scholarly journals An Integrative Multi-Omics Workflow to Address Multifactorial Toxicology Experiments

Metabolites ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 79 ◽  
Author(s):  
Víctor González-Ruiz ◽  
Domitille Schvartz ◽  
Jenny Sandström ◽  
Julian Pezzatti ◽  
Fabienne Jeanneret ◽  
...  
Keyword(s):  
Analytical Techniques ◽  
Reversed Phase ◽  
Analysis Tool ◽  
Toxicant Exposure ◽  
Glutamatergic Neurons ◽  
Proteomic Data ◽  
Pathway Analysis Tool ◽  
Negative Ionization ◽  
Maturation State ◽  
Analytical Platforms

Toxicology studies can take advantage of omics approaches to better understand the phenomena underlying the phenotypic alterations induced by different types of exposure to certain toxicants. Nevertheless, in order to analyse the data generated from multifactorial omics studies, dedicated data analysis tools are needed. In this work, we propose a new workflow comprising both factor deconvolution and data integration from multiple analytical platforms. As a case study, 3D neural cell cultures were exposed to trimethyltin (TMT) and the relevance of the culture maturation state, the exposure duration, as well as the TMT concentration were simultaneously studied using a metabolomic approach combining four complementary analytical techniques (reversed-phase LC and hydrophilic interaction LC, hyphenated to mass spectrometry in positive and negative ionization modes). The ANOVA multiblock OPLS (AMOPLS) method allowed us to decompose and quantify the contribution of the different experimental factors on the outcome of the TMT exposure. Results showed that the most important contribution to the overall metabolic variability came from the maturation state and treatment duration. Even though the contribution of TMT effects represented the smallest observed modulation among the three factors, it was highly statistically significant. The MetaCore™ pathway analysis tool revealed TMT-induced alterations in biosynthetic pathways and in neuronal differentiation and signaling processes, with a predominant deleterious effect on GABAergic and glutamatergic neurons. This was confirmed by combining proteomic data, increasing the confidence on the mechanistic understanding of such a toxicant exposure.

scholarly journals Determination of Ten Corticosteroids in Illegal Cosmetic Products by a Simple, Rapid, and High-Performance LC-MS/MS Method

2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Vita Giaccone ◽  
Giuseppe Polizzotto ◽  
Andrea Macaluso ◽  
Gaetano Cammilleri ◽  
Vincenzo Ferrantelli
Keyword(s):  
High Performance ◽  
Skin Diseases ◽  
Gradient Elution ◽  
Reversed Phase ◽  
Cosmetic Products ◽  
Chromatography Method ◽  
Esi Ms ◽  
Negative Ionization Mode ◽  
Negative Ionization

The aim of our present work was the development of a rapid high-performance liquid chromatography method with electrospray ionization and tandem mass spectrometry detection (LC-ESI-MS/MS) for the determination of several corticosteroids in cosmetic products. Corticosteroids are suspected to be illegally added in cosmetic preparations in order to enhance the curative effect against some skin diseases. Sample preparation step consists in a single extraction with acetonitrile followed by centrifugation and filtration. The compounds were separated by reversed-phase chromatography with water and acetonitrile (both with 0.1% formic acid) gradient elution and detected by ESI-MS positive and negative ionization mode. The method was validated at the validation level of 0.1 mg kg−1. Linearity was studied in the 5–250 μg L−1 range and linear coefficients (r2) were all over 0.99. The accuracy and precision of the method were satisfactory. The LOD ranged from 0.085 to 0.109 mg kg−1 and the LOQ from 0.102 to 0.121 mg kg−1. Mean recoveries for all the analytes were within the range 91.9–99.2%. The developed method is sensitive and useful for detection, quantification, and confirmation of these corticosteroids in cosmetic preparations and can be applied in the analysis of the suspected samples under investigation.

scholarly journals TriPOINT: a software tool to prioritize important genes in pathways and their non-coding regulators

2018 ◽  
Vol 35 (15) ◽  
pp. 2686-2689
Author(s):  
Asa Thibodeau ◽  
Dong-Guk Shin
Keyword(s):  
Gene Expression ◽  
Software Tool ◽  
Supplementary Information ◽  
Analysis Tool ◽  
Graph Representations ◽  
Expression Levels ◽  
Conducting Pathway ◽  
Pathway Analysis Tool ◽  
Pathway Analyses ◽  
Gene Expression Levels

Abstract Summary Current approaches for pathway analyses focus on representing gene expression levels on graph representations of pathways and conducting pathway enrichment among differentially expressed genes. However, gene expression levels by themselves do not reflect the overall picture as non-coding factors play an important role to regulate gene expression. To incorporate these non-coding factors into pathway analyses and to systematically prioritize genes in a pathway we introduce a new software: Triangulation of Perturbation Origins and Identification of Non-Coding Targets. Triangulation of Perturbation Origins and Identification of Non-Coding Targets is a pathway analysis tool, implemented in Java that identifies the significance of a gene under a condition (e.g. a disease phenotype) by studying graph representations of pathways, analyzing upstream and downstream gene interactions and integrating non-coding regions that may be regulating gene expression levels. Availability and implementation The TriPOINT open source software is freely available at https://github.uconn.edu/ajt06004/TriPOINT under the GPL v3.0 license. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Decomposing the Mechanism of Qishen Granules in the Treatment of Heart Failure by a Quantitative Pathway Analysis Method

Molecules ◽  
2018 ◽  
Vol 23 (7) ◽  
pp. 1829 ◽  
Author(s):  
Weiquan Ren ◽  
Sheng Gao ◽  
Huimin Zhang ◽  
Yinglu Ren ◽  
Xue Yu ◽  
...  
Keyword(s):  
Heart Failure ◽  
Energy Metabolism ◽  
Pathway Analysis ◽  
Ventricular Remodeling ◽  
Left Ventricular ◽  
Left Ventricular Ejection ◽  
Therapeutic Effects ◽  
Analysis Tool ◽  
Ventricular Ejection Fraction ◽  
Pathway Analysis Tool

Qishen granules (QSG) have beneficial therapeutic effects for heart failure, but the effects of decomposed recipes, including Wenyang Yiqi Huoxue (WYH) and Qingre Jiedu (QJ), are not clear. In this study, the efficacy of WYH and QJ on heart failure is evaluated by using transverse aortic constriction (TAC) induced mice and the significantly changed genes in heart tissues were screened with a DNA array. Furthermore, a new quantitative pathway analysis tool is developed to evaluate the differences of pathways in different groups and to identify the pharmacological contributions of the decomposed recipes. Finally, the related genes in the significantly changed pathways are verified by a real-time polymerase chain reaction and a Western blot. Our data show that both QJ and WYH improve the left ventricular ejection fraction, which explain their contributions to protect against heart failure. In the energy metabolism, QJ achieves the therapeutic effects of QSG through nicotinamide nucleotide transhydrogenase (Nnt)-mediated mechanisms. In ventricular remodeling and inflammation reactions, QJ and WYH undertake the therapeutic effects through 5′-nucleotidase ecto (Nt5e)-mediated mechanisms. Together, QJ and WYH constitute the therapeutic effects of QSG and play important roles in myocardial energy metabolism and inflammation, which can exert therapeutic effects for heart failure.

scholarly journals Determination of Nucleotides and Nucleosides in Milks and Pediatric Formulas: A Review

2007 ◽  
Vol 90 (5) ◽  
pp. 1354-1364 ◽  
Author(s):  
Brendon D Gill ◽  
Harvey E Indyk
Keyword(s):  
Complex Mixture ◽  
Analytical Techniques ◽  
Reversed Phase ◽  
Robust Methods ◽  
Structural Units ◽  
Chromatographic Separations ◽  
Analytical Technique ◽  
Minimal Sample ◽  
Nucleotides And Nucleosides

Abstract Nucleotides and nucleosides play important roles as structural units in nucleic acids, as coenzymes in biochemical pathways, and as sources of chemical energy. Milk contains a complex mixture of nucleotides, nucleosides, and nucleobases, and because of the reported differences in their relative levels in bovine and human milks, pediatric formulas are increasingly supplemented with nucleotides. Liquid chromatography is the dominant analytical technique used for the quantitation of nucleospecies and is commonly applied using either ion-exchange, reversed-phase, or ion-pair reversed-phase modes. Robust methods that incorporate minimal sample preparation and rapid chromatographic separations have been developed for routine product compliance analysis. This review summarizes the analytical techniques used to date in the analysis of nucleospecies in bovine and human milks and infant formulas.

scholarly journals Pathway-PDT: a flexible pathway analysis tool for nuclear families

2013 ◽  
Vol 14 (1) ◽  
pp. 267 ◽  
Author(s):  
Yo Park ◽  
Michael Schmidt ◽  
Eden R Martin ◽  
Margaret A Pericak-Vance ◽  
Ren-Hua Chung
Keyword(s):  
Pathway Analysis ◽  
Analysis Tool ◽  
Nuclear Families ◽  
Pathway Analysis Tool

scholarly journals A Pathway Analysis Tool for Analyzing Microarray Data of Species with Low Physiological Information

2008 ◽  
Vol 2008 ◽  
pp. 1-7 ◽  
Author(s):  
M. F. W. te Pas ◽  
S. van Hemert ◽  
B. Hulsegge ◽  
A. J. W. Hoekman ◽  
M. H. Pool ◽  
...  
Keyword(s):  
Microarray Data ◽  
Gene List ◽  
Microarray Experiment ◽  
Laboratory Animals ◽  
Specific Gene ◽  
Analysis Tool ◽  
Pathway Information ◽  
Pathway Analysis Tool ◽  
Species Specific ◽  
Specific Reactions

Pathway information provides insight into the biological processes underlying microarray data. Pathway information is widely available for humans and laboratory animals in databases through the internet, but less for other species, for example, livestock. Many software packages use species-specific gene IDs that cannot handle genomics data from other species. We developed a species-independent method to search pathways databases to analyse microarray data. Three PERL scripts were developed that use the names of the genes on the microarray. (1) Add synonyms of gene names by searching the Gene Ontology (GO) database. (2) Search the Kyoto Encyclopaedia of Genes and Genomes (KEGG) database for pathway information using this GO-enriched gene list. (3) Combine the pathway data with the microarray data and visualize the results using color codes indicating regulation. To demonstrate the power of the method, we used a previously reported chicken microarray experiment investigating line-specific reactions to Salmonella infection as an example.

scholarly journals Simultaneous Determination of Caffeine and Paracetamol in Commercial Formulations Using Greener Normal-Phase and Reversed-Phase HPTLC Methods: A Contrast of Validation Parameters

Molecules ◽  
2022 ◽  
Vol 27 (2) ◽  
pp. 405
Author(s):  
Prawez Alam ◽  
Faiyaz Shakeel ◽  
Abuzer Ali ◽  
Mohammed H. Alqarni ◽  
Ahmed I. Foudah ◽  
...  
Keyword(s):  
Thin Layer ◽  
Simultaneous Determination ◽  
High Performance ◽  
Analytical Techniques ◽  
Reversed Phase ◽  
Normal Phase ◽  
Validation Parameters ◽  
Analytical Approaches ◽  
Layer Chromatography

There has been no assessment of the greenness of the described analytical techniques for the simultaneous determination (SMD) of caffeine and paracetamol. As a result, in comparison to the greener normal-phase high-performance thin-layer chromatography (HPTLC) technique, this research was conducted to develop a rapid, sensitive, and greener reversed-phase HPTLC approach for the SMD of caffeine and paracetamol in commercial formulations. The greenness of both techniques was calculated using the AGREE method. For the SMD of caffeine and paracetamol, the greener normal-phase and reversed-phase HPTLC methods were linear in the 50–500 ng/band and 25–800 ng/band ranges, respectively. For the SMD of caffeine and paracetamol, the greener reversed-phase HPTLC approach was more sensitive, accurate, precise, and robust than the greener normal-phase HPTLC technique. For the SMD of caffeine paracetamol in commercial PANEXT and SAFEXT tablets, the greener reversed-phase HPTLC technique was superior to the greener normal-phase HPTLC approach. The AGREE scores for the greener normal-phase and reversed-phase HPTLC approaches were estimated as 0.81 and 0.83, respectively, indicated excellent greenness profiles for both analytical approaches. The greener reversed-phase HPTLC approach is judged superior to the greener normal-phase HPTLC approach based on numerous validation parameters and pharmaceutical assays.

Analytical Techniques to Measure Sethoxydim and Breakdown Products

Weed Science ◽  
1986 ◽  
Vol 34 (5) ◽  
pp. 745-751 ◽  
Author(s):  
Antony R. Shoaf ◽  
William C. Carlson
Keyword(s):  
High Performance ◽  
Limit Of Detection ◽  
Parent Compound ◽  
Analytical Techniques ◽  
Reversed Phase ◽  
Breakdown Product ◽  
Rapid Decomposition ◽  
Efficiency Decomposition ◽  
Alkaline Conditions ◽  
Sulfone Derivative

A method was developed for the quantitative determination of trace levels of the widely used herbicide sethoxydim {2-[1-(ethoxyimino)butyl]-5-[2-(ethylthio)propyl]-3-hydroxy-2-cyclohexen-1-one} and its metabolites in an aqueous solution using reversed-phase high-performance liquid chromatography (HPLC). Optimum extraction of sethoxydim was with dichloromethane and was only 15% efficient at pH 3. The limit of detection by HPLC for sethoxydim was 5 ng on column and <5 ppb in soil. At least five different compounds were detected in the commercial formulation, in EPA reference standards, and in commercial sethoxydim standards. Sethoxydim undergoes a rapid decomposition in the presence of water to form more polar products, which accounts for the low extraction efficiency. Decomposition was greatest under alkaline conditions. Acid pH and soil inhibited decomposition and gave greater recoveries of parent compound. At least one breakdown product cochromatographed with a known sulfone derivative. The procedures are directly applicable to soils, environmental waters, and plant and animal tissues.

Sign in / Sign up

Export Citation Format

Share Document