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Saarimäki LA, del Giudice G, Greco D. Expanding adverse outcome pathways towards one health models for nanosafety. Front Toxicol 2023; 5:1176745. [PMID: 37692900 PMCID: PMC10485555 DOI: 10.3389/ftox.2023.1176745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/15/2023] [Indexed: 09/12/2023] Open
Abstract
The ever-growing production of nano-enabled products has generated the need for dedicated risk assessment strategies that ensure safety for humans and the environment. Transdisciplinary approaches are needed to support the development of new technologies while respecting environmental limits, as also highlighted by the EU Green Deal Chemicals Strategy for Sustainability and its safe and sustainable by design (SSbD) framework. The One Health concept offers a holistic multiscale approach for the assessment of nanosafety. However, toxicology is not yet capable of explaining the interaction between chemicals and biological systems at the multiscale level and in the context of the One Health framework. Furthermore, there is a disconnect between chemical safety assessment, epidemiology, and other fields of biology that, if unified, would enable the adoption of the One Health model. The development of mechanistic toxicology and the generation of omics data has provided important biological knowledge of the response of individual biological systems to nanomaterials (NMs). On the other hand, epigenetic data have the potential to inform on interspecies mechanisms of adaptation. These data types, however, need to be linked to concepts that support their intuitive interpretation. Adverse Outcome Pathways (AOPs) represent an evolving framework to anchor existing knowledge to chemical risk assessment. In this perspective, we discuss the possibility of integrating multi-level toxicogenomics data, including toxicoepigenetic insights, into the AOP framework. We anticipate that this new direction of toxicogenomics can support the development of One Health models applicable to groups of chemicals and to multiple species in the tree of life.
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Affiliation(s)
- Laura Aliisa Saarimäki
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Giusy del Giudice
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Dario Greco
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Stein RA, Riber L. Epigenetic effects of short-chain fatty acids from the large intestine on host cells. Microlife 2023; 4:uqad032. [PMID: 37441522 PMCID: PMC10335734 DOI: 10.1093/femsml/uqad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/04/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023]
Abstract
Adult humans harbor at least as many microbial cells as eukaryotic ones. The largest compartment of this diverse microbial population, the gut microbiota, encompasses the collection of bacteria, archaea, viruses, and eukaryotic organisms that populate the gastrointestinal tract, and represents a complex and dynamic ecosystem that has been increasingly implicated in health and disease. The gut microbiota carries ∼100-to-150-times more genes than the human genome and is intimately involved in development, homeostasis, and disease. Of the several microbial metabolites that have been studied, short-chain fatty acids emerge as a group of molecules that shape gene expression in several types of eukaryotic cells by multiple mechanisms, which include DNA methylation changes, histone post-translational modifications, and microRNA-mediated gene silencing. Butyric acid, one of the most extensively studied short-chain fatty acids, reaches higher concentrations in the colonic lumen, where it provides a source of energy for healthy colonocytes, and its concentrations decrease towards the bottom of the colonic crypts, where stem cells reside. The lower butyric acid concentration in the colonic crypts allows undifferentiated cells, such as stem cells, to progress through the cell cycle, pointing towards the importance of the crypts in providing them with a protective niche. In cancerous colonocytes, which metabolize relatively little butyric acid and mostly rely on glycolysis, butyric acid preferentially acts as a histone deacetylase inhibitor, leading to decreased cell proliferation and increased apoptosis. A better understanding of the interface between the gut microbiota metabolites and epigenetic changes in eukaryotic cells promises to unravel in more detail processes that occur physiologically and as part of disease, help develop novel biomarkers, and identify new therapeutic modalities.
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Affiliation(s)
- Richard A Stein
- Corresponding author. Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA. Tel: +1-917-684-9438; E-mail: ;
| | - Leise Riber
- Department of Plant & Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
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Munnia A, Bollati V, Russo V, Ferrari L, Ceppi M, Bruzzone M, Dugheri S, Arcangeli G, Merlo F, Peluso M. Traffic-Related Air Pollution and Ground-Level Ozone Associated Global DNA Hypomethylation and Bulky DNA Adduct Formation. Int J Mol Sci 2023; 24:ijms24032041. [PMID: 36768368 PMCID: PMC9916664 DOI: 10.3390/ijms24032041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/09/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
Studies have indicated that air pollution, including surface-level ozone (O3), can significantly influence the risk of chronic diseases. To better understand the carcinogenic mechanisms of air pollutants and identify predictive disease biomarkers, we examined the association between traffic-related pollutants with DNA methylation alterations and bulky DNA adducts, two biomarkers of carcinogen exposure and cancer risk, in the peripheral blood of 140 volunteers-95 traffic police officers, and 45 unexposed subjects. The DNA methylation and adduct measurements were performed by bisulfite-PCR and pyrosequencing and 32P-postlabeling assay. Airborne levels of benzo(a)pyrene [B(a)P], carbon monoxide, and tropospheric O3 were determined by personal exposure biomonitoring or by fixed monitoring stations. Overall, air pollution exposure was associated with a significant reduction (1.41 units) in global DNA methylation (95% C.I. -2.65-0.04, p = 0.026). The decrement in ALU repetitive elements was greatest in the policemen working downtown (95% C.I. -3.23--0.49, p = 0.008). The DNA adducts were found to be significantly increased (0.45 units) in the municipal officers with respect to unexposed subjects (95% C.I. 0.02-0.88, p = 0.039), mainly in those who were controlling traffic in downtown areas (95% C.I. 0.39-1.29, p < 0.001). Regression models indicated an increment of ALU methylation at higher B(a)P concentrations (95% C.I. 0.03-0.60, p = 0.032). Moreover, statistical models showed a decrement in ALU methylation and an increment of DNA damage only above the cut-off value of 30 µg/m3 O3. A significant increment of 0.73 units of IL-6 gene methylation was also found in smokers with respect to non-smokers. Our results highlighted the role of air pollution on epigenetic alterations and genotoxic effects, especially above the target value of 30 µg/m3 surface-level O3, supporting the necessity for developing public health strategies aimed to reduce traffic-related air pollution molecular alterations.
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Affiliation(s)
- Armelle Munnia
- Research Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy
| | - Valentina Bollati
- EPIGET Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, 20122 Milan, Italy
- Occupational Health Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Valentina Russo
- Research Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy
| | - Luca Ferrari
- EPIGET Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, 20122 Milan, Italy
- Occupational Health Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Marcello Ceppi
- Clinical Epidemiology Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Marco Bruzzone
- Clinical Epidemiology Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Stefano Dugheri
- Laboratorio di Igiene e Tossicologia Industriale, Azienda Ospedaliero-Universitaria Careggi, 50134 Florence, Italy
| | - Giulio Arcangeli
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi di Firenze, 50121 Florence, Italy
| | - Franco Merlo
- Research and Statistics Infrastructure, Azienda Unità Sanitaria Locale, IRCCS, 42121 Reggio Emilie, Italy
| | - Marco Peluso
- Research Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy
- Correspondence:
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Rietze AH, Conley YP, Ren D, Anderson CM, Roberts JM, Jeyabalan A, Hubel CA, Schmella MJ. DNA Methylation of Endoglin Pathway Genes in Pregnant Women With and Without Preeclampsia. Epigenet Insights 2020; 13:2516865720959682. [PMID: 33103056 PMCID: PMC7550939 DOI: 10.1177/2516865720959682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 08/25/2020] [Indexed: 11/15/2022] Open
Abstract
Objective We compared blood-based DNA methylation levels of endoglin (ENG) and transforming growth factor beta receptor 2 (TGFβR2) gene promoter regions between women with clinically-overt preeclampsia and women with uncomplicated, normotensive pregnancies. Methods We used EpiTect Methyl II PCR Assays to evaluate DNA methylation of CpG islands located in promoter regions of ENG (CpG Island 114642) and TGFβR2 (CpG Island 110111). Preeclampsia was diagnosed based on blood pressure, protein, and uric acid criteria. N = 21 nulliparous preeclampsia case participants were 1:1 frequency matched to N = 21 nulliparous normotensive control participants on gestational age at sample collection (±2 weeks), smoking status, and labor status at sample collection. Methylation values were compared between case and control participant groups [(ENG subset: n = 20 (9 cases, 11 controls); TGFβR2 subset: n = 28 (15 cases, 13 controls)]. Results The majority of the preeclampsia cases delivered at ⩾34 weeks' gestation (83%). Average methylation levels for ENG ([M ± (SD)]; Case Participant Group = 6.54% ± 4.57 versus Control Participant group = 4.81% ± 5.08; P = .102) and TGFβR2 (Case Participant Group = 1.50% ± 1.37 vs Control Participant Group = 1.70% ± 1.40; P = .695) promoter CpG islands did not differ significantly between the participant groups. Removal of 2 extreme outliers in the ENG analytic subset revealed a trend between levels of ENG methylation and pregnancy outcome (Case Participant Group = 5.17% ± 2.16 vs Control Participant Group = 3.36% ± 1.73; P = .062). Conclusion Additional epigenetic studies that include larger sample sizes, investigate preeclampsia subtypes, and capture methylation status of CpG island shores and shelves are needed to further inform us of the potential role that ENG and TGFβR2 DNA methylation plays in preeclampsia pathophysiology.
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Affiliation(s)
- Allison H Rietze
- Department of Health Promotion and Development (School of Nursing), University of Pittsburgh, Pittsburgh, PA, USA
| | - Yvette P Conley
- Department of Health Promotion and Development (School of Nursing), University of Pittsburgh, Pittsburgh, PA, USA.,Department of Human Genetics (Graduate School of Public Health), University of Pittsburgh, Pittsburgh, PA, USA
| | - Dianxu Ren
- Department of Health and Community Systems (School of Nursing), University of Pittsburgh, Pittsburgh, PA, USA
| | - Cindy M Anderson
- Martha S Pitzer Center for Women, Children, and Youth (College of Nursing), The Ohio State University, Columbus, OH, USA
| | - James M Roberts
- Department of Obstetrics, Gynecology, & Reproductive Sciences (School of Medicine), University of Pittsburgh, PA, USA.,Magee-Womens Research Institute, Pittsburgh, PA, USA.,Department of Epidemiology (Graduate School of Public Health), University of Pittsburgh, Pittsburgh, PA, USA.,Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Arun Jeyabalan
- Department of Obstetrics, Gynecology, & Reproductive Sciences (School of Medicine), University of Pittsburgh, PA, USA.,Magee-Womens Research Institute, Pittsburgh, PA, USA.,Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carl A Hubel
- Department of Obstetrics, Gynecology, & Reproductive Sciences (School of Medicine), University of Pittsburgh, PA, USA.,Magee-Womens Research Institute, Pittsburgh, PA, USA
| | - Mandy J Schmella
- Department of Health Promotion and Development (School of Nursing), University of Pittsburgh, Pittsburgh, PA, USA
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Wagner MA, Erickson KI, Bender CM, Conley YP. The Influence of Physical Activity and Epigenomics On Cognitive Function and Brain Health in Breast Cancer. Front Aging Neurosci 2020; 12:123. [PMID: 32457596 PMCID: PMC7225270 DOI: 10.3389/fnagi.2020.00123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/14/2020] [Indexed: 12/17/2022] Open
Abstract
The risk of breast cancer increases with age, with the majority of women diagnosed with breast cancer being postmenopausal. It has been estimated that 25-75% of women with breast cancer experience changes in cognitive function (CF) related to disease and treatment, which compromises psychological well-being, decision making, ability to perform daily activities, and adherence to cancer therapy. Unfortunately, the mechanisms that underlie neurocognitive changes in women with breast cancer remain poorly understood, which in turn limits the development of effective treatments and prevention strategies. Exercise has great potential as a non-pharmaceutical intervention to mitigate the decline in CF in women with breast cancer. Evidence suggests that DNA methylation, an epigenetic mechanism for gene regulation, impacts CF and brain health (BH), that exercise influences DNA methylation, and that exercise impacts CF and BH. Although investigating DNA methylation has the potential to uncover the biologic foundations for understanding neurocognitive changes within the context of breast cancer and its treatment as well as the ability to understand how exercise mitigates these changes, there is a dearth of research on this topic. The purpose of this review article is to compile the research in these areas and to recommend potential areas of opportunity for investigation.
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Affiliation(s)
- Monica A. Wagner
- School of Nursing, University of Pittsburgh, Pittsburgh, PA, United States
| | - Kirk I. Erickson
- Department of Psychology, University of Pittsburgh, Pittsburgh, PA, United States
- Discipline of Exercise Science, College of Science, Health, Engineering and Education, Murdoch University, Perth Campus, Murdoch, WA, Australia
| | | | - Yvette P. Conley
- School of Nursing, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, United States
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Abstract
Nurse scientists are ideally positioned to perform environmental health research and it is critical that the role of omics in the complex relationships between environmental exposures and an individual's unique physiology in human health outcomes be appreciated. Importantly, omics can offer nurse scientists a tool to measure exposure, demonstrate molecular phenotypic changes associated with exposure, and potentially uncover mechanisms of exposure-related disease or negative health outcomes. The purpose of this summary is to serve as an overview of omics methodologies for nurse scientists conducting environmental health research and provides future directions of this work as well as exemplar funding opportunities that demonstrate the growing need and interest in this area. The intersection of nursing and exposure science will accelerate the work in environmental health and bring forth translation of research findings into clinical and community practice. Importantly, this information can better help us understand the variation in response to the environment and support environmental health policy change at the local, state, and federal level to improve community health and well-being.
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Taylor JY, Ware EB, Wright ML, Smith JA, Kardia SLR. Using Genetic Burden Scores for Gene-by-Methylation Interaction Analysis on Metabolic Syndrome in African Americans. Biol Res Nurs 2019; 21:279-285. [PMID: 30781968 PMCID: PMC6700897 DOI: 10.1177/1099800419828486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
With the rapid advancement of omics-based research, particularly big data such as genome- and epigenome-wide association studies that include extensive environmental and clinical variables, data analytics have become increasingly complex. Researchers face significant challenges regarding how to analyze multifactorial data and make use of the findings for clinical translation. The purpose of this article is to provide a scientific exemplar for use of genetic burden scores as a data analysis method for studies with both genotype and DNA methylation data in which the goal is to evaluate associations with chronic conditions such as metabolic syndrome (MetS). This study included 739 African American men and women from the Genetic Epidemiology Network of Arteriopathy Study who met diagnostic criteria for MetS and had available genetic and epigenetic data. Genetic burden scores for evaluated genes were not significant after multiple testing corrections, but DNA methylation at 2 CpG sites (dihydroorotate dehydrogenase cg22381196 pFDR = .014; CTNNA3 cg00132141 pFDR = .043) was significantly associated with MetS after controlling for multiple comparisons. Interactions between the marginally significant CpG sites and burden scores, however, were not significant. More work is required in this area to identify intermediate biological pathways influenced by environmental, genetic, and epigenetic variation that may explain the high prevalence of MetS among African Americans. This study does serve, however, as an example of the use of the genetic burden score as an alternative data analysis approach for complex studies involving the analysis of genetic and epigenetic data simultaneously.
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Affiliation(s)
| | - Erin B. Ware
- Institute for Social Research, University of Michigan, Ann Arbor, MI,
USA
| | | | - Jennifer A. Smith
- School of Public Health and Institute for Social Research, University of
Michigan, Ann Arbor, MI, USA
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Rosa R, Cristoferi L, Tanaka A, Invernizzi P. Geoepidemiology and (epi-)genetics in primary biliary cholangitis. Best Pract Res Clin Gastroenterol 2018; 34-35:11-5. [PMID: 30343705 DOI: 10.1016/j.bpg.2018.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/14/2018] [Indexed: 01/31/2023]
Abstract
Primary biliary cholangitis (PBC) is a rare female preponderant chronic autoimmune cholestatic liver disease, characterized by intrahepatic ductopenia and progressive fibrosis. During last decades incidence and prevalence showed an increasing rate which vary widely worldwide demonstrating an important interaction between environmental and genetic factors. Heritability suggested by familial occurrence and monozygotic twins concordance have been confirmed in more studies. Epigenetics mechanisms such as histone modification and DNA methylation can partially explain predisposition and inheritance of this disease. Nevertheless, an association with specific class II human leukocyte antigen (HLA) variants have been reported, showing an increase risk in susceptibility. More recently, data regarding a strong protective association between PBC and HLA alleles confirmed this association. After recent genome-wide association studies (GWAS), a more intricate interaction between PBC and the HLA region has been shown. Furthermore, GWAS also identified several immune-related-genes implicated. More genome-wide association studies on this disease are needed to reach a complete and systematic knowledge of this disease. In this review we discuss more recent issued data on geoepidemiology of PBC and the role of (epi-)genetic mechanisms in its pathogenesis.
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Park JM, Kim YJ, Song MK, Lee JM, Kim YJ. Genome‑wide DNA methylation profiling in a rat model with vascular dementia. Mol Med Rep 2018; 18:123-130. [PMID: 29749552 PMCID: PMC6059660 DOI: 10.3892/mmr.2018.8990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 04/04/2018] [Indexed: 12/12/2022] Open
Abstract
Vascular dementia (VaD), the second most prevalent type of dementia, is caused by reduced blood supply to the brain that results in cognitive impairment. Despite the efforts of numerous studies, the pathological mechanisms behind VaD remain unclear. The aim of the present study was to identify candidate genes that undergo changes in hippocampal DNA methylation owing to VaD. A genome‑wide DNA methylation analysis was performed, using methylated DNA‑binding domain sequencing. VaD model rats with cognitive impairment induced by bilateral common carotid artery occlusion were confirmed using the radial arm maze test. A total of 1,180 differentially methylated genes (DMGs) were identified, and functional annotation analysis revealed the DMGs to be enriched in 10 Gene Ontology biological processes. Network analysis using the STRING database indicated that seven genes were closely connected. Rats in the VaD model group demonstrated relative hypomethylation in the promoter region and increased mRNA expression of the hippocampal genes vascular endothelial growth factor (VEGFA) and kinase insert domain receptor, but only differences in VEGFA mRNA expression levels were determined to be statistically significant. In conclusion, these preliminary data from the functional annotation of hippocampal DMGs in the promoter region highlighted candidate genes for VaD that may contribute to the elucidation of its pathophysiology.
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Affiliation(s)
- Jong-Min Park
- Department of Nursing, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Yoon Ju Kim
- Department of Nursing, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Min Kyung Song
- Department of Nursing, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jae-Min Lee
- Department of Physiology, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Youn-Jung Kim
- College of Nursing Science, Kyung Hee University, Seoul 02447, Republic of Korea
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Alexander SA. Primer in Genetics and Genomics Series: Final Remarks. Biol Res Nurs 2018; 20:253-254. [PMID: 29635940 DOI: 10.1177/1099800418766616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Sheila A Alexander
- 1 International Society of Nurses in Genetics (ISONG), Pittsburgh, PA, USA.,2 Acute & Tertiary Care, School of Nursing, University of Pittsburgh, Pittsburgh, PA, USA.,3 Critical Care Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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