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Related Concept Videos

Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Toxic Reactions: Overview01:26

Toxic Reactions: Overview

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When toxic substances penetrate the human body, they disseminate to various tissues, undergoing metabolic changes. This process yields reactive metabolites that may covalently bind with specific target molecules, resulting in toxicity.
Toxicity falls into two primary categories: local and systemic.
Local toxicity appears at the exposure site, such as protein denaturation caused by caustic substances.
In contrast, systemic toxicity requires the toxic agent's absorption and distribution,...
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Toxicogenomic Analysis.

Taisa Magnani Dinamarco1, Paula Fagundes de Gouvêa2, Emerson de Souza Santos3

  • 1FFCLRP-USP, Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil. tdinamarco@ffclrp.usp.br.

Methods in Molecular Biology (Clifton, N.J.)
|January 10, 2021
PubMed
Summary

Toxicogenomics uses genomics and proteomics to understand how chemicals affect cell functions. This study details methods for RNA sequencing and proteomic analysis to assess these toxic impacts.

Keywords:
1D SDS-PAGELC-MS/MSRNA-seqReal-time qPCRToxicogenomics

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Area of Science:

  • Environmental toxicology
  • Molecular biology
  • Biochemistry

Background:

  • Cellular functions are altered by toxic agents.
  • Toxicogenomics integrates genomics, transcriptomics, and proteomics.
  • Understanding chemical impacts on gene and protein expression is crucial.

Purpose of the Study:

  • To describe a method for transcriptomic analysis using RNA sequencing.
  • To detail a method for proteomic analysis via 1D SDS-PAGE and LC-MS/MS.
  • To provide insights into toxicogenomic analysis.

Main Methods:

  • Transcriptomic analysis: RNA sequencing (Illumina HiSeq, NextSeq, NovaSeq) with qPCR validation.
  • Proteomic analysis: 1D SDS-PAGE followed by sample preparation for LC-MS/MS.
  • Methodological considerations for LC-MS/MS.

Main Results:

  • Established protocols for transcriptomic and proteomic analyses in toxicogenomics.
  • Demonstrated the utility of RNA sequencing and LC-MS/MS for studying chemical effects.
  • Identified key steps and considerations for robust toxicogenomic studies.

Conclusions:

  • The described methods provide a framework for toxicogenomic investigations.
  • Accurate assessment of chemical impacts on cellular systems is achievable.
  • These techniques aid in understanding cellular responses to toxicants.