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Omics to Field Bioremediation
Published in Vineet Kumar, Vinod Kumar Garg, Sunil Kumar, Jayanta Kumar Biswas, Omics for Environmental Engineering and Microbiology Systems, 2023
As the name suggests, metabolomics is the study of small metabolites such as lipids and vitamins in a sample or organism. Metabolites represent the energy transfer intermediates in the cell and in between different cells. This study mainly comprises the metabolite profiling in a sample. Metabolic phenotypes are the result of different processes that a cell undergoes due to the relationship between the genome and the factors affecting it. This study has not been developed yet like other studies as qualitative and quantitative study of metabolites is challenging due to perturbations in the metabolites profile due to changes in environmental conditions (Claudino et al., 2007). But it has some advantages over other systems as the metabolite is the closest to the phenotype a system exhibits, which can be studied easily if any changes happen. Also, it is the last product to be formed, and the changes in metabolome can be related to the changes in the genome quite comfortably. And also due to the large number of molecules to be studied, it is the most complex of all other omics (Horgan and Kenny, 2011).
Extending constraint-based approaches
Published in Karthik Raman, An Introduction to Computational Systems Biology, 2021
For batch cultures, biomass and glucose concentration are measured at different time-points and can be used to determine the growth rate of cells, the substrate uptake rate, the biomass yields, as well as product secretion rates and yields. Metabolite labelling is measured using a variety of experimental techniques, viz. HPLC (high-performance liquid chromatography), GC–MS (gas chromatography–mass spectrometry), LC–MS (liquid chromatography–mass spectrometry), tandem mass spectrometry, or even NMR (nuclear magnetic resonance). Typical metabolites studied are biomass components, amino acids, fatty acids, and sugar constituents.
Clinical Pharmacology of Parenteral Dosage Forms
Published in Sandeep Nema, John D. Ludwig, Parenteral Medications, 2019
Most drugs begin to be metabolized after they enter the body. The majority of small-molecule drug metabolism is carried out in the liver by redox enzymes, termed cytochrome (CYP) P450 enzymes (ubiquitously expressed in the body). As metabolism occurs, a (parent) drug is chemically converted to metabolites. Metabolism eliminates the administered dose of a parent drug. When metabolites are pharmacologically inert, metabolism reduces pharmacological effects in the body as a parent drug is eliminated. Metabolites may also be pharmacologically active, sometimes more so than a parent drug (active metabolites).
Multiple inhibitory effects of succinic acid on Microcystis aeruginosa: morphology, metabolomics, and gene expression
Published in Environmental Technology, 2022
Yi-dong Chen, Chu Zhao, Xiao-yu Zhu, Yuan Zhu, Ru-nan Tian
The PLS-DA analysis method provides the VIP (variable importance in the projection) value, which represents the contribution rate of the difference in metabolites for different groups. Fold change (FC) is the ration of the mean content of certain metabolites in the treatment group to the control group. To screen the differential metabolites, we set the thresholds at VIP > 1.0, FC > 2.0 or FC < 0.5, and P value < 0.05 (t test). The screened differential metabolites are shown in a volcano plot (Figure 4(B)). There were 167 differential metabolites with VIP > 1 (shown in Table S2), 48 of which were up-regulated and 119 were down-regulated. The metabolites included 31 amino acids and derivatives, 24 fatty acids and derivatives, 20 nucleotides and analogs, 9 organic acids and derivatives, 2 carbohydrates, and other organic oxygen compounds. The identified differential metabolites were analysed based on the KEGG database (https://www.kegg.jp/). The metabolic pathways in which the differential metabolites were enriched included galactose metabolism, purine metabolism, arginine biosynthesis, tyrosine metabolism, aminoacyl-tRNA biosynthesis, and 2-Oxocarboxylic acid metabolism.
Incorporation of chemical and toxicological availability into metal mixture toxicity modeling: State of the art and future perspectives
Published in Critical Reviews in Environmental Science and Technology, 2022
Bing Gong, Hao Qiu, Ana Romero-Freire, Cornelis A. M. Van Gestel, Erkai He
Together, genomics, transcriptomics, and proteomics can provide information on processes at the cellular level, however, in order to further connect genotype to phenotype another layer of information is needed (Fell, 2001). Metabolomics can bridge this gap and provide quantitative information at the intracellular metabolic level which stands for the supreme level of functional components of cellular processes (Fiehn, 2002; Halama, 2014). The metabolites, defined as the metabolome, act as the cell’s supplements composed of small and low molecular weight compounds, which are necessary for growth, function and maintenance (Quanbeck et al. 2012). The goal of metabolomics is to systematically identify and quantify these compounds and to report the most relevant information to the phenotype under genetic and/or environmental changes in the biological system (Barupal et al., 2012; Fiehn, 2002; Mashego et al., 2007). Previously, the omics-based approach was often used alone in practical applications. Nowadays, the multiomics methodology has become a popular and revolutionary approach in comparison to single omics, which gathers information from multiple layers and allows to understand better the complex mechanisms of intoxication and defense that act in organisms.
Methods of Metabolite Identification Using MS/MS Data
Published in Journal of Computer Information Systems, 2022
Myungjae Kwak, Kyungwoo Kang, Yingfeng Wang
Metabolites are the intermediate and end products of metabolism, which is the set of life-sustaining chemical reactions in living organisms.2 A metabolite is typically a small-molecular compound less than 1500 Da in the metabolome.2 A diverse set of metabolites exist in nature. For example, it was reported that there are more than 200,000 plant metabolites alone.3,4 The number of metabolites predicted in HMDB (Human Metabolome Database) 4.0 is. 114,1005 It is well known that physiological and pathological changes in human body are mapped to specific metabolic changes. For example, certain metabolic changes are identified in cancerous tissues.1,6 Once those mappings are completely identified, it would be possible to greatly improve disease diagnosis, prognosis, and selection of therapeutic strategies by profiling metabolites. Metabolomics is a scientific branch of studying the set of metabolites present within a living organism, cell, or tissue. It focuses on identifying the complete set of metabolites in a biological system.7 It also studies metabolic changes to disease, disease progression, medication, or environmental effects.7 Profiling metabolites can be used as a direct way of observing metabolic activities. Metabolomics is a study for detecting, identifying, and quantifying metabolites. It has advanced many medical and scientific areas such as microbiology8–10, pharmacy11–14, and medical science.15–19