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      Stage-specific exposure of Caenorhabditis elegans to cadmium identifies unique transcriptomic response cascades and an uncharacterized cadmium responsive transcript

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          Abstract

          Age/stage sensitivity is considered a significant factor in toxicity assessments. Previous studies investigated cadmium (Cd) toxicosis in Caenorhabditis elegans, and a plethora of metal-responsive genes/proteins have been identified and characterized in fine detail; however, most of these studies neglected age sensitivity and stage-specific response to toxicants at the molecular level. This present study compared the transcriptome response between C. elegans L3 vs L4 larvae exposed to 20 µM Cd to explore the transcriptional hallmarks of stage sensitivity. The results showed that the transcriptome of the L3 stage, despite being exposed to Cd for a shorter period, was more affected than the L4 stage, as demonstrated by differences in transcriptional changes and magnitude of induction. Additionally, T08G5.1, a hitherto uncharacterized gene located upstream of metallothionein ( mtl-2), was transcriptionally hyperresponsive to Cd exposure. Deletion of one or both metallothioneins ( mtl-1 and/or mtl-2) increased T08G5.1 expression, suggesting that its expression is linked to the loss of metallothionein. The generation of an extrachromosomal transgene (P T08G5.1:: GFP) revealed that T08G5.1 is constitutively expressed in the head neurons and induced in gut cells upon Cd exposure, not unlike mtl-1 and mtl-2. The low abundance of cysteine residues in T08G5.1 suggests, however, that it may not be involved directly in Cd sequestration to limit its toxicity like metallothionein, but might be associated with a parallel pathway, possibly an oxidative stress response.

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          C. elegans were exposed from L1 to L3 or L4 stage to identify development-specific changes of the transcriptome.

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          Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

          The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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            Cytoscape: a software environment for integrated models of biomolecular interaction networks.

            Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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              Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

              Background System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes/proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries. While many enrichment analysis tools and gene-set libraries databases have been developed, there is still room for improvement. Results Here, we present Enrichr, an integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. We applied Enrichr to analyze nine cancer cell lines by comparing their enrichment signatures to the enrichment signatures of matched normal tissues. We observed a common pattern of up regulation of the polycomb group PRC2 and enrichment for the histone mark H3K27me3 in many cancer cell lines, as well as alterations in Toll-like receptor and interlukin signaling in K562 cells when compared with normal myeloid CD33+ cells. Such analyses provide global visualization of critical differences between normal tissues and cancer cell lines but can be applied to many other scenarios. Conclusions Enrichr is an easy to use intuitive enrichment analysis web-based tool providing various types of visualization summaries of collective functions of gene lists. Enrichr is open source and freely available online at: http://amp.pharm.mssm.edu/Enrichr.
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                Author and article information

                Contributors
                Journal
                Metallomics
                Metallomics
                metallomics
                Metallomics: Integrated Biometal Science
                Oxford University Press
                1756-5901
                1756-591X
                May 2024
                28 March 2024
                28 March 2024
                : 16
                : 5
                : mfae016
                Affiliations
                Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London , London, UK
                Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London , London, UK
                Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London , London, UK
                Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London , London, UK
                Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London , London, UK
                Author notes
                Correspondence: Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK. E-mail: stephen.sturzenbaum@ 123456kcl.ac.uk

                Current address: Toxicology Department, GAB Consulting GmbH, 69126 Heidelberg, Germany.

                Author information
                https://orcid.org/0000-0002-9336-9290
                Article
                mfae016
                10.1093/mtomcs/mfae016
                11066929
                38549424
                44e453ee-d64f-454c-91f9-8031ef508121
                © The Author(s) 2024. Published by Oxford University Press.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 31 October 2023
                : 26 March 2024
                : 03 May 2024
                Page count
                Pages: 10
                Funding
                Funded by: Biotechnology and Biological Sciences Research Council, DOI 10.13039/501100000268;
                Award ID: BB/E025099
                Categories
                Paper
                AcademicSubjects/SCI00980
                AcademicSubjects/SCI01180
                AcademicSubjects/SCI00340
                AcademicSubjects/SCI00840

                c. elegans,l3 stage,l4 stage,cadmium,transcriptomics,metallothionein

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