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Application of Metabolomics to Discover the Implications of Nanomaterials for Crop Plants
Published in Ramesh Raliya, Nanoscale Engineering in Agricultural Management, 2019
Yuxiong Huang, Lijuan Zhao, Arturo A. Keller
In additional studies, with cucumber plants exposed throughout their entire life-cycle (seed to fruit harvest), we detected 239 metabolites using GC-TOF-MS, identifying 107 metabolites conclusively (An et al. 2016). The metabolites were ranked based on their variable importance in projection (VIP). VIP is the weighted sum of the squares of the PLS-DA analysis, which indicates the importance of a variable (metabolite) to the entire model (Garcia-Sevillano et al. 2014). Forty compounds were identified as discriminating metabolites (VIP > 1) between treatments of different nCu concentrations, for example, carbohydrates (1-kestose, xylose and fructose), amino acids and their derivatives (ornithine, citrulline, glycine, proline, oxoproline, methionine and aspartic acids), carboxylic acids (citric, glutaric, shikimic, benzoic and pelargonic acids) and fatty acids (arachidic, linolenic and caprylic acids). nCu clearly perturbed 15 metabolic pathways (Fig. 4). Five of these pathways (galactose metabolism, inositol phosphate metabolism, tricarboxylic acid (TCA) cycle, glyoxylate and dicarboxylate metabolism, starch and sucrose metabolism) are related to carbohydrate metabolism. Six pathways (arginine and proline metabolism; lysine biosynthesis; phenylalanine metabolism; phenylalanine, tyrosine and tryptophan biosynthesis; tyrosine metabolism; glycine, serine and threonine metabolism) are related to amino acid synthesis and metabolism. In addition, alpha-linolenic acid metabolism, isoquinoline alkaloid biosynthesis, and methane metabolism were also disturbed; these pathways are related to lipid metabolism, biosynthesis of other secondary metabolites, and energy metabolism, respectively. These results indicate that accumulated nCu may have a significant impact on carbohydrate and amino acid metabolism for cucumber plants. Interestingly, exposure to nCu reduced photosynthetic rate. In addition, stomatal conductance and transpiration rates tended to increase in nCu treatments compared to the control. The decline in carbon assimilation and increase in transpiration rates resulted in a statistically significantly decline in water use efficiency. However, root, stem, leaf and fruit biomass were not statistically impacted. Thus, these early results indicate the importance of understanding the extent to which organisms may be affected at lower doses than previously considered in previous studies of ENM ecotoxicity.
Assessment of oxidative DNA damage, apoptosis and histopathological alterations on zebrafish exposed with green silver nanoparticle
Published in Chemistry and Ecology, 2022
Mine Kokturk, Serkan Yıldırım, Muhammed Atamanalp, Mehmet Harbi Calimli, Mehmet Salih Nas, Ismail Bolat, Gunes Ozhan, Gonca Alak
By comparative analysis, there are fourteen impaired metabolic pathways, related to phosphorus assimilation under Ag NP exposures. Among them, five metabolic pathways were significantly affected, including inositol phosphate metabolism, phosphatidylinositol signalling system, and glutathione metabolism in algal cells. Moreover, enrichment analysis showed that AgNPs significantly affected metabolic pathways related to carbohydrate metabolism, amino acid metabolism and fatty acid metabolism [31]. These pathways are closely related to cellular functions such as cell growth, migration and differentiation, and disruptions in these mechanisms lead to strong adverse effects [26]. In our study findings, it is thought that the determined for VA-Ag/AC NPs toxicity is mainly caused by dissolved Ag +.
RNA-Seq analysis of Phanerochaete sordida YK-624 degrades neonicotinoid pesticide acetamiprid
Published in Environmental Technology, 2023
Jianqiao Wang, Yilin Liu, Ru Yin, Nana Wang, Tangfu Xiao, Hirofumi Hirai
On the other hand, the KEGG enrichment analysis of the upregulated DEGs showed that tryptophan metabolism, arginine and proline metabolism, inositol phosphate metabolism, MAPK signalling pathway-yeast and thiamine metabolism were the top 5 enriched genes. Relationships to metabolic pathways were the most enriched in upregulated DEGs according to the KEGG pathway analysis (Figure 4).
Transcriptome analysis reveals that yeast extract inhibits synthesis of prodigiosin by Serratia marcescens SDSPY-136
Published in Preparative Biochemistry & Biotechnology, 2023
Junqing Wang, Tingting Zhang, Yang Liu, Shanshan Wang, Zerun Li, Ping Sun, Hui Xu
The majority of the enriched DEGs involved in the TCA cycle (ko00020), propanoate metabolism (ko00640), inositol phosphate metabolism (ko00562), pyruvate metabolism (ko00620), and butanoate metabolism (ko00650). TCA showed the greatest enrichment, and the majority of the genes associated in pyruvate metabolism were enriched (Table S1). Pyruvate and malonyl-CoA in the carbon metabolism pathway are important intermediates in prodigiosin synthesis.[13] Two key enzymes in the glycolysis pathway were downregulated: 6-phosphofructokinase (EC:2.7.1.11) and glyceraldehyde 3-phosphate dehydrogenase (phosphorylation) (EC:1.2.1.12). Changes in these enzymes affect pyruvate production. In the TCA cycle, we observed downregulation of pyruvate ferredoxin oxidoreductase (porA, B, C, D, G), which provides thiamin pyrophosphate and catalyzes the oxidative decarboxylation of pyruvate to acetyl-CoA and CO2.[35] Notably, pyruvate dehydrogenase (aceE), pyruvate dehydrogenase E1 (PDHA, B), and dihydrolipoamide dehydrogenase (DLD) were slightly upregulated (Figure 5). These genes are critical for maintaining normal TCA cycle turnover and increasing pyruvate-to-acetyl-CoA flow.[36] Other genes in the citric acid cycle, such as isocitrate dehydrogenase (icd), 2-ketoglutarate dehydrogenase (OGDH; kgd; DLST), succinyl-CoA synthase (sucCD; LSC1, 2), fumarate hydration enzymes (fumA, B, C, D, E), malate dehydrogenase (mqo), and malate dehydrogenase (MDH1, 2) were also upregulated. The products of these genes are involved in providing energy and carbon skeletons for metabolism in S. marcescens. The expression of phosphoenol pyruvate carboxykinase, which is involved in carbon fixation via pyruvate metabolism, showed an increasing trend at the gene level. The conversion of malonyl-CoA to acetyl-CoA was enhanced, whereas the derivatization of pyruvate to formic and acetic acids was weakened. The regulation of other pyruvate genes is shown in Figure 5. The upregulation of these carbon metabolism genes suggests that S. marcescens carbon metabolism is regulated to compensate for the energy deficit. This may indirectly affect prodigiosin biosynthesis.