN and TP (P < 0.05) and for Enterococcus and TP (P < 0.05). The results clearly show that the amount of pathogenic bacteria in the sediment in Shahe Reservoir is most likely due to water eutrophication.

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Evolutionary Approach for Relative Gene Expression Algorithms

The Scientific World JOURNAL ◽

10.1155/2014/593503 ◽

2014 ◽

Vol 2014 ◽

pp. 1-7 ◽

Cited By ~ 3

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.

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

10.1101/2021.04.29.442033 ◽

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.

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

Applied Sciences ◽

10.3390/app11157144 ◽

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.

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Adaptation of Lactobacillus plantarum IMDO 130201, a Wheat Sourdough Isolate, to Growth in Wheat Sourdough Simulation Medium at Different pH Values through Differential Gene Expression

Applied and Environmental Microbiology ◽

10.1128/aem.02668-10 ◽

2011 ◽

Vol 77 (10) ◽

pp. 3406-3412 ◽

Cited By ~ 15

Author(s):

Gino Vrancken ◽

Luc De Vuyst ◽

Tom Rimaux ◽

Joke Allemeersch ◽

Stefan Weckx

Keyword(s):

Gene Expression ◽

Lactobacillus Plantarum ◽

Differential Gene Expression ◽

Lipoteichoic Acid ◽

Low Ph ◽

Exponential Growth Phase ◽

Cellular Mechanisms ◽

Content Type ◽

Ph Values ◽

Differential Gene

ABSTRACTSourdough is a very competitive and challenging environment for microorganisms. Usually, a stable microbiota composed of lactic acid bacteria (LAB) and yeasts dominates this ecosystem. Although sourdough is rich in carbohydrates, thus providing an ideal environment for microorganisms to grow, its low pH presents a particular challenge. The nature of the adaptation to this low pH was investigated forLactobacillus plantarumIMDO 130201, an isolate from a laboratory wheat sourdough fermentation. Batch fermentations were carried out in wheat sourdough simulation medium, and total RNA was isolated from mid-exponential-growth-phase cultures, followed by differential gene expression analysis using a LAB functional gene microarray. At low pH values, an increased expression of genes involved in peptide and amino acid metabolism was found as well as that of genes involved in plantaricin production and lipoteichoic acid biosynthesis. The results highlight cellular mechanisms that allowL. plantarumto function at a low environmental pH.

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