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Garcia DR, Souza FR, Guimarães AP, Valis M, Pavelek Z, Kuca K, Ramalho TC, França TCC. In Silico Studies of Potential Selective Inhibitors of Thymidylate Kinase from Variola virus. Pharmaceuticals (Basel) 2021; 14:ph14101027. [PMID: 34681251 PMCID: PMC8537287 DOI: 10.3390/ph14101027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/22/2021] [Accepted: 09/30/2021] [Indexed: 11/17/2022] Open
Abstract
Continuing the work developed by our research group, in the present manuscript, we performed a theoretical study of 10 new structures derived from the antivirals cidofovir and ribavirin, as inhibitor prototypes for the enzyme thymidylate kinase from Variola virus (VarTMPK). The proposed structures were subjected to docking calculations, molecular dynamics simulations, and free energy calculations, using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method, inside the active sites of VarTMPK and human TMPK (HssTMPK). The docking and molecular dynamic studies pointed to structures 2, 3, 4, 6, and 9 as more selective towards VarTMPK. In addition, the free energy data calculated through the MM-PBSA method, corroborated these results. This suggests that these compounds are potential selective inhibitors of VarTMPK and, thus, can be considered as template molecules to be synthesized and experimentally evaluated against smallpox.
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Affiliation(s)
- Danielle R. Garcia
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Praça General Tiburcio 80, Urca, Rio de Janeiro 22290-270, Brazil;
| | - Felipe R. Souza
- Department of Chemistry, Pontifical Catholic University of Rio de Janeiro, Rio de Janeiro 22541-041, Brazil;
| | - Ana P. Guimarães
- Department of Chemistry, Federal University of Viçosa, Avenida P. H. Rolfs, s/n, Centro, Viçosa 36570-000, MG, Brazil;
| | - Martin Valis
- Department of Neurology of the Medical Faculty of Charles University and University Hospital in Hradec Kralove, Sokolska 581, 50005 Hradec Kralove, Czech Republic; (M.V.); (Z.P.)
| | - Zbyšek Pavelek
- Department of Neurology of the Medical Faculty of Charles University and University Hospital in Hradec Kralove, Sokolska 581, 50005 Hradec Kralove, Czech Republic; (M.V.); (Z.P.)
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003 Hradec Kralove, Czech Republic;
- Biomedical Research Center, University Hospital in Hradec Kralove, Sokolska 581, 50005 Hradec Kralove, Czech Republic
- Correspondence: (K.K.); (T.C.C.F.)
| | - Teodorico C. Ramalho
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003 Hradec Kralove, Czech Republic;
- Laboratory of Computational Chemistry, Department of Chemistry, UFLA, Lavras 37200-000, MG, Brazil
| | - Tanos C. C. França
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Praça General Tiburcio 80, Urca, Rio de Janeiro 22290-270, Brazil;
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003 Hradec Kralove, Czech Republic;
- Correspondence: (K.K.); (T.C.C.F.)
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Rehman S, Aatif M, Rafi Z, Khan MY, Shahab U, Ahmad S, Farhan M. Effect of non-enzymatic glycosylation in the epigenetics of cancer. Semin Cancer Biol 2020; 83:543-555. [DOI: 10.1016/j.semcancer.2020.11.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 02/09/2023]
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3
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Yan S, Hou W, Wu H, Jiang W, Li Y, Zhang Y, Li H, Yang S, Sun C, Han T, Li Y. Prenatal exposure to the Chinese famine and the risk of metabolic syndrome in adulthood across consecutive generations. Eur J Clin Nutr 2020; 74:1229-1236. [DOI: 10.1038/s41430-020-0561-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 12/16/2019] [Accepted: 01/14/2020] [Indexed: 12/26/2022]
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Qiu Z, Nakamura S, Fujimoto K. Reversible photo-cross-linking of the GCN4 peptide containing 3-cyanovinylcarbazole amino acid to double-stranded DNA. Org Biomol Chem 2019; 17:6277-6283. [PMID: 31192345 DOI: 10.1039/c9ob00372j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Interaction analysis in vivo greatly promotes the analyses and understanding of biological functions. The interaction between DNA and peptides or proteins is very important in terms of readout and amplifying information from genomic DNA. In this study, we designed and synthesized a photo-cross-linkable amino acid, l-3-cyanovinlycarbazole amino acid (l-CNVA), to double-stranded DNA. Reversible photo-cross-linking between DNA and peptides containing CNVA, having 3-cyanovinylcarbazole moieties capable of photo-cross-linking to nucleic acids, was demonstrated. As a result, it was shown that the GCN4 peptide, containing CNVA, can be photo-cross-linked to DNA, and its adduct was photo-split into the original peptide and DNA with 312 nm-irradiation. This is the first report that reversibly manipulates photo-crosslinking between double stranded DNA and peptides. In addition, this reversible photo-cross-linking, using l-CNVA, is faster and with higher yield than that using diazirine and psoralen.
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Affiliation(s)
- Zhiyong Qiu
- School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology. Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan.
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Rodrigues Garcia D, Rodrigues de Souza F, Paula Guimarães A, Castro Ramalho T, Palermo de Aguiar A, Celmar Costa França T. Design of inhibitors of thymidylate kinase from Variola virus as new selective drugs against smallpox: part II. J Biomol Struct Dyn 2019; 37:4569-4579. [PMID: 30488769 PMCID: PMC9491145 DOI: 10.1080/07391102.2018.1554510] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Acknowledging the importance of studies toward the development of measures against terrorism and bioterrorism, this study aims to contribute to the design of new prototypes of potential drugs against smallpox. Based on a former study, nine synthetic feasible prototypes of selective inhibitors for thymidylate kinase from Variola virus (VarTMPK) were designed and submitted to molecular docking, molecular dynamics simulations and binding energy calculations. The compounds are simplifications of two more complex scaffolds, with a guanine connected to an amide or alcohol through a spacer containing ether and/or amide groups, formerly suggested as promising for the design of selective inhibitors of VarTMPK. Our study showed that, despite the structural simplifications, the compounds presented effective energy values in interactions with VarTMPK and HssTMPK and that the guanine could be replaced by a simpler imidazole ring linked to a –NH2 group, without compromising the affinity for VarTMPK. It was also observed that a positive charge in the imidazole ring is important for the selectivity toward VarTMPK and that an amide group in the spacer does not contribute to selectivity. Finally, prototype 3 was pointed as the most promising to be synthesized and experimentally evaluated. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Danielle Rodrigues Garcia
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | - Felipe Rodrigues de Souza
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | | | - Teodorico Castro Ramalho
- Laboratory of Computational Chemistry, Department of Chemistry, UFLA, Lavras, MG, Brazil
- Faculty of Informatics and Management, Center for Basic and Applied Research, University of Hradec Králové, Hradec Králove, Czech Republic
| | | | - Tanos Celmar Costa França
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
- Faculty of Informatics and Management, Center for Basic and Applied Research, University of Hradec Králové, Hradec Králove, Czech Republic
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6
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Ji Y, Wu Z, Dai Z, Wang X, Li J, Wang B, Wu G. Fetal and neonatal programming of postnatal growth and feed efficiency in swine. J Anim Sci Biotechnol 2017; 8:42. [PMID: 28484595 PMCID: PMC5420136 DOI: 10.1186/s40104-017-0173-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 04/18/2017] [Indexed: 01/10/2023] Open
Abstract
Maternal undernutrition or overnutrition during pregnancy alters organ structure, impairs prenatal and neonatal growth and development, and reduces feed efficiency for lean tissue gains in pigs. These adverse effects may be carried over to the next generation or beyond. This phenomenon of the transgenerational impacts is known as fetal programming, which is mediated by stable and heritable alterations of gene expression through covalent modifications of DNA and histones without changes in DNA sequences (namely, epigenetics). The mechanisms responsible for the epigenetic regulation of protein expression and functions include chromatin remodeling; DNA methylation (occurring at the 5´-position of cytosine residues within CpG dinucleotides); and histone modifications (acetylation, methylation, phosphorylation, and ubiquitination). Like maternal malnutrition, undernutrition during the neonatal period also reduces growth performance and feed efficiency (weight gain:feed intake; also known as weight-gain efficiency) in postweaning pigs by 5-10%, thereby increasing the days necessary to reach the market body-weight. Supplementing functional amino acids (e.g., arginine and glutamine) and vitamins (e.g., folate) play a key role in activating the mammalian target of rapamycin signaling and regulating the provision of methyl donors for DNA and protein methylation. Therefore, these nutrients are beneficial for the dietary treatment of metabolic disorders in offspring with intrauterine growth restriction or neonatal malnutrition. The mechanism-based strategies hold great promise for the improvement of the efficiency of pork production and the sustainability of the global swine industry.
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Affiliation(s)
- Yun Ji
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, 100193 China
| | - Zhenlong Wu
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, 100193 China
| | - Zhaolai Dai
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, 100193 China
| | - Xiaolong Wang
- Henan Yinfa Animal Husbandry Co., Ltd., Xinzheng, Henan 451100 China
| | - Ju Li
- Henan Yinfa Animal Husbandry Co., Ltd., Xinzheng, Henan 451100 China
| | - Binggen Wang
- Henan Yinfa Animal Husbandry Co., Ltd., Xinzheng, Henan 451100 China
| | - Guoyao Wu
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, 100193 China.,Department of Animal Science and Center for Animal Genomics, Texas A&M University, Room 212, College Station, TX 77843 USA
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7
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Methods to Study Long Noncoding RNA Biology in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 927:69-107. [PMID: 27376732 DOI: 10.1007/978-981-10-1498-7_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Thousands of long noncoding RNAs (lncRNAs) have been discovered in recent years. The functions of lncRNAs range broadly from regulating chromatin structure and gene expression in the nucleus to controlling messenger RNA (mRNA) processing, mRNA posttranscriptional regulation, cellular signaling, and protein activity in the cytoplasm. Experimental and computational techniques have been developed to characterize lncRNAs in high-throughput scale, to study the lncRNA function in vitro and in vivo, to map lncRNA binding sites on the genome, and to capture lncRNA-protein interactions with the identification of lncRNA-binding partners, binding sites, and interaction determinants. In this chapter, we will discuss these technologies and their applications in decoding the functions of lncRNAs. Understanding these techniques including their advantages and disadvantages and developing them in the future will be essential to elaborate the roles of lncRNAs in cancer and other diseases.
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8
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Abstract
Acute and transient changes in gene transcription following a single exercise bout, if reinforced by repeated exercise stimuli, result in the longer lasting effects on protein expression and function that form the basis of skeletal muscle training adaptations. Changes in skeletal muscle gene expression occur in response to multiple stimuli associated with skeletal muscle contraction, various signaling kinases that respond to these stimuli, and numerous downstream pathways and targets of these kinases. In addition, DNA methylation, histone acetylation and phosphorylation, and micro-RNAs can alter gene expression via epigenetic mechanisms. Contemporary studies rely upon "big omics data," in combination with computational and systems biology, to interrogate, and make sense of, the complex interactions underpinning exercise adaptations. The exciting potential is a greater understanding of the integrative biology of exercise.
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Affiliation(s)
- Mark Hargreaves
- Department of Physiology, The University of Melbourne, Melbourne, Australia.
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9
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Dunlap KA, Brown JD, Keith AB, Satterfield MC. Factors controlling nutrient availability to the developing fetus in ruminants. J Anim Sci Biotechnol 2015; 6:16. [PMID: 25908972 PMCID: PMC4407308 DOI: 10.1186/s40104-015-0012-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 03/23/2015] [Indexed: 01/20/2023] Open
Abstract
Inadequate delivery of nutrients results in intrauterine growth restriction (IUGR), which is a leading cause of neonatal morbidity and mortality in livestock. In ruminants, inadequate nutrition during pregnancy is often prevalent due to frequent utilization of exensive forage based grazing systems, making them highly susceptible to changes in nutrient quality and availability. Delivery of nutrients to the fetus is dependent on a number of critical factors including placental growth and development, utero-placental blood flow, nutrient availability, and placental metabolism and transport capacity. Previous findings from our laboratory and others, highlight essential roles for amino acids and their metabolites in supporting normal fetal growth and development, as well as the critical role for amino acid transporters in nutrient delivery to the fetus. The focus of this review will be on the role of maternal nutrition on placental form and function as a regulator of fetal development in ruminants.
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Affiliation(s)
- Kathrin A Dunlap
- Department of Animal Science, Texas A&M University, 2471 TAMU, College Station, Texas 77843 USA
| | - Jacob D Brown
- Department of Animal Science, Texas A&M University, 2471 TAMU, College Station, Texas 77843 USA
| | - Ashley B Keith
- Department of Animal Science, Texas A&M University, 2471 TAMU, College Station, Texas 77843 USA
| | - M Carey Satterfield
- Department of Animal Science, Texas A&M University, 2471 TAMU, College Station, Texas 77843 USA
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Hudler P, Videtič Paska A, Komel R. Contemporary proteomic strategies for clinical epigenetic research and potential impact for the clinic. Expert Rev Proteomics 2015; 12:197-212. [PMID: 25719543 DOI: 10.1586/14789450.2015.1019479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Novel proteomic methods are revealing the intricacy of the epigenetic landscape affecting gene regulation and improving our knowledge of the pathogenesis of complex diseases. Despite the enormous amount of data regarding epigenetic modifications present in DNA and histones, deciphering their biological relevance in the context of the disease and health is currently still an ongoing process. Here, we consider the relationship between epigenetic research in tumorigenesis and the prospect of knowledge transfer to clinical use, focusing primarily on the epigenetic histone post-translational modifications, which could be used as biomarkers. We additionally focus on the use of proteomic techniques in research and evaluate their usefulness in clinical setting.
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Affiliation(s)
- Petra Hudler
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
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11
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Maze I, Shen L, Zhang B, Garcia BA, Shao N, Mitchell A, Sun H, Akbarian S, Allis CD, Nestler EJ. Analytical tools and current challenges in the modern era of neuroepigenomics. Nat Neurosci 2014; 17:1476-90. [PMID: 25349914 DOI: 10.1038/nn.3816] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/20/2014] [Indexed: 12/14/2022]
Abstract
Over the past decade, rapid advances in epigenomics research have extensively characterized critical roles for chromatin regulatory events during normal periods of eukaryotic cell development and plasticity, as well as part of aberrant processes implicated in human disease. Application of such approaches to studies of the CNS, however, is more recent. Here we provide a comprehensive overview of available tools for analyzing neuroepigenomics data, as well as a discussion of pending challenges specific to the field of neuroscience. Integration of numerous unbiased genome-wide and proteomic approaches will be necessary to fully understand the neuroepigenome and the extraordinarily complex nature of the human brain. This will be critical to the development of future diagnostic and therapeutic strategies aimed at alleviating the vast array of heterogeneous and genetically distinct disorders of the CNS.
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Affiliation(s)
- Ian Maze
- 1] Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [2] Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Li Shen
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ningyi Shao
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Amanda Mitchell
- 1] Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [2] Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - HaoSheng Sun
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Schahram Akbarian
- 1] Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [2] Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York, USA
| | - Eric J Nestler
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Fu M, Wu X, He J, Zhang Y, Hua S. Natrium fluoride influences methylation modifications and induces apoptosis in mouse early embryos. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:10398-10405. [PMID: 25102367 DOI: 10.1021/es503026e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This study epigenetically examined the effect of fluoride on early embryos of Kunming mice administered with 0, 20 (low), 60 (medium), and 120 mg/L (high) sodium fluoride (NaF). The results showed that NaF repressed oocyte maturation, fertilization and blastocyst formation in all NaF-treated groups. Meanwhile, TUNEL assay showed that embryo apoptosis was induced dramatically in blastocyst stage at either low or medium doses, and in 8-cell stage at high dose, compared to the control, suggesting a dose-dependent effect. Furthermore, the immunostaining displayed global increases of DNA methylation, H3K9m2 and H3K4m2 with increasing dose, which were consistent with gene expression results, exhibiting general increases of DNMT1, DNMT3a, G9a, LSD1, and MLL1 and a reduction of JHDM2a in transcription and protein levels. More closely, the differential methylation domain in parentally imprinted gene H19 showed low methylation, while materanlly imprinted gene IGF2 showed high methylaiton in NaF-treated groups compared to the control group, which corresponded with high expression of H19 and low expression of IGF2 confirmed by qPCR. Collectively, we demonstrated that fluoride epigenetically impaired mouse oocyte maturation and embryonic development, supplying a better knowledge of fluoride in toxicology and a deeper evaluation of its potential influence in physiological and clinical implications.
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Affiliation(s)
- Mingzhe Fu
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi Province The People's Republic of China 712100
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13
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DelCurto H, Wu G, Satterfield MC. Nutrition and reproduction: links to epigenetics and metabolic syndrome in offspring. Curr Opin Clin Nutr Metab Care 2013; 16:385-91. [PMID: 23703295 DOI: 10.1097/mco.0b013e328361f96d] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
PURPOSE OF REVIEW Inappropriate exposure of gametes and/or products of conception to nutritional imbalance alters critical metabolic set points in the offspring and increases propensity to disease. This review will focus on recent findings highlighting clear links to epigenetic modifications in response to dietary manipulations as well as nutritional strategies with the potential to mitigate the effects of an otherwise poor nutritional environment. RECENT FINDINGS Maternal nutritional imbalance, either through global nutritional manipulation or deficiencies in select nutrients, predisposes the offspring to metabolic disease. Disease susceptibility is linked to global and/or specific modifications of the epigenome at key metabolic regulatory genes. Paternal nutritional imbalance also increases the likelihood of metabolic disease in offspring through similar epigenetic mechanisms. Finally, dietary intervention with select nutrients has been shown to ameliorate postnatal disease phenotypes in offspring, although the exact molecular mechanisms have not been elucidated. SUMMARY Select nutrients, such as amino acids and vitamins, not only serve as building blocks for growth but also mediate a myriad of physiological functions, including providing substrates for DNA synthesis. These nutrients hold great promise as intervention strategies to combat a suboptimal developmental environment.
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Affiliation(s)
- Hannah DelCurto
- Department of Animal Science, Texas A&M University, College Station, TX 77843–2471, USA
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Razafsha M, Behforuzi H, Harati H, Wafai RA, Khaku A, Mondello S, Gold MS, Kobeissy FH. An updated overview of animal models in neuropsychiatry. Neuroscience 2013; 240:204-18. [PMID: 23473749 DOI: 10.1016/j.neuroscience.2013.02.045] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/28/2013] [Accepted: 02/20/2013] [Indexed: 12/20/2022]
Abstract
Animal models are vital tools to study the genetic, molecular, cellular, and environmental parameters involved in several neuropsychiatric disorders. Over the years, these models have expanded our understanding of the pathogenesis of many neuropsychiatric disorders and neurodegenerative diseases. Although animal models have been widely used in psychiatry, and despite several years of extensive research with these models, their validity is still being investigated and presents a challenge to both investigators and clinicians as well. In this concise review, we will describe the most common animal models utilized in neuropsychiatry, including animal models of depression, anxiety, and psychosis. In addition, we will also discuss the validity and reliability of these models and current challenges in this domain. Furthermore, this work will discuss the role of gene-environment interaction as an additional contributing factor that modulates neuropsychological outcome and its implication on animal models. This overview will give a succinct summary of animal models in psychiatry which will be useful both to the seasoned researcher, as well as novices in the field.
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Affiliation(s)
- M Razafsha
- Residency Program, Department of Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA.
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15
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Baumgartel K, Zelazny J, Timcheck T, Snyder C, Bell M, Conley YP. Molecular genomic research designs. ANNUAL REVIEW OF NURSING RESEARCH 2012; 29:1-26. [PMID: 22891496 DOI: 10.1891/0739-6686.29.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genetic and genomic research approaches have the capability to expand our understanding of the complex pathophysiology of disease susceptibility, susceptibility to complications related to disease, trajectory of recovery from acquired injuries and infections, patient response to interventions and therapeutics, as well as informing diagnoses and prognoses. Nurse scientists are actively involved in all of these fields of inquiry, and the goal of this chapter is to assist with incorporation of genetic and genomic trajectories into their research and facilitate the design and execution of these studies. New studies that are going to embark on recruitment, phenotyping, and sample collection will benefit from forethought about research design to ensure that it addresses the research questions or hypotheses being tested. Studies that will use existing data or samples will also benefit from forethought about research design for the same reason but will also address the fact that some designs may not be feasible with the available data or samples. This chapter discusses candidate gene association, genome-wide association, candidate gene expression, global gene expression, and epigenetic/epigenomic study designs. Information provided includes rationale for selecting an appropriate study design, important methodology considerations for each design, key technologies available to accomplish each type of study, and online resources available to assist in executing each type of study design.
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16
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Brunner AM, Tweedie-Cullen RY, Mansuy IM. Epigenetic modifications of the neuroproteome. Proteomics 2012; 12:2404-20. [PMID: 22696459 DOI: 10.1002/pmic.201100672] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 03/12/2012] [Accepted: 04/12/2012] [Indexed: 01/17/2023]
Abstract
In the central nervous system, epigenetic processes are involved in a multitude of brain functions ranging from the development and differentiation of the nervous system through to higher-order cognitive processes such as learning and memory. This review summarises the current state of the art for the proteomic analysis of the epigenetic regulation of gene expression, in particular the PTM of histones, in the brain and cellular model systems. It describes the MS technologies that have helped the identification and analysis of histones, histone variants and PTMs in the brain. Strategies for the isolation of histones that allow the qualitative analysis of PTMs and their combinatorial patterns are introduced, methods for the relative and absolute quantification of histone PTMs are described, and future challenges are discussed.
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Affiliation(s)
- Andrea M Brunner
- Brain Research Institute, University of Zürich and Department of Biology, ETH Zürich, Zürich, Switzerland
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17
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Wang J, Wu Z, Li D, Li N, Dindot SV, Satterfield MC, Bazer FW, Wu G. Nutrition, epigenetics, and metabolic syndrome. Antioxid Redox Signal 2012; 17:282-301. [PMID: 22044276 PMCID: PMC3353821 DOI: 10.1089/ars.2011.4381] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 11/01/2011] [Indexed: 01/21/2023]
Abstract
SIGNIFICANCE Epidemiological and animal studies have demonstrated a close link between maternal nutrition and chronic metabolic disease in children and adults. Compelling experimental results also indicate that adverse effects of intrauterine growth restriction on offspring can be carried forward to subsequent generations through covalent modifications of DNA and core histones. RECENT ADVANCES DNA methylation is catalyzed by S-adenosylmethionine-dependent DNA methyltransferases. Methylation, demethylation, acetylation, and deacetylation of histone proteins are performed by histone methyltransferase, histone demethylase, histone acetyltransferase, and histone deacetyltransferase, respectively. Histone activities are also influenced by phosphorylation, ubiquitination, ADP-ribosylation, sumoylation, and glycosylation. Metabolism of amino acids (glycine, histidine, methionine, and serine) and vitamins (B6, B12, and folate) plays a key role in provision of methyl donors for DNA and protein methylation. CRITICAL ISSUES Disruption of epigenetic mechanisms can result in oxidative stress, obesity, insulin resistance, diabetes, and vascular dysfunction in animals and humans. Despite a recognized role for epigenetics in fetal programming of metabolic syndrome, research on therapies is still in its infancy. Possible interventions include: 1) inhibition of DNA methylation, histone deacetylation, and microRNA expression; 2) targeting epigenetically disturbed metabolic pathways; and 3) dietary supplementation with functional amino acids, vitamins, and phytochemicals. FUTURE DIRECTIONS Much work is needed with animal models to understand the basic mechanisms responsible for the roles of specific nutrients in fetal and neonatal programming. Such new knowledge is crucial to design effective therapeutic strategies for preventing and treating metabolic abnormalities in offspring born to mothers with a previous experience of malnutrition.
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Affiliation(s)
- Junjun Wang
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China
| | - Zhenlong Wu
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China
| | - Defa Li
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China
| | - Ning Li
- State Key Laboratory of AgroBiotechnology, China Agricultural University, Beijing, China
| | - Scott V. Dindot
- Center for Animal Biotechnology and Genomics, Texas A&M University, College Station, Texas
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas
| | - M. Carey Satterfield
- Center for Animal Biotechnology and Genomics, Texas A&M University, College Station, Texas
- Department of Animal Science, Texas A&M University, College Station, Texas
| | - Fuller W. Bazer
- Center for Animal Biotechnology and Genomics, Texas A&M University, College Station, Texas
- Department of Animal Science, Texas A&M University, College Station, Texas
| | - Guoyao Wu
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China
- Center for Animal Biotechnology and Genomics, Texas A&M University, College Station, Texas
- Department of Animal Science, Texas A&M University, College Station, Texas
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18
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Abstract
PURPOSE OF REVIEW Eating disorders are complex psychiatric disorders in which genes, environment, and gene-environment interactions (G×E) have a role. Such G×E may occur in adulthood or during development. They may also be modified by factors such as (mal)nutrition or stress and this may result in acute or long-term epigenetic modifications. This review discusses the potential for recent developments in epigenetics to address ongoing aetiological issues in eating disorders. RECENT FINDINGS Epigenetic studies in eating disorders have focussed on the DNA methylation status of promoter regions of candidate genes: differences have been reported between people with eating disorders and healthy controls, and between subtypes of eating disorders. Animal studies related to eating disorders have focussed on understanding the acute and long-term effects of environmental manipulation on epigenetic changes and on the resultant phenotypes: these studies are promising, but they have also identified some of the complexity of epigenetic processing. SUMMARY Because of the difficulties in obtaining brain samples, epigenetic studies in eating disorders (like in other psychiatric illnesses) have used peripheral tissues, usually blood: this raises various problems. It is likely, therefore, that in the immediate future, animal, rather than human studies will guide the progress in epigenetics studies of eating disorders and other psychiatric disorders.
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Affiliation(s)
- Eneda Pjetri
- Rudolf Magnus Institute of Neuroscience, Department of Neuroscience and Pharmacology, University Medical Centre Utrecht, Utrecht, The Netherlands
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19
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Britton LMP, Gonzales-Cope M, Zee BM, Garcia BA. Breaking the histone code with quantitative mass spectrometry. Expert Rev Proteomics 2012; 8:631-43. [PMID: 21999833 DOI: 10.1586/epr.11.47] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Histone post-translational modifications (PTMs) comprise one of the most intricate nuclear signaling networks that govern gene expression in a long-term and dynamic fashion. These PTMs are considered to be 'epigenetic' or heritable from one cell generation to the next and help establish genomic expression patterns. While much of the analyses of histones have historically been performed using site-specific antibodies, these methods are replete with technical obstacles (i.e., cross-reactivity and epitope occlusion). Mass spectrometry-based proteomics has begun to play a significant role in the interrogation of histone PTMs, revealing many new aspects of these modifications that cannot be easily determined with standard biological approaches. Here, we review the accomplishments of mass spectrometry in the histone field, and outline the future roadblocks that must be overcome for mass spectrometry-based proteomics to become the method of choice for chromatin biologists.
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Affiliation(s)
- Laura-Mae P Britton
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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20
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Baranowski T, Baranowski JC, Watson KB, Jago R, Islam N, Beltran A, Martin SJ, Nguyen N, Tepper BJ. 6-n-propylthiouracil taster status not related to reported cruciferous vegetable intake among ethnically diverse children. Nutr Res 2011; 31:594-600. [PMID: 21925344 DOI: 10.1016/j.nutres.2011.07.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 07/20/2011] [Accepted: 07/21/2011] [Indexed: 12/13/2022]
Abstract
Sensitivity to the taste of 6-n-propylthiouracil (PROP) (a bitter chemical related to the phenylthiocarbamide found in cruciferous vegetables) has been related to dietary intake or preferences of cruciferous vegetables among adults and young children but not middle-aged children or adolescents. We hypothesized that PROP taste sensitivity is related to lower reported dietary intake of cruciferous vegetables, primarily among younger children (ie, a moderating effect of child age). This study examined the relationship of PROP sensitivity to reported dietary intake across 3 days in 2 age groups of youth (9-10 and 17-18 years) while statistically controlling for physical activity, social desirability, and reporting bias. Cross-sectional design was used with a multiethnic (white, African American, Hispanic, etc) sample of 843 men and women. Children were recruited from and data were collected in local elementary and high schools that had at least 30% ethnic minority enrollment. Children providing nonplausible reports of dietary intake were deleted from the analyses. Body mass index was calculated and expressed in z scores. Energy intake and physical activity were measured by 3 telephone-conducted 24-hour dietary recalls with the Nutrient Data System for Research and 5 days of Actigraph (ActiGraph, Shalimar, Florida) activity monitor. The primary analyses included 347 students. 6-n-Propylthiouracil sensitivity was not related to intake of cruciferous vegetables. Intakes of the cruciferous vegetables were low, which may explain the lack of relationship.
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Affiliation(s)
- Tom Baranowski
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX 77030, USA.
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21
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Plazas-Mayorca MD, Vrana KE. Proteomic investigation of epigenetics in neuropsychiatric disorders: a missing link between genetics and behavior? J Proteome Res 2010; 10:58-65. [PMID: 20735116 DOI: 10.1021/pr100463y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Neuropsychiatric disorders affect a large segment of the human population and result in large costs to society. The majority of such disorders have unknown underlying causes. Recent evidence suggests an important role for epigenetic regulation in the emergence of neuropsychiatric disease. Epigenetics may provide a link between genetic and environmental factors and behavior. Epigenetic signaling involves changes on the structure of chromatin; such changes are often triggered and maintained by the post-translational modification of chromatin proteins and/or DNA. Recent proteomic technologies have enabled the study of epigenetic mechanisms in a high-throughput manner. This review will provide an overview of the major epigenetic pathways and modern techniques for their study, before focusing on experimental evidence supporting a strong role for epigenetics in selected psychiatric disorders such as depression, schizophrenia, and drug addiction. These results highlight a great need for the inclusion of the proteomic characterization of epigenetic mechanisms in the study of gene/disease associations in psychiatric disorders.
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Affiliation(s)
- Mariana D Plazas-Mayorca
- Department of Pharmacology, Penn State University College of Medicine, Hershey, Pennsylvania, USA
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22
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Tweedie-Cullen RY, Mansuy IM. Towards a better understanding of nuclear processes based on proteomics. Amino Acids 2010; 39:1117-30. [PMID: 20730591 DOI: 10.1007/s00726-010-0723-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 08/09/2010] [Indexed: 12/25/2022]
Abstract
The complex structural and functional organisation of the brain warrants the application of high-throughput approaches to study its functional alterations in physiological and pathological conditions. Such approaches have greatly benefited from advances in proteomics and genomics, and from their combination with computational modelling. They have been particularly instrumental for the analysis of processes such as the post-translational modification (PTM) of proteins, a critical biological process in the nervous system that remains not well studied. Protein PTMs are dynamic covalent marks that can be induced by activity and allow the maintenance of a trace of this activity. In the nucleus, they can modulate histone proteins and the components of the transcriptional machinery, and thereby contribute to regulating gene expression. PTMs do however need to be tightly controlled for proper chromatin functions. This review provides a synopsis of methods available to study PTMs and protein expression based on high-throughput mass spectrometry (MS), and covers basic concepts of traditional 'shot-gun'-based MS. It describes classical and emerging proteomic approaches such as multiple reaction monitoring and electron transfer dissociation, and their application to the analyses of nuclear processes in the brain.
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Affiliation(s)
- Ry Y Tweedie-Cullen
- Department of Biology of the ETH Zurich and Medical Faculty of the University Zurich, 8057, Zurich, Switzerland.
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23
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Ytterberg AJ, Jensen ON. Modification-specific proteomics in plant biology. J Proteomics 2010; 73:2249-66. [PMID: 20541636 DOI: 10.1016/j.jprot.2010.06.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 05/18/2010] [Accepted: 06/01/2010] [Indexed: 10/19/2022]
Abstract
Post-translational modifications (PTMs) are involved in the regulation of a wide range of biological processes, and affect e.g. protein structure, activity and stability. Several hundred PTMs have been described in the literature, but relatively few have been studied using mass spectrometry and proteomics. In general, methods for PTM characterization are developed to study yeast and mammalian biology and later adopted to investigate plants. Our point of view is that it is advantageous to enrich for PTMs on the peptide level as part of a quantitative proteomics strategy to not only identify the PTM, but also to determine the functional relevance in the context of regulation, response to abiotic stress etc. Protein phosphorylation is the only PTM that has been studied extensively at the proteome wide level in plants using mass spectrometry based methods. We review phosphoproteomics studies in plants and discuss the redox mediated PTMs (S-nitrosylation, tyrosine nitration and S-glutathionylation), ubiquitylation, SUMOylation, and glycosylation, including GPI anchors, and the quantitative proteomics methods that are used to study these modification in plants. Where appropriate we contrast the methods to those used for mammalian PTM characterization.
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Affiliation(s)
- A Jimmy Ytterberg
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark.
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24
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Abstract
Cell-free circulating DNA carries not only tumor-specific changes in its sequence but also distinctive epigenetic marks, namely DNA methylation, in certain GC-rich fragments. These fragments are usually located within the promoters and first exons of many genes, comprising CpG islands. Analysis of DNA methylation using cell-free circulating DNA can facilitate development of very accurate biomarkers for detection, diagnosis, prediction of response to therapy and prognosis of outcomes. Recent data suggest that benign and inflammatory diseases have very specific methylation patterns within cell-free circulating DNA, which are different from the pattern of a malignant tumor of the same organ. In addition, specific methylation patterns have been detected for cancers of different organs, so a differential diagnosis of site-specific cancer appears feasible. Currently, cancer-related applications dominate the field, although methylation-based biomarkers may also be possible for other diseases, including neurodegenerative and psychiatric disorders.
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Affiliation(s)
- Victor V Levenson
- Department of Radiation Oncology, Rush University Medical Center, Chicago, IL 60612, USA.
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25
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