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Mastrolorito F, Togo MV, Gambacorta N, Trisciuzzi D, Giannuzzi V, Bonifazi F, Liantonio A, Imbrici P, De Luca A, Altomare CD, Ciriaco F, Amoroso N, Nicolotti O. TISBE: A Public Web Platform for the Consensus-Based Explainable Prediction of Developmental Toxicity. Chem Res Toxicol 2024; 37:323-339. [PMID: 38200616 DOI: 10.1021/acs.chemrestox.3c00310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Despite being extremely relevant for the protection of prenatal and neonatal health, the developmental toxicity (Dev Tox) is a highly complex endpoint whose molecular rationale is still largely unknown. The lack of availability of high-quality data as well as robust nontesting methods makes its understanding even more difficult. Thus, the application of new explainable alternative methods is of utmost importance, with Dev Tox being one of the most animal-intensive research themes of regulatory toxicology. Descending from TIRESIA (Toxicology Intelligence and Regulatory Evaluations for Scientific and Industry Applications), the present work describes TISBE (TIRESIA Improved on Structure-Based Explainability), a new public web platform implementing four fundamental advancements for in silico analyses: a three times larger dataset, a transparent XAI (explainable artificial intelligence) framework employing a fragment-based fingerprint coding, a novel consensus classifier based on five independent machine learning models, and a new applicability domain (AD) method based on a double top-down approach for better estimating the prediction reliability. The training set (TS) includes as many as 1008 chemicals annotated with experimental toxicity values. Based on a 5-fold cross-validation, a median value of 0.410 for the Matthews correlation coefficient was calculated; TISBE was very effective, with a median value of sensitivity and specificity equal to 0.984 and 0.274, respectively. TISBE was applied on two external pools made of 1484 bioactive compounds and 85 pediatric drugs taken from ChEMBL (Chemical European Molecular Biology Laboratory) and TEDDY (Task-Force in Europe for Drug Development in the Young) repositories, respectively. Notably, TISBE gives users the option to clearly spot the molecular fragments responsible for the toxicity or the safety of a given chemical query and is available for free at https://prometheus.farmacia.uniba.it/tisbe.
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Affiliation(s)
- Fabrizio Mastrolorito
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Maria Vittoria Togo
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Nicola Gambacorta
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Daniela Trisciuzzi
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Viviana Giannuzzi
- Fondazione per la Ricerca Farmacologica Gianni Benzi Onlus, 70010 Valenzano (BA), Italy
| | - Fedele Bonifazi
- Fondazione per la Ricerca Farmacologica Gianni Benzi Onlus, 70010 Valenzano (BA), Italy
| | - Antonella Liantonio
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Paola Imbrici
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Annamaria De Luca
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Cosimo Damiano Altomare
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Fulvio Ciriaco
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Nicola Amoroso
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, 70125 Bari, Italy
| | - Orazio Nicolotti
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
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Shi M, Pei H, Sun L, Chen W, Zong Y, Zhao Y, Du R, He Z. Optimization of the Flavonoid Extraction Process from the Stem and Leaves of Epimedium Brevicornum and Its Effects on Cyclophosphamide-Induced Renal Injury. Molecules 2023; 29:207. [PMID: 38202790 PMCID: PMC10780727 DOI: 10.3390/molecules29010207] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/09/2023] [Accepted: 11/27/2023] [Indexed: 01/12/2024] Open
Abstract
Cyclophosphamide (CTX) is a broad-spectrum alkylated antitumor drug. It is clinically used in the treatment of a variety of cancers, and renal toxicity is one of the adverse reactions after long-term or repeated use, which not only limits the therapeutic effect of CTX, but also increases the probability of kidney lesions. The total flavonoids of Epimedium stem and leaf (EBF) and Icariin (ICA) are the main medicinal components of Epimedium, and ICA is one of the main active substances in EBF. Modern pharmacological studies have shown that EBF has a variety of biological activities such as improving osteoporosis, promoting cell proliferation, antioxidant and anti-inflammatory properties, etc. However, few studies have been conducted on the nephrotoxicity caused by optimized CTX extraction, and protein-ligand binding has not been involved. This research, through the response surface optimization extraction of EBF, obtained the best extraction conditions: ethanol concentration was 60%, solid-liquid ratio of 25:1, ultrasonic time was about 25 min. Combined with mass spectrometry (MS) analysis, EBF contained ICA, ichopidin A, ichopidin B, ichopidin C, and other components. In this study, we adopted a computational chemistry method called molecular docking, and the results show that Icariin was well bound to the antioxidant target proteins KEAP1 and NRF2, and the anti-inflammatory target proteins COX-2 and NF-κB, with free binding energies of -9.8 kcal/mol, -11.0 kcal/mol, -10.0 kcal/mol, and -8.1 kcal/mol, respectively. To study the protective effect of EBF on the nephrotoxicity of CTX, 40 male Kunming mice (weight 18 ± 22) were injected with CTX (80 mg/kg) for 7 days to establish the nephrotoxicity model and were treated with EBF (50 mg/kg, 100 mg/kg) for 8 days by gavage. After CTX administration, MDA, BUN, Cre, and IL-6 levels in serum increased, MDA increased in kidney, GPT/ALT and IL-6 increased in liver, and IL-6 increased in spleen and was significant ((p < 0.05 or (p < 0.01)). Histopathological observation showed that renal cortex glomerular atrophy necrosis, medullary inflammatory cell infiltration, and other lesions. After administration of EBF, CTX-induced increase in serum level of related indexes was reduced, and MDA in kidney, GPT/ALT and IL-6 in liver, and IL-6 in spleen were increased. At the same time, histopathological findings showed that the necrosis of medullary and corticorenal tubular epithelium was relieved at EBF (50 mg/kg) dose compared with the CTX group, and the glomerular tubular necrosis gradually became normal at EBF (100 mg/kg) dose. Western blot analysis of Keap1 and Nrf2 protein expression in kidney tissue showed that compared with model CTX group, the drug administration group could alleviate the high expression of Keap1 protein and low expression of Nrf2 protein in kidney tissue. Conclusion: After the optimal extraction of total flavonoids from the stems and leaves of Epimedium, the molecular docking technique combined with animal experiments suggested that the effective component of the total flavonoids of Epimedium might activate the Keap1-Nrf2 signaling pathway after treatment to reduce the inflammation and oxidative stress of kidney tissue, so as to reduce kidney damage and improve kidney function. Therefore, EBF may become a new natural protective agent for CTX chemotherapy in the future.
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Affiliation(s)
- Meiling Shi
- College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun 130118, China; (M.S.); (H.P.); (L.S.); (W.C.); (Y.Z.); (Y.Z.); (R.D.)
| | - Hongyan Pei
- College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun 130118, China; (M.S.); (H.P.); (L.S.); (W.C.); (Y.Z.); (Y.Z.); (R.D.)
| | - Li Sun
- College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun 130118, China; (M.S.); (H.P.); (L.S.); (W.C.); (Y.Z.); (Y.Z.); (R.D.)
| | - Weijia Chen
- College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun 130118, China; (M.S.); (H.P.); (L.S.); (W.C.); (Y.Z.); (Y.Z.); (R.D.)
| | - Ying Zong
- College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun 130118, China; (M.S.); (H.P.); (L.S.); (W.C.); (Y.Z.); (Y.Z.); (R.D.)
| | - Yan Zhao
- College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun 130118, China; (M.S.); (H.P.); (L.S.); (W.C.); (Y.Z.); (Y.Z.); (R.D.)
- Engineering Research Center for Efficient Breeding and Product Development of Sika Deer, Changchun 130118, China
| | - Rui Du
- College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun 130118, China; (M.S.); (H.P.); (L.S.); (W.C.); (Y.Z.); (Y.Z.); (R.D.)
- Engineering Research Center for Efficient Breeding and Product Development of Sika Deer, Changchun 130118, China
| | - Zhongmei He
- College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun 130118, China; (M.S.); (H.P.); (L.S.); (W.C.); (Y.Z.); (Y.Z.); (R.D.)
- Engineering Research Center for Efficient Breeding and Product Development of Sika Deer, Changchun 130118, China
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Shi J, Zhao J, Zhang Y, Wang Y, Tan CP, Xu YJ, Liu Y. Windows Scanning Multiomics: Integrated Metabolomics and Proteomics. Anal Chem 2023; 95:18793-18802. [PMID: 38095040 DOI: 10.1021/acs.analchem.3c03785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Metabolomics and proteomics offer significant advantages in understanding biological mechanisms at two hierarchical levels. However, conventional single omics analysis faces challenges due to the high demand for specimens and the complexity of intrinsic associations. To obtain comprehensive and accurate system biological information, we developed a multiomics analytical method called Windows Scanning Multiomics (WSM). In this method, we performed simultaneous extraction of metabolites and proteins from the same sample, resulting in a 10% increase in the coverage of the identified biomolecules. Both metabolomics and proteomics analyses were conducted by using ultrahigh-performance liquid chromatography mass spectrometry (UPLC-MS), eliminating the need for instrument conversions. Additionally, we designed an R-based program (WSM.R) to integrate mathematical and biological correlations between metabolites and proteins into a correlation network. The network created from simultaneously extracted biomolecules was more focused and comprehensive compared to those from separate extractions. Notably, we excluded six pairs of false-positive relationships between metabolites and proteins in the network established using simultaneously extracted biomolecules. In conclusion, this study introduces a novel approach for multiomics analysis and data processing that greatly aids in bioinformation mining from multiomics results. This method is poised to play an indispensable role in systems biology research.
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Affiliation(s)
- Jiachen Shi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Jialiang Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Yu Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Yanan Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Chin Ping Tan
- Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
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Grzeszczak K, Łanocha-Arendarczyk N, Malinowski W, Ziętek P, Kosik-Bogacka D. Oxidative Stress in Pregnancy. Biomolecules 2023; 13:1768. [PMID: 38136639 PMCID: PMC10741771 DOI: 10.3390/biom13121768] [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] [Received: 10/23/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Recent years have seen an increased interest in the role of oxidative stress (OS) in pregnancy. Pregnancy inherently heightens susceptibility to OS, a condition fueled by a systemic inflammatory response that culminates in an elevated presence of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in the circulatory system. The amplified OS in pregnancy can trigger a series of detrimental outcomes such as underdevelopment, abnormal placental function, and a host of pregnancy complications, including pre-eclampsia, embryonic resorption, recurrent pregnancy loss, fetal developmental anomalies, intrauterine growth restriction, and, in extreme instances, fetal death. The body's response to mitigate the uncontrolled increase in RNS/ROS levels requires trace elements that take part in non-enzymatic and enzymatic defense processes, namely, copper (Cu), zinc (Zn), manganese (Mn), and selenium (Se). Determination of ROS concentrations poses a challenge due to their short half-lives, prompting the use of marker proteins, including malondialdehyde (MDA), superoxide dismutase (SOD), glutathione peroxidase (GPx), glutathione reductase (GR), catalase (CAT), and glutathione (GSH). These markers, indicative of oxidative stress intensity, can offer indirect assessments of pregnancy complications. Given the limitations of conducting experimental studies on pregnant women, animal models serve as valuable substitutes for in-depth research. This review of such models delves into the mechanism of OS in pregnancy and underscores the pivotal role of OS markers in their evaluation.
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Affiliation(s)
- Konrad Grzeszczak
- Department of Biology and Medical Parasitology, Pomeranian Medical University in Szczecin, Powstanców Wielkopolskich 72, 70-111 Szczecin, Poland; (K.G.); (N.Ł.-A.)
- Department of Laboratory Diagnostics, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Natalia Łanocha-Arendarczyk
- Department of Biology and Medical Parasitology, Pomeranian Medical University in Szczecin, Powstanców Wielkopolskich 72, 70-111 Szczecin, Poland; (K.G.); (N.Ł.-A.)
| | - Witold Malinowski
- Faculty of Health Sciences, The Masovian. Public University in Płock, Plac Dąbrowskiego 2, 09-402 Płock, Poland;
| | - Paweł Ziętek
- Department of Orthopaedics, Traumatology and Orthopaedic Oncology, Pomeranian Medical University, Unii Lubelskiej 1, 71-252 Szczecin, Poland;
| | - Danuta Kosik-Bogacka
- Independent Laboratory of Pharmaceutical Botany, Department of Biology and Medical Parasitology, Pomeranian Medical University in Szczecin, Powstanców Wielkopolskich 72, 70-111 Szczecin, Poland
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Santorelli L, Caterino M, Costanzo M. Proteomics and Metabolomics in Biomedicine. Int J Mol Sci 2023; 24:16913. [PMID: 38069240 PMCID: PMC10706996 DOI: 10.3390/ijms242316913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
The technological advances of recent years have significantly enhanced medical discoveries [...].
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Affiliation(s)
- Lucia Santorelli
- Department of Oncology and Hematology-Oncology, University of Milano, 20122 Milan, Italy;
| | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy;
- CEINGE–Biotecnologie Avanzate Franco Salvatore, 80145 Naples, Italy
| | - Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy;
- CEINGE–Biotecnologie Avanzate Franco Salvatore, 80145 Naples, Italy
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Ortiz-García RG, Gómez-Meda BC, Gutiérrez-Sevilla JE, Gallegos-Arreola MP, Zamora-Perez AL, Ortiz-García YM, García-Arias VE, Torres-Mendoza BM, Zúñiga-González GM. Micronuclei and nuclear buds in amniotic tissue of rats treated with cyclophosphamide. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2023; 890:503659. [PMID: 37567649 DOI: 10.1016/j.mrgentox.2023.503659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 06/27/2023] [Accepted: 07/11/2023] [Indexed: 08/13/2023]
Abstract
Fetal development can be altered by DNA damage caused by maternal exposure to chemical, physical, or biological agents during gestation. One method of assessing genotoxicity is to detect micronuclei (MNs) and/or nuclear abnormalities. This can be performed in vivo and requires only frequently dividing tissues, such as amniotic tissue (AT), which is in contact with the fetal environment and is composed of very thin layers of cells. This study evaluated the presence of MNs, nucleoplasmic bridges, and nuclear buds (NBs) in the fetal AT following maternal exposure to cyclophosphamide (CP) during pregnancy. Pregnant Wistar rats were divided into a negative control group and an experimental group that was orally administered CP (10 mg/kg). Daily blood smears were obtained from pregnant rats on days 14-19 of gestation. The rats were dissected, and fetal ATs were obtained on the 19th day of gestation. The MN and NB frequencies in AT cells were analyzed using a fluorescence microscope (100 ×). Micronucleated erythrocytes in the peripheral blood of the control rats were also assessed. Micronucleated polychromatic erythrocyte frequencies were significantly higher than those in the controls. Polychromatic erythrocyte frequencies were lower in CP-treated rats than in controls at 48-120 h. Fetuses in the CP-treated group also showed a significant increase in MNs and NBs in AT cells. In conclusion, AT could be used for analyzing MNs and NBs in rats following maternal exposure to a genotoxic agent and as a viable alternative for analyzing the integrity of fetal DNA during gestation.
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Affiliation(s)
- Ramón Guillermo Ortiz-García
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico; Laboratorio de Mutagénesis, División de Medicina Molecular, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, Mexico
| | - Belinda Claudia Gómez-Meda
- Instituto de Genética Humana "Dr. Enrique Corona Rivera", Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Juan Ernesto Gutiérrez-Sevilla
- Laboratorio de Inmunodeficiencias y retrovirus humanos, División de Neurociencias, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, Mexico; Departamento de Clínicas Medicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Martha Patricia Gallegos-Arreola
- Laboratorio de Genética Molecular, División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, Mexico
| | - Ana Lourdes Zamora-Perez
- Instituto de Investigación en Odontología, Departamento de Clínicas Odontológicas Integrales, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Yveth Marlene Ortiz-García
- Instituto de Investigación en Odontología, Departamento de Clínicas Odontológicas Integrales, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico; Laboratorio de Apoyo a la Vigilancia e Investigación Epidemiológica, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, Mexico
| | - Víctor Eduardo García-Arias
- Laboratorio de Mutagénesis, División de Medicina Molecular, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, Mexico
| | - Blanca Miriam Torres-Mendoza
- Laboratorio de Inmunodeficiencias y retrovirus humanos, División de Neurociencias, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, Mexico; Departamento de Clínicas Medicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Guillermo Moisés Zúñiga-González
- Laboratorio de Mutagénesis, División de Medicina Molecular, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, Mexico.
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