Influences of sea water on the ethylene-biosynthesis, senescence-associated gene expressions, and antioxidant characteristics of Arabidopsis plants

We evaluated the physiological and antioxidant characteristics of Arabidopsis thaliana (At) plants grown in different sea water (SW) products containing trace elements, namely RO3, 300K, and 340K, at various dilutions. The synthetic water (namely 300K-Test), a mixture of the main ions of SW including 143.08 mg L-1 Mg2+, 5.74 mg L-1 Na+, 170 mg L-1 K+, and 33.5 mg L-1 Ca2+ with equal concentrations to those in 300K SW without trace elements, was also used to culture At plants and study the influences that the major ions had on regulating ethylene production. The ethylene-biosynthesis (ACS7 and ACO2) and senescence-associated (NAP, SAG113, and WRKY6) gene expressions in SW- and ionic-treated At plants in response to transcriptional signaling pathways of ethylene response mechanisms were also investigated. Our results show that down-regulation of the ACS7 gene in 300K-treated plants significantly reduced the ethylene content but remarkably increased chlorophyll, total phenol, and DPPH radical scavenging accumulations and strengthened the salt tolerance of 300K-treated plants. The expression of the ACS7 gene of At plants under 300K, Ca2+, Mg2+, and Na+ treatments was correlated with decreases in NAP, SAG113, and WRKY6 gene expressions. The application of Ca2+ increased total phenol content and reduced the accumulation of superoxide, which in combination decreases plant aging brought on by ethylene. However, K+ treatment inhibited SGA113 gene expression, resulting in reducing ACS7 gene expression and ethylene content. The characterization and functional analysis of these genes should facilitate our understanding of ethylene response mechanisms in plants.

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Expression of Ethylene Biosynthesis and Signaling Genes during Differential Abscission Responses of Sweet Orange Leaves and Mature Fruit

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.135.5.456 ◽

2010 ◽

Vol 135 (5) ◽

pp. 456-464 ◽

Cited By ~ 11

Author(s):

Karthik-Joseph John-Karuppiah ◽

Jacqueline K. Burns

Keyword(s):

Gene Expression ◽

Sweet Orange ◽

Ethylene Biosynthesis ◽

Differential Response ◽

Leaf Abscission ◽

Mature Fruit ◽

Fruit Abscission ◽

Ethylene Sensitivity ◽

Ethylene Response ◽

Significant Difference

When applying abscission agents to tree fruit to facilitate harvest, it is desirable to loosen fruit and not leaves or other organs, but mechanisms controlling leaf and fruit drop are not fully understood. The effect of 450 μL·L−1 ethephon (ethylene-releasing agent) alone or in combination with 1-methylcyclopropene [1-MCP (ethylene perception inhibitor)] on leaf and mature fruit abscission of ‘Valencia’ sweet orange (Citrus sinensis) was studied. Leaf abscission increased and fruit detachment force (FDF) decreased significantly especially 4 days after ethephon treatment. Leaf drop rose to over 80% 7 days after application, whereas FDF was only 30% less than untreated control fruit. When 1-MCP was combined with ethephon and applied to ‘Valencia’ sweet orange canopies, leaf abscission was greatly reduced, but reduction in FDF proceeded unabated. We hypothesized that differential response of ‘Valencia’ sweet orange fruit and leaves to 1-MCP was correlated with expression of ethylene biosynthetic and signaling genes and their downstream action. Partial or full-length nucleotide sequences were obtained for ‘Valencia’ sweet orange homologs of 1-amino-cyclopropane-1-carboxylate synthase-1 (CsACS1), 2 (CsACS2), 1-amino-cyclopropane-1-carboxylate oxidase (CsACO), ethylene response sensor-1 (CsERS1), ethylene response-1 (CsETR1), 2 (CsETR2), 3 (CsETR3), constitutive triple response-1 (CsCTR1), ethylene insensitive-2 (CsEIN2), and ethylene insensitive 3-like-1 (CsEIL1) and 2 (CsEIL2). Ethephon application increased expression of biosynthesis genes CsACS1 and CsACO and receptors CsERS1 and CsETR2 in the abscission zones of leaves and mature fruit. Ethephon-induced increase in gene expression was completely suppressed by 1-MCP application in all but CsACS1 and CsACO in fruit abscission zones. Although gene expression was suppressed initially, CsACS1 and CsACO expression in fruit abscission zones treated with 1-MCP in the presence or absence of ethephon increased over the 7-day measurement period, suggesting that CsACS1 and CsACO expression were negatively regulated by basal ethylene production in this tissue. However, 1-MCP treatment alone did not loosen fruit, indicating that CsACS1 and CsACO played minor roles in fruit abscission. To determine if the difference in ethylene sensitivity was the basis of differential response to ethylene within the same organ, potted ‘Valencia’ sweet orange plants were treated with ethylene, and rates of blade and petiole drop and detachment forces at the laminar and petiolar abscission zones were studied. Although leaf blades abscised earlier than petioles, the force of detachment was similar, indicating no differences in ethylene sensitivity. Overall, the most significant difference between fruit and leaf abscission zones was seen in the expression of CsACS1 and CsACO genes, but the expression pattern was poorly correlated with abscission.

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Mechanisms of ethylene biosynthesis and response in plants

Essays in Biochemistry ◽

10.1042/bse0580061 ◽

2015 ◽

Vol 58 ◽

pp. 61-70 ◽

Cited By ~ 11

Author(s):

Paul B. Larsen

Keyword(s):

Plant Growth ◽

Growth And Development ◽

Ethylene Biosynthesis ◽

Unsaturated Hydrocarbon ◽

Flower Senescence ◽

Detailed Knowledge ◽

Plant Growth And Development ◽

Step Process ◽

Ethylene Response ◽

Ethylene Signalling

Ethylene is the simplest unsaturated hydrocarbon, yet it has profound effects on plant growth and development, including many agriculturally important phenomena. Analysis of the mechanisms underlying ethylene biosynthesis and signalling have resulted in the elucidation of multistep mechanisms which at first glance appear simple, but in fact represent several levels of control to tightly regulate the level of production and response. Ethylene biosynthesis represents a two-step process that is regulated at both the transcriptional and post-translational levels, thus enabling plants to control the amount of ethylene produced with regard to promotion of responses such as climacteric flower senescence and fruit ripening. Ethylene production subsequently results in activation of the ethylene response, as ethylene accumulation will trigger the ethylene signalling pathway to activate ethylene-dependent transcription for promotion of the response and for resetting the pathway. A more detailed knowledge of the mechanisms underlying biosynthesis and the ethylene response will ultimately enable new approaches to be developed for control of the initiation and progression of ethylene-dependent developmental processes, many of which are of horticultural significance.

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The Mechanisms Behind the Biological Activity of Flavonoids

Current Medicinal Chemistry ◽

10.2174/0929867325666180706104829 ◽

2019 ◽

Vol 26 (39) ◽

pp. 6976-6990 ◽

Cited By ~ 12

Author(s):

Ana María González-Paramás ◽

Begoña Ayuda-Durán ◽

Sofía Martínez ◽

Susana González-Manzano ◽

Celestino Santos-Buelga

Keyword(s):

Gene Expression ◽

Biological Activity ◽

Phenolic Compounds ◽

Intracellular Signaling ◽

Molecular Mechanisms ◽

Radical Scavenging ◽

Model Organism ◽

Stress Theory ◽

Radical Scavenging Properties

: Flavonoids are phenolic compounds widely distributed in the human diet. Their intake has been associated with a decreased risk of different diseases such as cancer, immune dysfunction or coronary heart disease. However, the knowledge about the mechanisms behind their in vivo activity is limited and still under discussion. For years, their bioactivity was associated with the direct antioxidant and radical scavenging properties of phenolic compounds, but nowadays this assumption is unlikely to explain their putative health effects, or at least to be the only explanation for them. New hypotheses about possible mechanisms have been postulated, including the influence of the interaction of polyphenols and gut microbiota and also the possibility that flavonoids or their metabolites could modify gene expression or act as potential modulators of intracellular signaling cascades. This paper reviews all these topics, from the classical view as antioxidants in the context of the Oxidative Stress theory to the most recent tendencies related with the modulation of redox signaling pathways, modification of gene expression or interactions with the intestinal microbiota. The use of C. elegans as a model organism for the study of the molecular mechanisms involved in biological activity of flavonoids is also discussed.

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Chemoprotective Effects of Propolis on Aflatoxin B1-Induced Hepatotoxicity in Rats: Oxidative Damage and Hepatotoxicity by Modulating TP53, Oxidative Stress

Current Proteomics ◽

10.2174/1570164617666190925121720 ◽

2020 ◽

Vol 17 (3) ◽

pp. 191-199

Author(s):

Seval Yilmaz ◽

Fatih Mehmet Kandemir ◽

Emre Kaya ◽

Mustafa Ozkaraca

Keyword(s):

Oxidative Stress ◽

Gene Expression ◽

Oxidative Damage ◽

Aflatoxin B1 ◽

Tp53 Gene ◽

Control Group ◽

Glutathione S Transferase ◽

Gene Expressions ◽

Cat Gene ◽

Gst Activity

Objective: This study aimed to detect hepatic oxidative damage caused by aflatoxin B1 (AFB1), as well as to examine how propolis protects against hepatotoxic effects of AFB1. Method: Rats were split into four groups as control group, AFB1 group, propolis group, AFB1+ propolis group. Results: There was significant increase in malondialdehyde (MDA) level and tumor suppressor protein (TP53) gene expression, Glutathione (GSH) level, Catalase (CAT) activity, CAT gene expression decreased in AFB1 group in blood. MDA level and Glutathione-S-Transferase (GST) activity, GST and TP53 gene expressions increased in AFB1 group, whereas GSH level and CAT activity alongside CAT gene expression decreased in liver. AFB1+propolis group showed significant decrease in MDA level, GST activity, TP53 and GST gene expressions, GSH level and CAT activity and CAT gene expression increased in liver compared to AFB1 group. Conclusion: These results suggest that propolis may potentially be natural agent that prevents AFB1- induced oxidative stress and hepatotoxicity.

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Mining The Cancer Genome Atlas gene expression data for lineage markers in distinguishing bladder urothelial carcinoma and prostate adenocarcinoma

Scientific Reports ◽

10.1038/s41598-021-85993-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ewe Seng Ch’ng

Keyword(s):

Gene Expression ◽

Gene Expression Data ◽

The Cancer Genome Atlas ◽

Relative Importance ◽

Expression Data ◽

Gene Expressions ◽

Urothelial Carcinomas ◽

Cancer Genome Atlas ◽

Lineage Markers ◽

Genome Atlas

AbstractDistinguishing bladder urothelial carcinomas from prostate adenocarcinomas for poorly differentiated carcinomas derived from the bladder neck entails the use of a panel of lineage markers to help make this distinction. Publicly available The Cancer Genome Atlas (TCGA) gene expression data provides an avenue to examine utilities of these markers. This study aimed to verify expressions of urothelial and prostate lineage markers in the respective carcinomas and to seek the relative importance of these markers in making this distinction. Gene expressions of these markers were downloaded from TCGA Pan-Cancer database for bladder and prostate carcinomas. Differential gene expressions of these markers were analyzed. Standard linear discriminant analyses were applied to establish the relative importance of these markers in lineage determination and to construct the model best in making the distinction. This study shows that all urothelial lineage genes except for the gene for uroplakin III were significantly expressed in bladder urothelial carcinomas (p < 0.001). In descending order of importance to distinguish from prostate adenocarcinomas, genes for uroplakin II, S100P, GATA3 and thrombomodulin had high discriminant loadings (> 0.3). All prostate lineage genes were significantly expressed in prostate adenocarcinomas(p < 0.001). In descending order of importance to distinguish from bladder urothelial carcinomas, genes for NKX3.1, prostate specific antigen (PSA), prostate-specific acid phosphatase, prostein, and prostate-specific membrane antigen had high discriminant loadings (> 0.3). Combination of gene expressions for uroplakin II, S100P, NKX3.1 and PSA approached 100% accuracy in tumor classification both in the training and validation sets. Mining gene expression data, a combination of four lineage markers helps distinguish between bladder urothelial carcinomas and prostate adenocarcinomas.

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Stablization of ACOs by NatB mediated N-terminal acetylation is required for ethylene homeostasis

BMC Plant Biology ◽

10.1186/s12870-021-03090-7 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Hai-qing Liu ◽

Ya-jie Zou ◽

Xiao-feng Li ◽

Lei Wu ◽

Guang-qin Guo

Keyword(s):

Protein Modification ◽

Normal Growth ◽

Ethylene Biosynthesis ◽

Regulation Mechanism ◽

Biological Functions ◽

Loss Of Function ◽

Auxiliary Subunit ◽

Ethylene Content ◽

Endogenous Ethylene ◽

Exogenous Ethylene

AbstractN-terminal acetylation (NTA) is a highly abundant protein modification catalyzed by N-terminal acetyltransferases (NATs) in eukaryotes. However, the plant NATs and their biological functions have been poorly explored. Here we reveal that loss of function of CKRC3 and NBC-1, the auxiliary subunit (Naa25) and catalytic subunit (Naa20) of Arabidopsis NatB, respectively, led to defects in skotomorphogenesis and triple responses of ethylene. Proteome profiling and WB test revealed that the 1-amincyclopropane-1-carboxylate oxidase (ACO, catalyzing the last step of ethylene biosynthesis pathway) activity was significantly down-regulated in natb mutants, leading to reduced endogenous ethylene content. The defective phenotypes could be fully rescued by application of exogenous ethylene, but less by its precursor ACC. The present results reveal a previously unknown regulation mechanism at the co-translational protein level for ethylene homeostasis, in which the NatB-mediated NTA of ACOs render them an intracellular stability to maintain ethylene homeostasis for normal growth and responses.

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Histochemical Characterisation and Gene Expression Analysis of Skeletal Muscles from Maremmana and Aubrac Steers Reared on Grazing and Feedlot Systems

Animals ◽

10.3390/ani11030656 ◽

2021 ◽

Vol 11 (3) ◽

pp. 656

Author(s):

Giulia Foggi ◽

Francesca Ciucci ◽

Maria Conte ◽

Laura Casarosa ◽

Andrea Serra ◽

...

Keyword(s):

Gene Expression ◽

Physical Activity ◽

Muscle Fibre ◽

Skeletal Muscles ◽

Gene Expression Analysis ◽

Type I ◽

Triceps Brachii ◽

Gene Expressions ◽

Muscle Properties ◽

Voluntary Physical Activity

This study aimed to characterise the fibre composition of Triceps brachii (TB) and Semimembranosus (SM) muscles from 20 Maremmana (MA) and 20 Aubrac (AU) steers, and the effect of grazing activity in comparison with feedlot system. The histochemical method was performed with the m-ATPase method with an acid pre-incubation, thus allowing to distinguish type I, IIA, and IIB fibres. Additionally, on total RNA extracted from SM muscle, the expressions of atp1a1, mt-atp6, and capn1 genes were evaluated, in order to find potential associations with muscle fibre histochemical characteristics. In SM muscle, the MA steers had the greater frequency of oxidative fibres (type I and IIA) and the higher atp1a1 expression, in comparison to AU steers. Conversely, AU steers had a greater frequency of type IIB fibres, and the higher capn1 expression. A similar histochemical pattern was observed in TB muscle. The grazing activity was probably insufficient to determine differences both for fibre proportion and size, and gene expressions, except for mt-atp6 expression that was surprisingly highest in feedlot MA in comparison to other steers. These findings further the knowledge of muscle properties belonging to these breeds, and the effect of voluntary physical activity since few studies were available in this regard.

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Microarray analysis identification of key pathways and interaction network of differential gene expressions during osteogenic differentiation

Human Genomics ◽

10.1186/s40246-020-00293-1 ◽

2020 ◽

Vol 14 (1) ◽

Author(s):

Fatemeh Khodabandehloo ◽

Sara Taleahmad ◽

Reza Aflatoonian ◽

Farzad Rajaei ◽

Zahra Zandieh ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Signaling Pathway ◽

Expression Profiles ◽

Wnt Signaling Pathway ◽

Hub Genes ◽

Gene Expressions ◽

Cell Based Therapy ◽

Wnt Pathways ◽

Key Pathways

Abstract Background Adult bone marrow-derived mesenchymal stem cells (BM-MSCs) are multipotent stem cells that can differentiate into three lineages. They are suitable sources for cell-based therapy and regenerative medicine applications. This study aims to evaluate the hub genes and key pathways of differentially expressed genes (DEGs) related to osteogenesis by bioinformatics analysis in three different days. The DEGs were derived from the three different days compared with day 0. Results Gene expression profiles of GSE37558 were obtained from the Gene Expression Omnibus (GEO) database. A total of 4076 DEGs were acquired on days 8, 12, and 25. Gene ontology (GO) enrichment analysis showed that the non-canonical Wnt signaling pathway and lipopolysaccharide (LPS)-mediated signaling pathway were commonly upregulated DEGs for all 3 days. KEGG pathway analysis indicated that the PI3K-Akt and focal adhesion were also commonly upregulated DEGs for all 3 days. Ten hub genes were identified by CytoHubba on days 8, 12, and 25. Then, we focused on the association of these hub genes with the Wnt pathways that had been enriched from the protein-protein interaction (PPI) by the Cytoscape plugin MCODE. Conclusions These findings suggested further insights into the roles of the PI3K/AKT and Wnt pathways and their association with osteogenesis. In addition, the stem cell microenvironment via growth factors, extracellular matrix (ECM), IGF1, IGF2, LPS, and Wnt most likely affect osteogenesis by PI3K/AKT.

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Effects of glutamine supplementation on oxidative stress-related gene expression and antioxidant properties in rats with streptozotocin-induced type 2 diabetes

British Journal Of Nutrition ◽

10.1017/s0007114511004168 ◽

2011 ◽

Vol 107 (8) ◽

pp. 1112-1118 ◽

Cited By ~ 26

Author(s):

Pei-Hsuan Tsai ◽

Jun-Jen Liu ◽

Chui-Li Yeh ◽

Wan-Chun Chiu ◽

Sung-Ling Yeh

Keyword(s):

Oxidative Stress ◽

Gene Expression ◽

Amino Acid ◽

Oxidative Damage ◽

Antioxidant Capacity ◽

Enzyme Activities ◽

Antioxidant Enzyme Activities ◽

Related Gene ◽

Gene Expressions ◽

Oxidative Stress Related Gene

There are close links among hyperglycaemia, oxidative stress and diabetic complications. Glutamine (GLN) is an amino acid with immunomodulatory properties. The present study investigated the effect of dietary GLN on oxidative stress-relative gene expressions and tissue oxidative damage in diabetes. There were one normal control (NC) and two diabetic groups in the present study. Diabetes was induced by an intraperitoneal injection of nicotinamide followed by streptozotocin (STZ). Rats in the NC group were fed a regular chow diet. In the two diabetic groups, one group (diabetes mellitus, DM) was fed a common semi-purified diet while the other group received a diet in which part of the casein was replaced by GLN (DM-GLN). GLN provided 25 % of total amino acid N. The experimental groups were fed the respective diets for 8 weeks, and then the rats were killed for further analysis. The results showed that blood thioredoxin-interacting protein (Txnip) mRNA expression in the diabetic groups was higher than that in the NC group. Compared with the DM group, the DM-GLN group had lower glutamine fructose-6-phosphate transaminase 1, a receptor of advanced glycation end products, and Txnip gene expressions in blood mononuclear cells. The total antioxidant capacity was lower and antioxidant enzyme activities were altered by the diabetic condition. GLN supplementation increased antioxidant capacity and normalised antioxidant enzyme activities. Also, the renal nitrotyrosine level and Txnip mRNA expression were lower when GLN was administered. These results suggest that dietary GLN supplementation decreases oxidative stress-related gene expression, increases the antioxidant potential and may consequently attenuate renal oxidative damage in rats with STZ-induced diabetes.

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Discovering Distinct Patterns in Gene Expression Profiles

Journal of Integrative Bioinformatics ◽

10.1515/jib-2008-105 ◽

2008 ◽

Vol 5 (2) ◽

Cited By ~ 1

Author(s):

Li Teng ◽

Laiwan Chan

Keyword(s):

Gene Expression ◽

Large Scale ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Clustering Methods ◽

Gene Expressions ◽

Real Gene ◽

Large Scale Dataset ◽

Coexpressed Genes

SummaryTraditional analysis of gene expression profiles use clustering to find groups of coexpressed genes which have similar expression patterns. However clustering is time consuming and could be diffcult for very large scale dataset. We proposed the idea of Discovering Distinct Patterns (DDP) in gene expression profiles. Since patterns showing by the gene expressions reveal their regulate mechanisms. It is significant to find all different patterns existing in the dataset when there is little prior knowledge. It is also a helpful start before taking on further analysis. We propose an algorithm for DDP by iteratively picking out pairs of gene expression patterns which have the largest dissimilarities. This method can also be used as preprocessing to initialize centers for clustering methods, like K-means. Experiments on both synthetic dataset and real gene expression datasets show our method is very effective in finding distinct patterns which have gene functional significance and is also effcient.

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