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Effects of a 12-week telehealth exercise intervention on gait speed and gait deviations in adults with Down syndrome. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2024; 68:598-609. [PMID: 38481070 DOI: 10.1111/jir.13132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/11/2024] [Accepted: 02/21/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND Altered gait patterns and reduced walking speed are commonly reported in adults with Down syndrome (DS). Research on the effects of DS-specific exercise programmes on adults with DS is lacking. The purpose of this quasi-experimental study was to evaluate the changes in gait deviations and walking speed in adults with DS after a DS-specific exercise programme. METHODS Twenty participants underwent a 12-week, DS-specific exercise programme in a telehealth format. Before and after the intervention, gait deviations were assessed with the Ranchos Los Amigos Observational Gait Analysis form, and comfortable walking speed was evaluated with the 4-m walk test. RESULTS We observed increased comfortable walking speed and reduced gait deviations in the whole gait cycle in adults with DS after the intervention. There were fewer gait deviations during single-leg stance and swing-limb advancement and at the hip, knee and ankle joints after the 12-week exercise programme. CONCLUSIONS Gait speed and observable gait impairments in adults with DS significantly improved following a 12-week telehealth exercise programme.
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2,4-D Herbicide-Induced Hepatotoxicity: Unveiling Disrupted Liver Functions and Associated Biomarkers. TOXICS 2024; 12:35. [PMID: 38250991 PMCID: PMC10818579 DOI: 10.3390/toxics12010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/22/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024]
Abstract
2,4-dichlorophenoxyacetic acid (2,4-D) is a widely used herbicide worldwide and is frequently found in water samples. This knowledge has prompted studies on its effects on non-target organisms, revealing significant alterations to liver structure and function. In this review, we evaluated the literature on the hepatotoxicity of 2,4-D, focusing on morphological damages, toxicity biomarkers and affected liver functions. Searches were conducted on PubMed, Web of Science and Scopus and 83 articles were selected after curation. Among these studies, 72% used in vivo models and 30% used in vitro models. Additionally, 48% used the active ingredient, and 35% used commercial formulations in exposure experiments. The most affected biomarkers were related to a decrease in antioxidant capacity through alterations in the activities of catalase, superoxide dismutase and the levels of malondialdehyde. Changes in energy metabolism, lipids, liver function, and xenobiotic metabolism were also identified. Furthermore, studies about the effects of 2,4-D in mixtures with other pesticides were found, as well as hepatoprotection trials. The reviewed data indicate the essential role of reduction in antioxidant capacity and oxidative stress in 2,4-D-induced hepatotoxicity. However, the mechanism of action of the herbicide is still not fully understood and further research in this area is necessary.
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Biochemical Markers for Liver Injury in Zebrafish Larvae. Methods Mol Biol 2024; 2753:469-482. [PMID: 38285360 DOI: 10.1007/978-1-0716-3625-1_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Liver plays a crucial role in detoxification processes and metabolism of xenobiotics, and therefore, it is a target organ of toxicity of different classes of chemicals. In this context, some key enzymes present in liver are considered to be good biochemical markers of hepatic damage and can have their activities determined via spectrophotometry. Aspartate and alanine aminotransferases, alkaline phosphatase, lactate dehydrogenase, and glutathione peroxidase are enzymes that have activities often changed in response to hepatotoxic compounds and can be accessed through the larval period of zebrafish (Danio rerio). In this chapter, we described methodologies for analyses of these five biomarkers in pooled zebrafish larvae through spectrophotometry.
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The First Steps on AOPs' Concepts, Development, and Applications in Teratology. Methods Mol Biol 2024; 2753:151-157. [PMID: 38285337 DOI: 10.1007/978-1-0716-3625-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
An Adverse Outcome Pathway (AOP) is an analytical model that describes, through a graphical representation, a linear sequence of biologically connected events at different levels of biological organization, causally leading to an adverse effect on human health or the environment. In general, AOPs are constructed based on five central principles: systematic development and review, chemical-agnostic, modular, networks, and living documents. Furthermore, AOPs have the potential to be used, for example, to investigate certain molecular targets; relate the regulation of specific genes or proteins among AOPs; extrapolate biological processes, pathways, or diseases from one species to another; and even predict adverse effects in particular populations. AOPs also emerge as an alternative to animal experimentation in studies of developmental malformations. It's even possible now to develop a quantitative AOP to predict teratogenic effects for some substances. However, the construction of high-quality AOPs requires standardization in the way these models are developed and reviewed, ensuring an adequate degree of flexibility and guaranteeing efficiency. The development of AOPs should strictly be based on the guidance documents developed by the OECD. Nevertheless, an important step for those developing AOPs is the choice of an apical endpoint or an initiating molecular event in order to initiate the construction of the pathway. Another crucial step is a systematic literature review based on the random combination of the blocks of information. With these two fundamental steps completed, it only remains to follow the guidance documents on Developing and Assessing Adverse Outcome Pathways and AOP Developers' Handbook supplement provided by the OECD to organize and construct an AOP. This modern approach will bring radical changes in the field of toxicity testing, regarding the prediction of apical toxic effects using molecular-level effects.
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AOP Report: Glutathione Conjugation Leading to Reproductive Dysfunction via Oxidative Stress. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:2519-2528. [PMID: 37849373 DOI: 10.1002/etc.5751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023]
Abstract
We propose an adverse outcome pathway (AOP) for reproductive dysfunction via oxidative stress (OS). The AOP was developed based on Organisation for Economic Co-operation and Development (OECD) Guidance Document 184 and on the specific considerations of the OECD users' handbook supplement to the guidance document for developing and assessing AOPs (no. 233). According to the qualitative and quantitative experimental data evaluation, glutathione (GSH) conjugation is the first upstream key event (KE) of this AOP to reproductive dysfunction triggering OS. This event causes depletion of GSH basal levels (KE2 ). Consequently, this drop of free GSH induces an increase of reactive oxygen species (KE3 ) generated by the natural cellular metabolic processes (cellular respiration) of the organism. Increased levels of these reactive species, in turn, induce an increase of lipid peroxidation (KE4 ). This KE consequently leads to a rise in the amount of toxic substances, such as malondialdehyde and hydroxynonenal, which are associated with decreased quality and competence of gamete cell division, consequently impairing fertility (KE5 and adverse outcome). The overall assessment of the general biological plausibility, the empirical support, and the essentiality of KE relationships was considered as high for this AOP. We conclude that GSH conjugation is able to lead to reproductive disorder in fishes and mammals, via OS, but that the amount of stressor needed to trigger the AOP differs between stressors. Environ Toxicol Chem 2023;42:2519-2528. © 2023 SETAC.
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Network Toxicology and Molecular Docking to Investigate the Non-AChE Mechanisms of Organophosphate-Induced Neurodevelopmental Toxicity. TOXICS 2023; 11:710. [PMID: 37624215 PMCID: PMC10458981 DOI: 10.3390/toxics11080710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023]
Abstract
Organophosphate pesticides (OPs) are toxic substances that contaminate aquatic environments, interfere with the development of the nervous system, and induce Neurodevelopmental Toxicity (NDT) in animals and humans. The canonical mechanism of OP neurotoxicity involves the inhibition of acetylcholinesterase (AChE), but other mechanisms non-AChE are also involved and not fully understood. We used network toxicology and molecular docking to identify molecular targets and toxicity mechanisms common to OPs. Targets related to diazinon-oxon, chlorpyrifos oxon, and paraoxon OPs were predicted using the Swiss Target Prediction and PharmMapper databases. Targets related to NDT were compiled from GeneCards and OMIM databases. In order to construct the protein-protein interaction (PPI) network, the common targets between OPs and NDT were imported into the STRING. Network topological analyses identified EGFR, MET, HSP90AA1, and SRC as hub nodes common to the three OPs. Using the Reactome pathway and gene ontology, we found that signal transduction, axon guidance, cellular responses to stress, and glutamatergic signaling activation play key roles in OP-induced NDT.
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Exposure to 2,4-D herbicide induces hepatotoxicity in zebrafish larvae. Comp Biochem Physiol C Toxicol Pharmacol 2021; 248:109110. [PMID: 34144256 DOI: 10.1016/j.cbpc.2021.109110] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 12/31/2022]
Abstract
2,4-Dichlorophenoxyacetic acid (2,4-D) herbicide is the main ingredient in over 1500 commercially available products such as Weedestroy® AM40 and DMA® 4 IVM. Although the liver has been identified as one of the organs that are affected by this herbicide, reports on its hepatotoxic effects available in the literature are restricted to rats. Thus, there is a gap in information on other organisms that may be vulnerable to 2,4-D exposure, such as fish. Therefore, the present work aimed to assess the hepatotoxic potential of 2,4-D in fish using zebrafish (Danio rerio) larvae as a model system. For this purpose, its acute toxicity to zebrafish embryos was assessed, as well as its sublethal effects (< LC50) on the activity of enzymes related to oxidative (GST, CAT and GPX) and metabolic (LDH) stress and liver parameters (AST, ALT and ALP) after 48 h of exposure. Morphological analyses of the liver were also assessed in zebrafish larvae. As a result, 2,4-D reduced larvae survival (LC50 15.010 mg/L in 96 h of exposure), induced malformations, altered the activity of LDH, GST and CAT enzymes and significantly increased the activity of all biomarkers for liver damage. Although no changes in the color or size of larval liver were observed, histopathological analysis revealed that treatment with 2,4-D caused severe changes in liver tissue, such as vacuolization of the cytosol, eccentric cell nucleus, loss of tissue architecture and cellular boundaries. Thus, the results showed that 2,4-D altered the enzymatic profile related to oxidative stress, and induces liver damage.
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Computed tomographic (CT) arthrogram contributes to the diagnosis of an osteochondroma of the distal calcaneus in a horse. EQUINE VET EDUC 2021. [DOI: 10.1111/eve.13276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Translational Proteomics Analysis of Anthracycline-Induced Cardiotoxicity From Cardiac Microtissues to Human Heart Biopsies. Front Genet 2021; 12:695625. [PMID: 34211507 PMCID: PMC8239409 DOI: 10.3389/fgene.2021.695625] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/24/2021] [Indexed: 01/17/2023] Open
Abstract
Anthracyclines, including doxorubicin, idarubicin, and epirubicin, are common antitumor drugs as well as well-known cardiotoxic agents. This study analyzed the proteomics alteration in cardiac tissues caused by these 3 anthracyclines analogs. The in vitro human cardiac microtissues were exposed to drugs in 2 weeks; the proteomic data were measured at 7 time points. The heart biopsy data were collected from heart failure patients, in which some patients underwent anthracycline treatment. The anthracyclines-affected proteins were separately identified in the in vitro and in vivo dataset using the WGCNA method. These proteins engage in different cellular pathways including translation, metabolism, mitochondrial function, muscle contraction, and signaling pathways. From proteins detected in 2 datasets, a protein-protein network was established with 4 hub proteins, and 7 weighted proteins from both cardiac microtissue and human biopsies data. These 11 proteins, which involve in mitochondrial functions and the NF-κB signaling pathway, could provide insights into the anthracycline toxic mechanism. Some of them, such as HSPA5, BAG3, and SH3BGRL, are cardiac therapy targets or cardiotoxicity biomarkers. Other proteins, such as ATP5F1B and EEF1D, showed similar responses in both the in vitro and in vivo data. This suggests that the in vitro outcomes could link to clinical phenomena in proteomic analysis.
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Assessing the effects of an acute exposure to worst-case concentration of Cry proteins on zebrafish using the embryotoxicity test and proteomics analysis. CHEMOSPHERE 2021; 264:128538. [PMID: 33038734 DOI: 10.1016/j.chemosphere.2020.128538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/24/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
Cry1C, Cry1F and Cry1Ab are insecticidal proteins from Bacillus thuringiensis (Bt) which are expressed in transgenic crops. Given the entry of these proteins into aquatic environments, it is relevant to evaluate their impacts on aquatic organisms. In this work, we sought to evaluate the effects of Cry1C, Cry1F and Cry1Ab on zebrafish embryos and larvae of a predicted worst-case scenario concentration of these proteins (set to 1.1 mg/L). For that, we coupled a traditional toxicity approach (the zebrafish embryotoxicity test and dosage of enzymatic biomarkers) to gel free proteomics analysis. At the concentration tested, these proteins did not cause adverse effects in the zebrafish early life stages, either by verifying phenotypic endpoints of toxicity or alterations in representative enzymatic biomarkers (catalase, glutathione-S-tranferase and lactate-dehydrogenase). At the molecular level, the Cry proteins tested lead to very small changes in the proteome of zebrafish larvae. In a global way, these proteins upregulated the expression of vitellogenins. Besides that, Cry1C e Cry1F deregulated heterogeneous nuclear ribonucleoproteins (Hnrnpa0l and Hnrnpaba, respectively), implicated in mRNA processing and gene regulation. Overall, these data lead to the conclusion that Cry1C, Cry1F and Cry1Ab proteins, even at a very high concentration, have limited effects in the early stages of zebrafish life.
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An ensemble learning approach for modeling the systems biology of drug-induced injury. Biol Direct 2021; 16:5. [PMID: 33435983 PMCID: PMC7805064 DOI: 10.1186/s13062-020-00288-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 12/09/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Drug-induced liver injury (DILI) is an adverse reaction caused by the intake of drugs of common use that produces liver damage. The impact of DILI is estimated to affect around 20 in 100,000 inhabitants worldwide each year. Despite being one of the main causes of liver failure, the pathophysiology and mechanisms of DILI are poorly understood. In the present study, we developed an ensemble learning approach based on different features (CMap gene expression, chemical structures, drug targets) to predict drugs that might cause DILI and gain a better understanding of the mechanisms linked to the adverse reaction. RESULTS We searched for gene signatures in CMap gene expression data by using two approaches: phenotype-gene associations data from DisGeNET, and a non-parametric test comparing gene expression of DILI-Concern and No-DILI-Concern drugs (as per DILIrank definitions). The average accuracy of the classifiers in both approaches was 69%. We used chemical structures as features, obtaining an accuracy of 65%. The combination of both types of features produced an accuracy around 63%, but improved the independent hold-out test up to 67%. The use of drug-target associations as feature obtained the best accuracy (70%) in the independent hold-out test. CONCLUSIONS When using CMap gene expression data, searching for a specific gene signature among the landmark genes improves the quality of the classifiers, but it is still limited by the intrinsic noise of the dataset. When using chemical structures as a feature, the structural diversity of the known DILI-causing drugs hampers the prediction, which is a similar problem as for the use of gene expression information. The combination of both features did not improve the quality of the classifiers but increased the robustness as shown on independent hold-out tests. The use of drug-target associations as feature improved the prediction, specially the specificity, and the results were comparable to previous research studies.
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COVID-19 Therapies in Brazil: Should We Be Concerned with the Impacts on Aquatic Wildlife? ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2020; 39:2348-2350. [PMID: 33006776 PMCID: PMC7537244 DOI: 10.1002/etc.4888] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 09/27/2020] [Indexed: 05/06/2023]
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Correlation between kidney function and muscle wasting in hospitalized patients. Clin Nutr ESPEN 2020. [DOI: 10.1016/j.clnesp.2020.09.618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Analysis of the small chromosomal Prionium serratum (Cyperid) demonstrates the importance of reliable methods to differentiate between mono- and holocentricity. Chromosoma 2020; 129:285-297. [PMID: 33165742 PMCID: PMC7665975 DOI: 10.1007/s00412-020-00745-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 12/21/2022]
Abstract
For a long time, the Cyperid clade (Thurniceae-Juncaceae-Cyperaceae) was considered a group of species possessing holocentromeres exclusively. The basal phylogenetic position of Prionium serratum (Thunb.) Drège (Thurniceae) within Cyperids makes this species an important specimen to understand the centromere evolution within this clade. In contrast to the expectation, the chromosomal distribution of the centromere-specific histone H3 (CENH3), alpha-tubulin and different centromere-associated post-translational histone modifications (H3S10ph, H3S28ph and H2AT120ph) demonstrate a monocentromeric organisation of P. serratum chromosomes. Analysis of the high-copy repeat composition resulted in the identification of two centromere-localised satellite repeats. Hence, monocentricity was the ancestral condition for the Juncaceae-Cyperaceae-Thurniaceae Cyperid clade, and holocentricity in this clade has independently arisen at least twice after differentiation of the three families, once in Juncaceae and the other one in Cyperaceae. In this context, methods suitable for the identification of holocentromeres are discussed.
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In performance horses undergoing surgical treatment for nonstrangulating large intestinal displacements, will performance be reduced compared to before surgery? EQUINE VET EDUC 2020. [DOI: 10.1111/eve.13378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Drug-induced gene expression profile changes in relation to intestinal toxicity: State-of-the-art and new approaches. Cancer Treat Rev 2019; 77:57-66. [DOI: 10.1016/j.ctrv.2019.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/22/2022]
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Corrigendum to "A sequential analysis of motivational interviewing technical skills and client responses" [Journal of Substance Abuse Treatment 92 (2018 Sep) 27-34]. J Subst Abuse Treat 2019; 98:26-27. [PMID: 30665600 DOI: 10.1016/j.jsat.2018.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury. Front Genet 2018; 9:527. [PMID: 30515189 PMCID: PMC6255978 DOI: 10.3389/fgene.2018.00527] [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: 07/12/2018] [Accepted: 10/19/2018] [Indexed: 12/03/2022] Open
Abstract
In toxicogenomics, functional annotation is an important step to gain additional insights into genes with aberrant expression that drive pathophysiological mechanisms. Nevertheless, there exists a gap on annotation of these genes which often hampers the interpretation of results and limits their applicability in translational medicine. In this study, we evaluated the coverage of functional annotations of differentially expressed genes (DEGs) induced by 10 selected compounds from the TG-GATEs database identified as high- or no-risk in causing drug-induced liver injury (most-DILI or no-DILI, respectively) using in vitro human data. Functional roles of DEGs not present in the most common biological annotation databases – termed “dark genes” – were unveiled via literature mining and via the identification of shared regulatory transcription factors or signaling pathways. Our results demonstrated that there were approximately 13% of dark genes induced by these compounds in vitro and we were able to obtain additional relevant information for up to 76% of those. Using interactome data from several sources, we have uncovered genes such as LRBA, and WDR26 as highly connected in the protein network that play roles in drug response. Genes such as MALAT1, H19, and MIR29C – whose links to hepatotoxicity have been confirmed – were identified as markers for the most-DILI group and appeared as top hits across all literature-based mining methods. Furthermore, we investigated the potential impact of dark genes on liver toxicity by identifying their rat orthologs in combination with their correlation to drug-induced liver pathologies observed in vivo following chemical exposure. We identified a set of important regulatory transcription factors of dark genes for all most-DILI compounds including E2F1 and JUND with supporting evidences in literature and we found Magee1 correlated with chemically induced bile duct hyperplasia and adverse responses at 29 days in rats in vivo. In conclusion, in this study we show the potential role of these poorly annotated genes in mechanisms underlying hepatotoxicity and offer a number of computational approaches that may help to minimize current gaps in gene annotation and highlight their values as potential biomarkers in toxicological studies.
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IL17A polymorphism and elevated IL17A serum levels are associated with oral lichen planus. Oral Dis 2017; 24:377-383. [DOI: 10.1111/odi.12718] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 07/06/2017] [Accepted: 07/10/2017] [Indexed: 12/13/2022]
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Identification of essential transcription factors for adequate DNA damage response after benzo(a)pyrene and aflatoxin B1 exposure by combining transcriptomics with functional genomics. Toxicology 2017; 390:74-82. [PMID: 28882572 DOI: 10.1016/j.tox.2017.09.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/15/2017] [Accepted: 09/01/2017] [Indexed: 01/09/2023]
Abstract
DNA damage mediates widespread changes in transcription through activation or repression of transcription factors (TFs). However, the consequences of regulating specific TFs for the outcome of the DNA repair process remain incompletely understood. Here, we combined transcriptomics and TF binding prediction with functional genomics to identify TFs essential for adequate DNA repair in HepG2 liver cells after a non-cytotoxic dose of carcinogens benzo(a)pyrene (BaP) (2μM) and aflatoxin B1 (AFB1) (5μM). BaP and AFB1 induced a largely common transcriptional response, mediated by similar TFs. A lentiviral shRNA screen knocking down the top31 identified TFs, was performed to determine their effect on DNA repair by assessing phosphorylation of H2AX (γ-H2AX). In addition to the top candidate p53, we identified several other interesting TFs that modulated γ-H2AX after BaP and AFB1 treatment. Validation studies confirmed the role of p53 in reducing γ-H2AX formation and DNA breaks measured by COMET assay after BaP and AFB1 exposure. Expression of the cell cycle inhibitor p21 was profoundly impaired upon p53 knock-down. In addition, the expression of 2 genes involved in nucleotide exchange repair, DDB2 and XPC was significantly reduced in p53 knock-down cells. Although p63 knock-down affected DNA damage upon BaP treatment this was not associated with altered expression of DDB2 or XPC. Finally, knock-down of ARNT reduced γ-H2AX in response to BaP, which was associated with reduced CYP1A1 expression. Importantly, our results suggest a new role for ARNT and its dimerization partner AHR in the occurrence of H2AX phosphorylation after AFB1 treatment. These data show that modulation of TF activity impacts on the repair of BaP- and AFB1-induced DNA damage. Our study also demonstrates the potential of combining functional genomics with genome-wide expression analysis to identify yet unknown causal relationships, thereby aiding in the interpretation of complex biological systems.
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ESTUDO DA ASSOCIAÇÃO ENTRE LÍNGUA GEOGRÁFICA E DOENÇA PSORIÁSICA PELA ANÁLISE DAS FREQUENCIAS DOS GENES HLA E KIR EM UMA POPULAÇÃO MISCIGENADA. REVISTA BRASILEIRA DE REUMATOLOGIA 2017. [DOI: 10.1016/j.rbr.2017.07.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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DTNI: a novel toxicogenomics data analysis tool for identifying the molecular mechanisms underlying the adverse effects of toxic compounds. Arch Toxicol 2016; 91:2343-2352. [PMID: 28032149 PMCID: PMC5429357 DOI: 10.1007/s00204-016-1922-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 12/15/2016] [Indexed: 01/29/2023]
Abstract
Unravelling gene regulatory networks (GRNs) influenced by chemicals is a major challenge in systems toxicology. Because toxicant-induced GRNs evolve over time and dose, the analysis of global gene expression data measured at multiple time points and doses will provide insight in the adverse effects of compounds. Therefore, there is a need for mathematical methods for GRN identification from time-over-dose-dependent data. One of the current approaches for GRN inference is Time Series Network Identification (TSNI). TSNI is based on ordinary differential equations (ODE), describing the time evolution of the expression of each gene, which is assumed to be dependent on the expression of other genes and an external perturbation (i.e. chemical exposure). Here, we present Dose-Time Network Identification (DTNI), a method extending TSNI by including ODE describing how the expression of each gene evolves with dose, which is supposed to depend on the expression of other genes and the exposure time. We also adapted TSNI in order to enable inclusion of time-over-dose-dependent data from multiple compounds. Here, we show that DTNI outperforms TSNI in inferring a toxicant-induced GRN. Moreover, we show that DTNI is a suitable method to infer a GRN dose- and time-dependently induced by a group of compounds influencing a common biological process. Applying DTNI on experimental data from TG-GATEs, we demonstrate that DTNI provides in-depth information on the mode of action of compounds, in particular key events and potential molecular initiating events. Furthermore, DTNI also discloses several unknown interactions which have to be verified experimentally.
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Active syndromic surveillance program of arboviruses in Rio de Janeiro, Brazil. Int J Infect Dis 2016. [DOI: 10.1016/j.ijid.2016.11.345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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New insights into BaP-induced toxicity: role of major metabolites in transcriptomics and contribution to hepatocarcinogenesis. Arch Toxicol 2016; 90:1449-58. [PMID: 26238291 PMCID: PMC4873527 DOI: 10.1007/s00204-015-1572-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 07/20/2015] [Indexed: 12/23/2022]
Abstract
Benzo(a)pyrene (BaP) is a ubiquitous carcinogen resulting from incomplete combustion of organic compounds and also present at high levels in cigarette smoke. A wide range of biological effects has been attributed to BaP and its genotoxic metabolite BPDE, but the contribution to BaP toxicity of intermediary metabolites generated along the detoxification path remains unknown. Here, we report for the first time how 3-OH-BaP, 9,10-diol and BPDE, three major BaP metabolites, temporally relate to BaP-induced transcriptomic alterations in HepG2 cells. Since BaP is also known to induce AhR activation, we additionally evaluated TCDD to source the expression of non-genotoxic AhR-mediated patterns. 9,10-Diol was shown to activate several transcription factor networks related to BaP metabolism (AhR), oxidative stress (Nrf2) and cell proliferation (HIF-1α, AP-1) in particular at early time points, while BPDE influenced expression of genes involved in cell energetics, DNA repair and apoptotic pathways. Also, in order to grasp the role of BaP and its metabolites in chemical hepatocarcinogenesis, we compared expression patterns from BaP(-metabolites) and TCDD to a signature set of approximately nine thousand gene expressions derived from hepatocellular carcinoma (HCC) patients. While transcriptome modulation by TCDD appeared not significantly related to HCC, BaP and BPDE were shown to deregulate metastatic markers via non-genotoxic and genotoxic mechanisms and activate inflammatory pathways (NF-κβ signaling, cytokine-cytokine receptor interaction). BaP also showed strong repression of genes involved in cholesterol and fatty acid biosynthesis. Altogether, this study provides new insights into BaP-induced toxicity and sheds new light onto its mechanism of action as a hepatocarcinogen.
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Poster session 1: Wednesday 3 December 2014, 09:00-16:00 * Location: Poster area. Eur Heart J Cardiovasc Imaging 2014; 15:ii25-ii51. [DOI: 10.1093/ehjci/jeu248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
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Structural and functional analysis of a GH12 from Aspergillus terreus. Acta Crystallogr A 2012. [DOI: 10.1107/s0108767312096572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Structural characterization of trypanosomatids kinases: targets to drug discovery. Acta Crystallogr A 2012. [DOI: 10.1107/s0108767312096985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Lipid content and fatty acid profile of Senegalese sole (Solea senegalensis Kaup, 1858) juveniles as affected by feed containing different amounts of plant protein sources. Food Chem 2012; 134:1337-42. [PMID: 25005951 DOI: 10.1016/j.foodchem.2012.03.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 02/12/2012] [Accepted: 03/07/2012] [Indexed: 10/28/2022]
Abstract
A growth trial with Senegalese Sole (Solea senegalensis Kaup, 1858) juveniles fed with diets containing increasing replacement levels of fishmeal by mixtures of plant protein sources was conducted over 12 weeks. Total fat contents of muscle, liver, viscera, skin, fins and head tissues were determined, as well as fatty acid profiles of muscle and liver (GC-FID analysis). Liver was the preferential local for fat deposition (5.5-10.8% of fat) followed by fins (3.4-6.7% fat). Increasing levels of plant protein in the diets seems to be related to increased levels of total lipids in the liver. Sole muscle is lean (2.4-4.0% fat), with total lipids being similar among treatments. Liver fatty acid profile varied significantly among treatments. Plant protein diets induced increased levels of C16:1 and C18:2 n-6 and a decrease in ARA and EPA levels. Muscle fatty acid profile also evidenced increasing levels of C18:2 n-6, while ARA and DHA remained similar among treatments. Substitution of fishmeal by plant protein is hence possible without major differences on the lipid content and fatty acid profile of the main edible portion of the fish - the muscle.
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Moderated Poster Sessions 5: Cardiovascular remodeling: from bench to bedside * Saturday 10 December 2011, 08:30-12:30 * Location: Moderated Poster Area. EUROPEAN JOURNAL OF ECHOCARDIOGRAPHY 2011. [DOI: 10.1093/ejechocard/jer217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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SP5-31 Food and nutritional insecurity among collectors of recycled material in southern Brazil, 2010. Br J Soc Med 2011. [DOI: 10.1136/jech.2011.142976p.67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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New measurements of rearfoot, forefoot and shank-forefoot alignment in athletes. Br J Sports Med 2011. [DOI: 10.1136/bjsm.2011.084038.94] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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A correlational study of systemic blood pressure and intraocular pressure in a young South African adult population*. AFRICAN VISION AND EYE HEALTH 2009. [DOI: 10.4102/aveh.v68i4.176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Increased blood pressure (BP) and raised intraocular pressure (IOP) are probably both common oc-currences among the South African population. If left untreated both conditions have detrimentalcomplications. Previous cross-sectional studies suggested BP was positively related to IOP. This study therefore sets out to determine in a young South African adult population the correlation between systemic BP and IOP. Systemic BP was measured using an electronic sphygmomanometer and IOP using a Goldman applanation tonometer. For all subjects, two averages were obtained fromthree measurements each of BP and IOP. Other clinical procedures such as uncompensated visual acuity (VA), pinhole and direct ophthalmoscopy were done to exclude underlying factors possiblyaffecting either BP or IOP before the commencement of the investigation. Two hundred (N = 200)subjects were included in the study and their ages ranged from 18 to 30 years with a mean of 21 ± 3.9 years. The correlation coefficients between average IOP and average systolic or diastolic BP respectively were 0.67 and 0.55. These weak positivecorrelations suggested that with an increase in BP there is a corresponding increase in IOP. Also, similar correlation between IOP and BP was found toexist amongst both males and females with systolic BP having a greater effect. This study validates theimportance of evaluating either systemic BP or IOP amongst all patients seen by primary eye-care practitioners, and that such evaluations should form part of daily routine patient examination.
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Epidemiological analysis of patients with cerebral aneurysm submitted for an embolization at São José do Avaí Hospital. Crit Care 2009. [PMCID: PMC4083983 DOI: 10.1186/cc7261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Endoscopic ultrasound-guided ureterosigmoidostomy in malignant ureteral obstruction: description of a new method. Endoscopy 2008; 40:769-72. [PMID: 18668473 DOI: 10.1055/s-2008-1077447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
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[The role of the human histocompatibility antigens in the pathogenesis of neurological disorders]. Rev Neurol 2007; 44:298-302. [PMID: 17342681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
INTRODUCTION Several studies have been trying to define genetic markers of neurological disorders. Among them, antigens and alleles of the HLA (human leukocyte antigens) system are distinguished. The HLA exerts genetic influence on the susceptibility, clinical aspects and severity of many diseases. The discovery of new molecular methods to typify HLA alleles and the recent nomenclature updates have been contributing to a better understanding of this system. Unfortunately, this information has not been adequately published in the clinical literature. AIM To review the structure, function, nomenclature and methods of detection of the HLA polymorphism and its associations with common neurological disorders. DEVELOPMENT Articles that were published between 1990 and 2004 were searched in the MEDLINE and LILACS databases. This review demonstrated that although the HLA association is well established for some neurological disorders (e.g., HLA-DQB1*0602 with multiple sclerosis and narcolepsy; HLA-B7 e HLA-A2 with Alzheimer's disease; HLA-DR3-DR8 with Lamber-Eaton syndrome; and HLA class II Parkinson's disease and amyotrophic lateral sclerosis), these associations are not consistent and vary in different ethnic groups. CONCLUSIONS It is necessary to study populations from different ethnic backgrounds to identify new associations or to strength the ones already identified. This knowledge will contribute in the evaluation of the risk that a person carrying a particular allele or haplotype has to develop a neurological disease and therefore contribute towards a better understanding of its pathogenesis.
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P.502 Very low prevalence of hepatitis C and B virus infection in patients with idiopathic dilated cardiomyopathy in Brazil: a pilot study. J Clin Virol 2006. [DOI: 10.1016/s1386-6532(06)80675-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Human brain activation accompanying explicitly directed movement sequence learning. Exp Brain Res 2001; 141:269-80. [PMID: 11715072 DOI: 10.1007/s002210100822] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2001] [Accepted: 05/25/2001] [Indexed: 10/27/2022]
Abstract
We examined brain activation patterns occurring during the production and encoding of a motor sequence. Participants performed a variant of the serial reaction-time task under two conditions. The first condition was designed to foster the engagement of explicit mechanisms of knowledge acquisition. The second condition was intended to encourage the engagement of implicit learning mechanisms that would be more typical of the standard serial reaction-time task. In the first condition, the acquisition of explicit knowledge about an 8-element ordered sequence led to a significant and rapid decline in reaction time. By contrast, the second condition, the task in which a sequence was presented unbeknownst to participants, did not yield changes in reaction time. Several brain regions, including prefrontal cortex, superior and inferior parietal lobules, and cerebellum, exhibited explicit learning-related activation. The prefrontal cortex and inferior parietal lobules increased their levels of activation between the beginning and end of the experiment, while primary motor, primary sensory, and cerebellar cortex decreased their levels of activation from the beginning to the end of the experiment. We propose a model in which two processes, a learning-related increase and a habituation process might interact to produce the activation patterns observed during movement sequence acquisition. In short, the prefrontal cortex and inferior parietal lobule together direct and recruit superior parietal lobule and cerebellum to encode and perform the sequence. The increased activation in prefrontal cortex and inferior parietal lobule may represent the activity of a working memory circuit that functions in the acquisition and recall of sequence information.
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Testing problems in diagnosing HTLV infection among intravenous drug users with AIDS in São Paulo City, Brazil. AIDS Res Hum Retroviruses 1997; 13:1639-41. [PMID: 9430256 DOI: 10.1089/aid.1997.13.1639] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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