Omics Technology

Debnath, Mousumi; Prasad, G. V. R.; Bisen, Prakash S.

doi:10.1007/978-90-481-3261-4_2

Cited by 15 publications

(5 citation statements)

References 52 publications

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“…Omics technologies involved in reverse genetics approaches, such as transcriptomics, proteomics, and metabolomics will improve our understanding of biological processes and have become the new mantra in molecular research [ 23 ]. Thus, the application of these technologies could help us to discern how microorganisms respond to different environmental stresses and formulate ways to improve or modify their genotype to let them perform optimally in the presence of inhibitors.…”

Section: Introductionmentioning

confidence: 99%

Proteomic and metabolomic analysis of the cellular biomarkers related to inhibitors tolerance in Zymomonas mobilis ZM4

Chang

Islam

French

et al. 2018

Biotechnol Biofuels

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BackgroundToxic compounds present in both the hydrolysate and pyrolysate of lignocellulosic biomass severely hinder the further conversion of lignocellulose-derived fermentable sugars into useful chemicals by common biocatalysts like Zymomonas mobilis, which has remarkable advantages over yeast. Although the extra detoxification treatment prior to fermentation process can help biocatalysts to eliminate the inhibitory environment, it is not environment friendly and cost effective for industrial application. As also reported by previous studies, an ideal and holistic approach to solve this issue is to develop microbial strains with inhibitor tolerance. However, previously engineered strains had the limitation that they could not cope well with the synergistic effect of multiple inhibitors as they are resistant only to a single inhibitor. Hence, understanding the universal cellular responses of Z. mobilis to various inhibitors may guide the designing of rational strategies to obtain more robust engineered strains for biofuel production from lignocellulosic biomass.ResultsQuantitative proteomics and metabolomics approaches were used to determine the cellular responses of Z. mobilis ZM4 to representative biomass-derived inhibitors like formic acid, acetic acid, furfural, 5-hydroxymethylfurfural, and phenol. The differentially expressed proteins identified under the challenge of single and combined inhibitors were involved in cell wall/membrane biogenesis, energy production, DNA replication, DNA recombination, DNA repair, DNA transcription, RNA translation, posttranslational modification, biosynthesis of amino acids, central carbon metabolism, etc. Metabolomics analysis showed that the up- or down-regulation pattern of metabolites was changed consistently with that of relevant proteins.ConclusionFifteen up-regulated proteins (e.g., Isopropylmalate isomerase LeuC, transcription-repair-coupling factor Mfd, and phosphoglucose isomerase PGI) and thirteen down-regulated proteins (e.g., TonB-dependent transporter ZMO1522, transcription termination factor Rho, and S1/P1 nuclease ZMO0127) were identified as candidate proteins related to all the stress conditions, implying that these proteins are potential biomarkers for the improvement of Z. mobilis ZM4 to resist complex biomass-derived inhibitors. These data can be used to generate a database of inhibitor-tolerance biomarkers, which could provide a basis for engineering Z. mobilis that would be able to grow in the presence of multiple inhibitors and directly ferment the biomass-derived sugars into biofuels.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1287-5) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Proteomic and metabolomic analysis of the cellular biomarkers related to inhibitors tolerance in Zymomonas mobilis ZM4

Chang

Islam

French

et al. 2018

Biotechnol Biofuels

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“…The emergence of systems biology integrates high throughput data generation and analysis from many platforms to understand complex interactions between different levels of organization in a biological system [ 226 , 227 ]. Omics technology, an indispensable molecular technique in systems biology, incorporates genomics, transcriptomics, proteomics, and metabolomics techniques to foster a better understanding of biological processes [ 224 , 228 ]. The application of a systems biology paradigm in plant studies will provide a more holistic view of the antiviral potentials in medicinal plants.…”

Section: Future Directions For the Application Of Metabolomics To The...mentioning

confidence: 99%

Medicinal Plants against Viral Infections: A Review of Metabolomics Evidence for the Antiviral Properties and Potentials in Plant Sources

Adeosun,

Loots

2024

Viruses

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Most plants have developed unique mechanisms to cope with harsh environmental conditions to compensate for their lack of mobility. A key part of their coping mechanisms is the synthesis of secondary metabolites. In addition to their role in plants’ defense against pathogens, they also possess therapeutic properties against diseases, and their use by humans predates written history. Viruses are a unique class of submicroscopic agents, incapable of independent existence outside a living host. Pathogenic viruses continue to pose a significant threat to global health, leading to innumerable fatalities on a yearly basis. The use of medicinal plants as a natural source of antiviral agents has been widely reported in literature in the past decades. Metabolomics is a powerful research tool for the identification of plant metabolites with antiviral potentials. It can be used to isolate compounds with antiviral capacities in plants and study the biosynthetic pathways involved in viral disease progression. This review discusses the use of medicinal plants as antiviral agents, with a special focus on the metabolomics evidence supporting their efficacy. Suggestions are made for the optimization of various metabolomics methods of characterizing the bioactive compounds in plants and subsequently understanding the mechanisms of their operation.

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“…Various omics techniques, such as transcriptomics, proteomics, genomics, metabolomics, or other high-throughput screening methods, were used to identify potential disease biomarkers (Figure A). − An omics study involves the identification, quantification, and functional analysis of large-scale biological data from a particular biological system . In general for disease biomarker identification, the biological samples, such as tissues, blood, or urine, were collected from the patients with disease and healthy volunteers.…”

Section: Specificity Of Target Proteinsmentioning

confidence: 99%

Druggability of Targets for Diagnostic Radiopharmaceuticals

Wang

Chen

Yan

et al. 2023

ACS Pharmacol. Transl. Sci.

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Targets play an indispensable and pivotal role in the development of radiopharmaceuticals. However, the initial stages of drug discovery projects are often plagued by frequent failures due to inadequate information on druggability and suboptimal target selection. In this context, we aim to present a comprehensive review of the factors that influence target druggability for diagnostic radiopharmaceuticals. Specifically, we explore the crucial determinants of target specificity, abundance, localization, and positivity rate and their respective implications. Through a detailed analysis of existing protein targets, we elucidate the significance of each factor. By carefully considering and balancing these factors during the selection of targets, more efficacious and targeted radiopharmaceuticals are expected to be designed for the diagnosis of a wide range of diseases in the future.

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Omics Technology

Cited by 15 publications

References 52 publications

Proteomic and metabolomic analysis of the cellular biomarkers related to inhibitors tolerance in Zymomonas mobilis ZM4

Proteomic and metabolomic analysis of the cellular biomarkers related to inhibitors tolerance in Zymomonas mobilis ZM4

Medicinal Plants against Viral Infections: A Review of Metabolomics Evidence for the Antiviral Properties and Potentials in Plant Sources

Druggability of Targets for Diagnostic Radiopharmaceuticals

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