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Sharma BD, Olson DG, Giannone RJ, Hettich RL, Lynd LR. Characterization and Amelioration of Filtration Difficulties Encountered in Metabolomic Studies of Clostridium thermocellum at Elevated Sugar Concentrations. Appl Environ Microbiol 2023; 89:e0040623. [PMID: 37039651 PMCID: PMC10132107 DOI: 10.1128/aem.00406-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 04/12/2023] Open
Abstract
Clostridium thermocellum, a promising candidate for consolidated bioprocessing, has been subjected to numerous engineering strategies for enhanced bioethanol production. Measurements of intracellular metabolites at substrate concentrations high enough (>50 g/L) to allow the production of industrially relevant titers of ethanol would inform efforts toward this end but have been difficult due to the production of a viscous substance that interferes with the filtration and quenching steps during metabolite extraction. To determine whether this problem is unique to C. thermocellum, we performed filtration experiments with other organisms that have been engineered for high-titer ethanol production, including Escherichia coli and Thermoanaerobacterium saccharolyticum. We addressed the problem through a series of improvements, including active pH control (to reduce problems with viscosity), investigation of different filter materials and pore sizes (to increase the filtration capacity), and correction for extracellular metabolite concentrations, and we developed a technique for more accurate intracellular metabolite measurements at elevated substrate concentrations. IMPORTANCE The accurate measurement of intracellular metabolites (metabolomics) is an integral part of metabolic engineering for the enhanced production of industrially important compounds and a useful technique to understand microbial physiology. Previous work tended to focus on model organisms under laboratory conditions. As we try to perform metabolomic studies with a wider range of organisms under conditions that more closely represent those found in nature or industry, we have found limitations in existing techniques. For example, fast filtration is an important step in quenching metabolism in preparation for metabolite extraction; however, it does not work for cultures of C. thermocellum at high substrate concentrations. In this work, we characterize the extent of the problem and develop techniques to overcome it.
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Affiliation(s)
- Bishal D. Sharma
- Thayer School of Engineering at Dartmouth College, Hanover, New Hampshire, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Daniel G. Olson
- Thayer School of Engineering at Dartmouth College, Hanover, New Hampshire, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Richard J. Giannone
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Robert L. Hettich
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Lee R. Lynd
- Thayer School of Engineering at Dartmouth College, Hanover, New Hampshire, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Enchi Corporation, Holliston, Massachusetts, USA
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Optimized Fast Filtration-Based Sampling and Extraction Enables Precise and Absolute Quantification of the Escherichia coli Central Carbon Metabolome. Metabolites 2023; 13:metabo13020150. [PMID: 36837769 PMCID: PMC9965072 DOI: 10.3390/metabo13020150] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/07/2023] [Accepted: 01/15/2023] [Indexed: 01/20/2023] Open
Abstract
Precise and accurate quantification is a prerequisite for interpretation of targeted metabolomics data, but this task is challenged by the inherent instability of the analytes. The sampling, quenching, extraction, and sample purification conditions required to recover and stabilize metabolites in representative extracts have also been proven highly dependent on species-specific properties. For Escherichia coli, unspecific leakage has been demonstrated for conventional microbial metabolomics sampling protocols. We herein present a fast filtration-based sampling protocol for this widely applied model organism, focusing on pitfalls such as inefficient filtration, selective loss of biomass, matrix contamination, and membrane permeabilization and leakage. We evaluate the effect of and need for removal of extracellular components and demonstrate how residual salts can challenge analytical accuracy of hyphenated mass spectrometric analyses, even when sophisticated correction strategies are applied. Laborious extraction procedures are bypassed by direct extraction in cold acetonitrile:water:methanol (3:5:2, v/v%), ensuring compatibility with sample concentration and thus, any downstream analysis. By applying this protocol, we achieve and demonstrate high precision and low metabolite turnover, and, followingly, minimal perturbation of the inherent metabolic state. This allows us to herein report absolute intracellular concentrations in E. coli and explore its central carbon metabolome at several commonly applied cultivation conditions.
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Gao Z, Batool R, Xie W, Huang X, Wang Z. Transcriptome and Metabolome Analysis Reveals the Importance of Amino-Acid Metabolism in Spodoptera Frugiperda Exposed to Spinetoram. INSECTS 2022; 13:insects13090852. [PMID: 36135553 PMCID: PMC9504701 DOI: 10.3390/insects13090852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 05/31/2023]
Abstract
Pests are inevitably exposed to sublethal and lethal doses in the agroecosystem following the application of pesticides indispensable to protect food sources. The effect of spinetoram on amino-acid metabolism of fall armyworm, Spodoptera frugiperda (J.E. Smith), was investigated, at the dose of LC10 and LC90, by transcriptome and LC-MS/MS analysis. Using statistics-based analysis of both POS and NEG mode, a total of 715,501 metabolites in S. frugiperda were significantly changed after spinetoram treatment. The enhancement of glucose metabolism provides energy support for detoxification in larvae. The decrease in valine and isoleucine is associated with an increase in leucine, without maintaining the conservation of citric acid in the larvae. The down-regulation of phenylalanine may retard the tricarboxylic acid cycle to produce GTP. The abundance of lysine was decreased in response to spinetoram exposure, which damages the nervous system of the larvae. The abundance of arginine increases and causes non-functional contraction of the insect's muscles, causing the larva to expend excess energy. Tryptophan provides an important substrate for eliminating ROS. The changes in glutamic acid, aspartic acid, and lysine cause damage to the nerve centers of the larvae. The results of transcriptome and LC-MS/MS analysis revealed the effects of pesticide exposure on amino-acid metabolism of S. frugiperda successfully and provide a new overview of the response of insect physio-biochemistry against pesticides.
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Affiliation(s)
- Zupeng Gao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Raufa Batool
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Weifeng Xie
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Engineering Research Center of Natural Enemy Insects/Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Xiaodan Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Engineering Research Center of Natural Enemy Insects/Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Zhenying Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Allahghadry T, Bojesen AM, Whitehead BJ, Antenucci F. Clarification of large-volume bacterial cultures using a centrifuge-free protocol. J Appl Microbiol 2022; 133:870-882. [PMID: 35503033 PMCID: PMC9542984 DOI: 10.1111/jam.15608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 11/30/2022]
Abstract
Aims To provide a reliable, reproducible and centrifuge‐free filtration protocol for clarification of large volumes of bacterial cultures. Methods and Results Four experiments were designed to compare different techniques enabling clarification of Escherichia coli cultures using as a benchmark the concentration and quality of bacterial outer membrane vesicles (OMVs). The experiments were designed to examine the performance of different extraction methods on large volume (≥1 L) filtrations of bacterial culture media. Performance parameters included filtration flow rates, sterility testing and characterization of the filtrates by: (i) SDS‐PAGE, (ii) cryogenic transmission electron microscopy, (iii) nanoparticle tracking analysis and (iv) Qubit protein quantification. The experiments revealed that: (i) addition of the filter aid Diatomaceous Earth to the bacterial cultures improved filtration flow rates significantly and eliminated the need for centrifugation prior to filtration; (ii) sterile filtration was successful as no bacterial passage was identified through the membrane filter; (iii) centrifuge‐free filtrates contained an increased amount of OMVs compared to centrifuged filtrates. Conclusions In comparison to conventional centrifuge‐based protocols, the clarification method presented has universal applicability for a broad range of microbial extraction procedures, regardless of the volume of culture harvested. Moreover, the decreased amount of OMVs presented in the filtrates following centrifugation step provides an additional argument in favour of a centrifuge‐free approach. Significance and Impact of the Study Sterile filtration is a universal method for the clarification of bacterial cultures. Common challenges related to filtration include filter clogging and long processing times, due to limited centrifugation capacity, which can affect product quality. The proposed protocol is likely to ensure a highly effective filtration process and could be a novel approach in improving the filtrate products without the need of centrifugation.
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Affiliation(s)
- Toloe Allahghadry
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Miki Bojesen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bradley Joseph Whitehead
- Department of Clinical Medicine, Department of Infectious Diseases, Aarhus University, Aarhus N, Denmark
| | - Fabio Antenucci
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Mohd Kamal K, Mahamad Maifiah MH, Abdul Rahim N, Hashim YZHY, Abdullah Sani MS, Azizan KA. Bacterial Metabolomics: Sample Preparation Methods. Biochem Res Int 2022; 2022:9186536. [PMID: 35465444 PMCID: PMC9019480 DOI: 10.1155/2022/9186536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/31/2022] [Indexed: 12/03/2022] Open
Abstract
Metabolomics is a comprehensive analysis of metabolites existing in biological systems. As one of the important "omics" tools, the approach has been widely employed in various fields in helping to better understand the complex cellular metabolic states and changes. Bacterial metabolomics has gained a significant interest as bacteria serve to provide a better subject or model at systems level. The approach in metabolomics is categorized into untargeted and targeted which serves different paradigms of interest. Nevertheless, the bottleneck in metabolomics has been the sample or metabolite preparation method. A custom-made method and design for a particular species or strain of bacteria might be necessary as most studies generally refer to other bacteria or even yeast and fungi that may lead to unreliable analysis. The paramount aspect of metabolomics design comprises sample harvesting, quenching, and metabolite extraction procedures. Depending on the type of samples and research objective, each step must be at optimal conditions which are significantly important in determining the final output. To date, there are no standardized nor single designated protocols that have been established for a specific bacteria strain for untargeted and targeted approaches. In this paper, the existing and current developments of sample preparation methods of bacterial metabolomics used in both approaches are reviewed. The review also highlights previous literature of optimized conditions used to propose the most ideal methods for metabolite preparation, particularly for bacterial cells. Advantages and limitations of methods are discussed for future improvement of bacterial metabolomics.
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Affiliation(s)
- Khairunnisa Mohd Kamal
- International Institute for Halal Research and Training (INHART), Level 3, KICT Building, International Islamic University Malaysia (IIUM), Jalan Gombak, Selangor 53100, Malaysia
| | - Mohd Hafidz Mahamad Maifiah
- International Institute for Halal Research and Training (INHART), Level 3, KICT Building, International Islamic University Malaysia (IIUM), Jalan Gombak, Selangor 53100, Malaysia
| | | | - Yumi Zuhanis Has-Yun Hashim
- International Institute for Halal Research and Training (INHART), Level 3, KICT Building, International Islamic University Malaysia (IIUM), Jalan Gombak, Selangor 53100, Malaysia
| | - Muhamad Shirwan Abdullah Sani
- International Institute for Halal Research and Training (INHART), Level 3, KICT Building, International Islamic University Malaysia (IIUM), Jalan Gombak, Selangor 53100, Malaysia
| | - Kamalrul Azlan Azizan
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, UKM, Bangi, Selangor 43600, Malaysia
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Metabolic profiling of attached and detached metformin and 2-deoxy-D-glucose treated breast cancer cells reveals adaptive changes in metabolome of detached cells. Sci Rep 2021; 11:21354. [PMID: 34725457 PMCID: PMC8560930 DOI: 10.1038/s41598-021-98642-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 09/06/2021] [Indexed: 02/05/2023] Open
Abstract
Anchorage-independent growth of cancer cells in vitro is correlated to metastasis formation in vivo. Metformin use is associated with decreased breast cancer incidence and currently evaluated in cancer clinical trials. The combined treatment with metformin and 2-deoxy-D-glucose (2DG) in vitro induces detachment of viable MDA-MB-231 breast cancer cells that retain their proliferation capacity. This might be important for cell detachment from primary tumors, but the metabolic changes involved are unknown. We performed LC/MS metabolic profiling on separated attached and detached MDA-MB-231 cells treated with metformin and/or 2DG. High 2DG and metformin plus 2DG altered the metabolic profile similarly to metformin, inferring that metabolic changes are necessary but not sufficient while the specific effects of 2DG are crucial for detachment. Detached cells had higher NADPH levels and lower fatty acids and glutamine levels compared to attached cells, supporting the role of AMPK activation and reductive carboxylation in supporting anchorage-independent survival. Surprisingly, the metabolic profile of detached cells was closer to untreated control cells than attached treated cells, suggesting detachment might help cells adapt to energy stress. Metformin treated cells had higher fatty and amino acid levels with lower purine nucleotide levels, which is relevant for understanding the anticancer mechanisms of metformin.
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Birk B, Haake V, Sperber S, Herold M, Wallisch SK, Huener HA, Verlohner A, Amma MM, Walk T, Hernandez TR, Hewitt NJ, Kamp H, van Ravenzwaay B. Use of in vitro metabolomics in NRK cells to help predicting nephrotoxicity and differentiating the MoA of nephrotoxicants. Toxicol Lett 2021; 353:43-59. [PMID: 34626816 DOI: 10.1016/j.toxlet.2021.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 08/06/2021] [Accepted: 09/29/2021] [Indexed: 12/25/2022]
Abstract
We describe a strategy using an in vitro metabolomics assay with tubular rat NRK-52E cells to investigate the Modes of Action (MoAs) of nephrotoxic compounds. Chemicals were selected according to their MoAs based on literature information: acetaminophen, 4-aminophenol and S-(trichlorovinyl-)L-cysteine (TCVC), (covalent protein binding); gentamycin, vancomycin, polymycin B and CdCl2 (lysosomal overload) and tenofovir and cidofovir (mitochondrial DNA-interaction). After treatment and harvesting of the cells, intracellular endogenous metabolites were quantified relative to vehicle control. Metabolite patterns were evaluated in a purely data-driven pattern generation process excluding published information. This strategy confirmed the assignment of the chemicals to the respective MoA except for TCVC and CdCl2. Finally, TCVC was defined as unidentified and CdCl2 was reclassified to the MoA "covalent protein binding". Hierarchical cluster analysis of 58 distinct metabolites from the patterns enabled a clear visual separation of chemicals in each MoA. The assay reproducibility was very good and metabolic responses were consistent. These results support the use of metabolome analysis in NRK-52E cells as a suitable tool for understanding and investigating the MoA of nephrotoxicants. This assay could enable the early identification of nephrotoxic compounds and finally reduce animal testing.
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Affiliation(s)
- Barbara Birk
- Experimental Toxicology and Ecology, BASF SE, Ludwigshafen, Germany.
| | | | - Saskia Sperber
- Experimental Toxicology and Ecology, BASF SE, Ludwigshafen, Germany
| | | | | | | | | | - Meike M Amma
- Experimental Toxicology and Ecology, BASF SE, Ludwigshafen, Germany
| | | | | | | | - Hennicke Kamp
- Experimental Toxicology and Ecology, BASF SE, Ludwigshafen, Germany; BASF Metabolome Solutions GmbH, Berlin, Germany
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Bowen TJ, Hall AR, Lloyd GR, Weber RJM, Wilson A, Pointon A, Viant MR. An Extensive Metabolomics Workflow to Discover Cardiotoxin-Induced Molecular Perturbations in Microtissues. Metabolites 2021; 11:644. [PMID: 34564460 PMCID: PMC8470535 DOI: 10.3390/metabo11090644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 11/29/2022] Open
Abstract
Discovering modes of action and predictive biomarkers of drug-induced structural cardiotoxicity offers the potential to improve cardiac safety assessment of lead compounds and enhance preclinical to clinical translation during drug development. Cardiac microtissues are a promising, physiologically relevant, in vitro model, each composed of ca. 500 cells. While untargeted metabolomics is capable of generating hypotheses on toxicological modes of action and discovering metabolic biomarkers, applying this technology to low-biomass microtissues in suspension is experimentally challenging. Thus, we first evaluated a filtration-based approach for harvesting microtissues and assessed the sensitivity and reproducibility of nanoelectrospray direct infusion mass spectrometry (nESI-DIMS) measurements of intracellular extracts, revealing samples consisting of 28 pooled microtissues, harvested by filtration, are suitable for profiling the intracellular metabolome and lipidome. Subsequently, an extensive workflow combining nESI-DIMS untargeted metabolomics and lipidomics of intracellular extracts with ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS/MS) analysis of spent culture medium, to profile the metabolic footprint and quantify drug exposure concentrations, was implemented. Using the synthetic drug and model cardiotoxin sunitinib, time-resolved metabolic and lipid perturbations in cardiac microtissues were investigated, providing valuable data for generating hypotheses on toxicological modes of action and identifying putative biomarkers such as disruption of purine metabolism and perturbation of polyunsaturated fatty acid levels.
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Affiliation(s)
- Tara J. Bowen
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (T.J.B.); (R.J.M.W.)
| | - Andrew R. Hall
- Functional and Mechanistic Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK; (A.R.H.); (A.P.)
| | - Gavin R. Lloyd
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
| | - Ralf J. M. Weber
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (T.J.B.); (R.J.M.W.)
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
| | - Amanda Wilson
- Clinical Pharmacology and Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, UK;
| | - Amy Pointon
- Functional and Mechanistic Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK; (A.R.H.); (A.P.)
| | - Mark R. Viant
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (T.J.B.); (R.J.M.W.)
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
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Diederen T, Delabrière A, Othman A, Reid ME, Zamboni N. Metabolomics. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Lv N, Ma K, Li R, Liang P, Liang P, Gao X. Sublethal and lethal effects of the imidacloprid on the metabolic characteristics based on high-throughput non-targeted metabolomics in Aphis gossypii Glover. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 212:111969. [PMID: 33561773 DOI: 10.1016/j.ecoenv.2021.111969] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
Sublethal effect considered as an emerging factor to assess the environmental risk of insecticides, which can impact the insects on both physiology and behavior. Lethal exposure can be causing near immediate mortality. Pests are inevitably exposed to sublethal and lethal dose in the agroecosystem following application of pesticides. Insecticides, widely used for the control of insect pests, are irreplaceable in insect pest management. The effects of imidacloprid by the method of high-throughput non-targeted metabolomics was investigated in Aphis gossypii Glover exposed to LC10 and LC90 doses of the imidacloprid, and the control group was treated with the same condition without imidacloprid. Pairwise comparisons showed that 111 metabolites changed significantly, 60 in the LC10 group, and 66 in the LC90 group compared to the control group, while only 16 changes in the LC10 were same with that in LC90 group. Among the changed metabolites, a total of 16 metabolites were identified as potential biomarkers, which represented the most influential pathways including glycolysis and gluconeogenesis, alanine, aspartate, and glutamate metabolism, ascorbate and aldarate metabolism, glutathione metabolism, phenylalanine metabolism, tyrosine metabolism, caffeine metabolism and parkinson's disease (PD), which could account for the sublethal and lethal effects on A. gossypii. These modified metabolic pathways demonstrated that high energy consumption, excitotoxicity and oxidative stress (OS) were appeared in both LC10 and LC90 groups, while PD was detected only in the LC90 group. The results of non-targeted metabolomics revealed the effects of neonicotinoid pesticide exposure on A. gossypii successfully, and provided a deep insight into the influenced physiology by the stress of neonicotinoid pesticide in the insect.
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Affiliation(s)
- Nannan Lv
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Kangsheng Ma
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Ren Li
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Pingzhuo Liang
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Pei Liang
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Xiwu Gao
- Department of Entomology, China Agricultural University, Beijing 100193, China.
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Deter HS, Hossain T, Butzin NC. Antibiotic tolerance is associated with a broad and complex transcriptional response in E. coli. Sci Rep 2021; 11:6112. [PMID: 33731833 PMCID: PMC7969968 DOI: 10.1038/s41598-021-85509-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/02/2021] [Indexed: 02/06/2023] Open
Abstract
Antibiotic treatment kills a large portion of a population, while a small, tolerant subpopulation survives. Tolerant bacteria disrupt antibiotic efficacy and increase the likelihood that a population gains antibiotic resistance, a growing health concern. We examined how E. coli transcriptional networks changed in response to lethal ampicillin concentrations. We are the first to apply transcriptional regulatory network (TRN) analysis to antibiotic tolerance by leveraging existing knowledge and our transcriptional data. TRN analysis shows that gene expression changes specific to ampicillin treatment are likely caused by specific sigma and transcription factors typically regulated by proteolysis. These results demonstrate that to survive lethal concentration of ampicillin specific regulatory proteins change activity and cause a coordinated transcriptional response that leverages multiple gene systems.
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Affiliation(s)
- Heather S Deter
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tahmina Hossain
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57006, USA
| | - Nicholas C Butzin
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57006, USA.
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12
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Li JH, Xu ZY, Li MJ, Zheng WL, Huang XM, Xiao F, Cui YH, Pan HW. LC-MS based metabolomics reveals metabolic pathway disturbance in retinal pigment epithelial cells exposed to hydroxychloroquine. Chem Biol Interact 2020; 328:109212. [DOI: 10.1016/j.cbi.2020.109212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/13/2020] [Accepted: 07/23/2020] [Indexed: 01/08/2023]
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Bacon K, Lavoie A, Rao BM, Daniele M, Menegatti S. Past, Present, and Future of Affinity-based Cell Separation Technologies. Acta Biomater 2020; 112:29-51. [PMID: 32442784 PMCID: PMC10364325 DOI: 10.1016/j.actbio.2020.05.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/29/2020] [Accepted: 05/05/2020] [Indexed: 02/06/2023]
Abstract
Progress in cell purification technology is critical to increase the availability of viable cells for therapeutic, diagnostic, and research applications. A variety of techniques are now available for cell separation, ranging from non-affinity methods such as density gradient centrifugation, dielectrophoresis, and filtration, to affinity methods such as chromatography, two-phase partitioning, and magnetic-/fluorescence-assisted cell sorting. For clinical and analytical procedures that require highly purified cells, the choice of cell purification method is crucial, since every method offers a different balance between yield, purity, and bioactivity of the cell product. For most applications, the requisite purity is only achievable through affinity methods, owing to the high target specificity that they grant. In this review, we discuss past and current methods for developing cell-targeting affinity ligands and their application in cell purification, along with the benefits and challenges associated with different purification formats. We further present new technologies, like stimuli-responsive ligands and parallelized microfluidic devices, towards improving the viability and throughput of cell products for tissue engineering and regenerative medicine. Our comparative analysis provides guidance in the multifarious landscape of cell separation techniques and highlights new technologies that are poised to play a key role in the future of cell purification in clinical settings and the biotech industry. STATEMENT OF SIGNIFICANCE: Technologies for cell purification have served science, medicine, and industrial biotechnology and biomanufacturing for decades. This review presents a comprehensive survey of this field by highlighting the scope and relevance of all known methods for cell isolation, old and new alike. The first section covers the main classes of target cells and compares traditional non-affinity and affinity-based purification techniques, focusing on established ligands and chromatographic formats. The second section presents an excursus of affinity-based pseudo-chromatographic and non-chromatographic technologies, especially focusing on magnetic-activated cell sorting (MACS) and fluorescence-activated cell sorting (FACS). Finally, the third section presents an overview of new technologies and emerging trends, highlighting how the progress in chemical, material, and microfluidic sciences has opened new exciting avenues towards high-throughput and high-purity cell isolation processes. This review is designed to guide scientists and engineers in their choice of suitable cell purification techniques for research or bioprocessing needs.
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Affiliation(s)
- Kaitlyn Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Ashton Lavoie
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Balaji M Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA; Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695-7928, USA
| | - Michael Daniele
- Joint Department of Biomedical Engineering, North Carolina State University - University of North Carolina Chapel Hill, North Carolina, United States
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA; Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695-7928, USA.
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Smith ML, Miguez AM, Styczynski MP. Gas Chromatography-Mass Spectrometry Microbial Metabolomics for Applications in Strain Optimization. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2019; 1927:179-189. [PMID: 30788792 DOI: 10.1007/978-1-4939-9142-6_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Metabolomics is the systems-scale measurement of biochemical intermediates in biological systems; by virtue of its deep and broad study of metabolism, it has great potential for applications in metabolic engineering. While a number of the analytical techniques used widely in metabolomics are familiar to metabolic engineers performing post hoc analyses of product titers, the requirements for accurately capturing metabolism at a systems scale rather than just measuring a single secreted product are much more complicated. Nonetheless, metabolomics (which is still not widely available as an affordable consumer service like many molecular biology services) is within reach of many properly equipped metabolic engineering groups. To this end, we present a detailed metabolomics protocol with application to strain optimization. Specifically, we focus on characterizing metabolism in the yeast Saccharomyces cerevisiae using gas chromatography coupled to mass spectrometry. The measurement of metabolic intermediates that results from such approaches has the potential to enable more informed and rational efforts towards pathway engineering and strain optimization.
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Affiliation(s)
- McKenzie L Smith
- Georgia Tech School of Chemical & Biomolecular Engineering, Atlanta, GA, USA
| | - April M Miguez
- Georgia Tech School of Chemical & Biomolecular Engineering, Atlanta, GA, USA
| | - Mark P Styczynski
- Georgia Tech School of Chemical & Biomolecular Engineering, Atlanta, GA, USA.
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Dhami N, Trivedi DK, Goodacre R, Mainwaring D, Humphreys DP. Mitochondrial aconitase is a key regulator of energy production for growth and protein expression in Chinese hamster ovary cells. Metabolomics 2018; 14:136. [PMID: 30830403 DOI: 10.1007/s11306-018-1430-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 09/21/2018] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Mammalian cells like Chinese hamster ovary (CHO) cells are routinely used for production of recombinant therapeutic proteins. Cells require a continuous supply of energy and nutrients to sustain high cell densities whilst expressing high titres of recombinant proteins. Cultured mammalian cells are primarily dependent on glucose and glutamine metabolism for energy production. OBJECTIVES The TCA cycle is the main source of energy production and its continuous flow is essential for cell survival. Modulated regulation of TCA cycle can affect ATP production and influence CHO cell productivity. METHODS To determine the key metabolic reactions of the cycle associated with cell growth in CHO cells, we transiently silenced each gene of the TCA cycle using RNAi. RESULTS Silencing of at least four TCA cycle genes was detrimental to CHO cell growth. With an exception of mitochondrial aconitase (or Aco2), all other genes were associated with ATP production reactions of the TCA cycle and their resulting substrates can be supplied by other anaplerotic and cataplerotic reactions. This study is the first of its kind to have established key role of aconitase gene in CHO cells. We further investigated the temporal effects of aconitase silencing on energy production, CHO cell metabolism, oxidative stress and recombinant protein production. CONCLUSION Transient silencing of mitochondrial aconitase inhibited cell growth, reduced ATP production, increased production of reactive oxygen species and reduced cell specific productivity of a recombinant CHO cell line by at least twofold.
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Affiliation(s)
- Neha Dhami
- Protein Sciences, UCB, 216 Bath Road, Slough, Berkshire, SL1 3WE, UK.
| | - Drupad K Trivedi
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Royston Goodacre
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - David Mainwaring
- Protein Sciences, UCB, 216 Bath Road, Slough, Berkshire, SL1 3WE, UK
- Pall Europe Limited, 5 Harbourgate Business Park, Southampton Road, Portsmouth, Hampshire, PO6 4BQ, UK
| | - David P Humphreys
- Protein Sciences, UCB, 216 Bath Road, Slough, Berkshire, SL1 3WE, UK
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Beatty A, Fink LS, Singh T, Strigun A, Peter E, Ferrer CM, Nicolas E, Cai KQ, Moran TP, Reginato MJ, Rennefahrt U, Peterson JR. Metabolite Profiling Reveals the Glutathione Biosynthetic Pathway as a Therapeutic Target in Triple-Negative Breast Cancer. Mol Cancer Ther 2017; 17:264-275. [PMID: 29021292 DOI: 10.1158/1535-7163.mct-17-0407] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 09/06/2017] [Accepted: 10/05/2017] [Indexed: 12/11/2022]
Abstract
Cancer cells can exhibit altered dependency on specific metabolic pathways and targeting these dependencies is a promising therapeutic strategy. Triple-negative breast cancer (TNBC) is an aggressive and genomically heterogeneous subset of breast cancer that is resistant to existing targeted therapies. To identify metabolic pathway dependencies in TNBC, we first conducted mass spectrometry-based metabolomics of TNBC and control cells. Relative levels of intracellular metabolites distinguished TNBC from nontransformed breast epithelia and revealed two metabolic subtypes within TNBC that correlate with markers of basal-like versus non-basal-like status. Among the distinguishing metabolites, levels of the cellular redox buffer glutathione were lower in TNBC cell lines compared to controls and markedly lower in non-basal-like TNBC. Significantly, these cell lines showed enhanced sensitivity to pharmacologic inhibition of glutathione biosynthesis that was rescued by N-acetylcysteine, demonstrating a dependence on glutathione production to suppress ROS and support tumor cell survival. Consistent with this, patients whose tumors express elevated levels of γ-glutamylcysteine ligase, the rate-limiting enzyme in glutathione biosynthesis, had significantly poorer survival. We find, further, that agents that limit the availability of glutathione precursors enhance both glutathione depletion and TNBC cell killing by γ-glutamylcysteine ligase inhibitors in vitro Importantly, we demonstrate the ability to this approach to suppress glutathione levels and TNBC xenograft growth in vivo Overall, these findings support the potential of targeting the glutathione biosynthetic pathway as a therapeutic strategy in TNBC and identify the non-basal-like subset as most likely to respond. Mol Cancer Ther; 17(1); 264-75. ©2017 AACR.
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Affiliation(s)
| | | | - Tanu Singh
- Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | | | - Erik Peter
- Metanomics GmbH & Metanomics Health GmbH, Berlin, Germany
| | - Christina M Ferrer
- Department of Biochemistry & Molecular Biology, Drexel College of Medicine, Philadelphia, Pennsylvania
| | | | - Kathy Q Cai
- Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | | | - Mauricio J Reginato
- Department of Biochemistry & Molecular Biology, Drexel College of Medicine, Philadelphia, Pennsylvania
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Prediction of liver toxicity and mode of action using metabolomics in vitro in HepG2 cells. Arch Toxicol 2017; 92:893-906. [PMID: 28965233 PMCID: PMC5818600 DOI: 10.1007/s00204-017-2079-6] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/21/2017] [Indexed: 11/17/2022]
Abstract
Liver toxicity is a leading systemic toxicity of drugs and chemicals demanding more human-relevant, high throughput, cost effective in vitro solutions. In addition to contributing to animal welfare, in vitro techniques facilitate exploring and understanding the molecular mechanisms underlying toxicity. New ‘omics technologies can provide comprehensive information on the toxicological mode of action of compounds, as well as quantitative information about the multi-parametric metabolic response of cellular systems in normal and patho-physiological conditions. Here, we combined mass-spectroscopy metabolomics with an in vitro liver toxicity model. Metabolite profiles of HepG2 cells treated with 35 test substances resulted in 1114 cell supernatants and 3556 intracellular samples analyzed by metabolomics. Control samples showed relative standard deviations of about 10–15%, while the technical replicates were at 5–10%. Importantly, this procedure revealed concentration–response effects and patterns of metabolome changes that are consistent for different liver toxicity mechanisms (liver enzyme induction/inhibition, liver toxicity and peroxisome proliferation). Our findings provide evidence that identifying organ toxicity can be achieved in a robust, reliable, human-relevant system, representing a non-animal alternative for systemic toxicology.
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Collection and Preparation of Clinical Samples for Metabolomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 965:19-44. [DOI: 10.1007/978-3-319-47656-8_2] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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