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Hatami Z, Yi S, Hall M. Well-being and relative deprivation in a digital era. Heliyon 2022; 8:e11233. [PMID: 36311371 PMCID: PMC9615042 DOI: 10.1016/j.heliyon.2022.e11233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/03/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Social unrest is a feature of the early 21st century, yet relatively little research binds theoretical aspects with empirical validation of the drivers of protests and revolutions. This study aims to empirically validate the Davies J-Curve considering the digital era, with economic, social, and political factors. Using big data techniques, network analysis, and theoretical analysis, we analyzed countries' similarities by analyzing Human Development Index (HDI) and Worldwide Governance Indicator (WGI) as proxies of social well-being. Results established the existence of a J-Curve during social crises in countries prior to an occurrence of large-scale social unrest. In addition, our results suggest that HDI was not a sufficient indicator regarding countries' experienced well-being, likely because it is missing the highly granular aspects of daily life. We further recommended that other indicators from political and psychological areas should be considered and treated in the data preparation phase for future society-wide well-being research for a more realistic baseline.
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Affiliation(s)
- Zahra Hatami
- College of Business, University of Louisville, United States of America
| | - Sue Yi
- School of Interdisciplinary Informatics, The University of Nebraska at Omaha, United States of America
| | - Margeret Hall
- Strategy and Innovation Department, Wirtschaftsuniversität Wien, Austria,Corresponding author
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2
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Hamezah HS, Durani LW, Yanagisawa D, Ibrahim NF, Aizat WM, Makpol S, Wan Ngah WZ, Damanhuri HA, Tooyama I. Modulation of Proteome Profile in AβPP/PS1 Mice Hippocampus, Medial Prefrontal Cortex, and Striatum by Palm Oil Derived Tocotrienol-Rich Fraction. J Alzheimers Dis 2020; 72:229-246. [PMID: 31594216 PMCID: PMC6839455 DOI: 10.3233/jad-181171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Tocotrienol-rich fraction (TRF) is a mixture of vitamin E analogs derived from palm oil. We previously demonstrated that supplementation with TRF improved cognitive function and modulated amyloid pathology in AβPP/PS1 mice brains. The current study was designed to examine proteomic profiles underlying the therapeutic effect of TRF in the brain. Proteomic analyses were performed on samples of hippocampus, medial prefrontal cortex (mPFC), and striatum using liquid chromatography coupled to Q Exactive HF Orbitrap mass spectrometry. From these analyses, we profiled a total of 5,847 proteins of which 155 proteins were differentially expressed between AβPP/PS1 and wild-type mice. TRF supplementation of these mice altered the expression of 255 proteins in the hippocampus, mPFC, and striatum. TRF also negatively modulated the expression of amyloid beta A4 protein and receptor-type tyrosine-protein phosphatase alpha protein in the hippocampus. The expression of proteins in metabolic pathways, oxidative phosphorylation, and those involved in Alzheimer’s disease were altered in the brains of AβPP/PS1 mice that received TRF supplementation.
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Affiliation(s)
- Hamizah Shahirah Hamezah
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Japan
| | - Lina Wati Durani
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Japan
| | - Daijiro Yanagisawa
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Japan
| | - Nor Faeizah Ibrahim
- Department of Biochemistry, Faculty of Medicine, UKMMC, Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latif, Cheras, Kuala Lumpur, Malaysia
| | - Wan Mohd Aizat
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Suzana Makpol
- Department of Biochemistry, Faculty of Medicine, UKMMC, Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latif, Cheras, Kuala Lumpur, Malaysia
| | - Wan Zurinah Wan Ngah
- Department of Biochemistry, Faculty of Medicine, UKMMC, Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latif, Cheras, Kuala Lumpur, Malaysia
| | - Hanafi Ahmad Damanhuri
- Department of Biochemistry, Faculty of Medicine, UKMMC, Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latif, Cheras, Kuala Lumpur, Malaysia
| | - Ikuo Tooyama
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Japan
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Thompson MJ, Chwiałkowska K, Rubbi L, Lusis AJ, Davis RC, Srivastava A, Korstanje R, Churchill GA, Horvath S, Pellegrini M. A multi-tissue full lifespan epigenetic clock for mice. Aging (Albany NY) 2019; 10:2832-2854. [PMID: 30348905 PMCID: PMC6224226 DOI: 10.18632/aging.101590] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/05/2018] [Indexed: 12/11/2022]
Abstract
Human DNA-methylation data have been used to develop highly accurate biomarkers of aging ("epigenetic clocks"). Recent studies demonstrate that similar epigenetic clocks for mice (Mus Musculus) can be slowed by gold standard anti-aging interventions such as calorie restriction and growth hormone receptor knock-outs. Using DNA methylation data from previous publications with data collected in house for a total 1189 samples spanning 193,651 CpG sites, we developed 4 novel epigenetic clocks by choosing different regression models (elastic net- versus ridge regression) and by considering different sets of CpGs (all CpGs vs highly conserved CpGs). We demonstrate that accurate age estimators can be built on the basis of highly conserved CpGs. However, the most accurate clock results from applying elastic net regression to all CpGs. While the anti-aging effect of calorie restriction could be detected with all types of epigenetic clocks, only ridge regression based clocks replicated the finding of slow epigenetic aging effects in dwarf mice. Overall, this study demonstrates that there are trade-offs when it comes to epigenetic clocks in mice. Highly accurate clocks might not be optimal for detecting the beneficial effects of anti-aging interventions.
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Affiliation(s)
- Michael J Thompson
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Karolina Chwiałkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Liudmilla Rubbi
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Aldons J Lusis
- Department of Microbiology, Immunology and Molecular Genetics, Department of Medicine, and Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Richard C Davis
- Department of Microbiology, Immunology and Molecular Genetics, Department of Medicine, and Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | | | - Ron Korstanje
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | - Steve Horvath
- Department of Human Genetics and Biostatistics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Matteo Pellegrini
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
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Xu J, Patassini S, Rustogi N, Riba-Garcia I, Hale BD, Phillips AM, Waldvogel H, Haines R, Bradbury P, Stevens A, Faull RLM, Dowsey AW, Cooper GJS, Unwin RD. Regional protein expression in human Alzheimer's brain correlates with disease severity. Commun Biol 2019; 2:43. [PMID: 30729181 PMCID: PMC6361956 DOI: 10.1038/s42003-018-0254-9] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 12/03/2018] [Indexed: 01/18/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that currently affects 36 million people worldwide with no effective treatment available. Development of AD follows a distinctive pattern in the brain and is poorly modelled in animals. Therefore, it is vital to widen the spatial scope of the study of AD and prioritise the study of human brains. Here we show that functionally distinct human brain regions display varying and region-specific changes in protein expression. These changes provide insights into the progression of disease, novel AD-related pathways, the presence of a gradient of protein expression change from less to more affected regions and a possibly protective protein expression profile in the cerebellum. This spatial proteomics analysis provides a framework which can underpin current research and open new avenues to enhance molecular understanding of AD pathophysiology, provide new targets for intervention and broaden the conceptual frameworks for future AD research.
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Affiliation(s)
- Jingshu Xu
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, Core Technology Facility (3rd Floor), 46 Grafton Street, Manchester, M13 9NT UK
- School of Biological Sciences, and Maurice Wilkins Centre for Molecular Biodiscovery, Faculty of Science, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Stefano Patassini
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, Core Technology Facility (3rd Floor), 46 Grafton Street, Manchester, M13 9NT UK
- School of Biological Sciences, and Maurice Wilkins Centre for Molecular Biodiscovery, Faculty of Science, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Nitin Rustogi
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, Core Technology Facility (3rd Floor), 46 Grafton Street, Manchester, M13 9NT UK
| | - Isabel Riba-Garcia
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, Core Technology Facility (3rd Floor), 46 Grafton Street, Manchester, M13 9NT UK
| | - Benjamin D. Hale
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, Core Technology Facility (3rd Floor), 46 Grafton Street, Manchester, M13 9NT UK
| | - Alexander M Phillips
- Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool, L69 3GJ UK
| | - Henry Waldvogel
- Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, 1142 New Zealand
| | - Robert Haines
- Research IT, The University of Manchester, Manchester, M13 9PL UK
| | - Phil Bradbury
- Research IT, The University of Manchester, Manchester, M13 9PL UK
| | - Adam Stevens
- Division of Developmental Biology & Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, M13 9PL UK
| | - Richard L. M. Faull
- Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, 1142 New Zealand
| | - Andrew W. Dowsey
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, Core Technology Facility (3rd Floor), 46 Grafton Street, Manchester, M13 9NT UK
- Department of Population Health Sciences and Bristol Veterinary School, Faculty of Health Sciences, University of Bristol, Bristol, BS8 2BN UK
| | - Garth J. S. Cooper
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, Core Technology Facility (3rd Floor), 46 Grafton Street, Manchester, M13 9NT UK
- School of Biological Sciences, and Maurice Wilkins Centre for Molecular Biodiscovery, Faculty of Science, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
- Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, 1142 New Zealand
| | - Richard D. Unwin
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, Core Technology Facility (3rd Floor), 46 Grafton Street, Manchester, M13 9NT UK
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Wang J, Li Q, Kong Y, Zhou F, Li J, Li W, Wang K, Wu T, Guan Y, Xie J, Wen T. Biosystems Study of the Molecular Networks Underlying Hippocampal Aging Progression and Anti-aging Treatment in Mice. Front Aging Neurosci 2018; 9:393. [PMID: 29311893 PMCID: PMC5735351 DOI: 10.3389/fnagi.2017.00393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/13/2017] [Indexed: 12/22/2022] Open
Abstract
Aging progression is a process that an individual encounters as they become older, and usually results from a series of normal physiological changes over time. The hippocampus, which contributes to the loss of spatial and episodic memory and learning in older people, is closely related to the detrimental effects of aging at the morphological and molecular levels. However, age-related genetic changes in hippocampal molecular mechanisms are not yet well-established. To provide additional insight into the aging process, differentially-expressed genes of 3- versus 24- and 29-month old mice were re-analyzed. The results revealed that a large number of immune and inflammatory response-related genes were up-regulated in the aged hippocampus, and membrane receptor-associated genes were down-regulated. The down-regulation of transmembrane receptors may indicate the weaker perception of environmental exposure in older people, since many transmembrane proteins participate in signal transduction. In addition, molecular interaction analysis of the up-regulated immune genes indicated that the hub gene, Ywhae, may play essential roles in immune and inflammatory responses during aging progression, as well as during hippocampal development. Our biological experiments confirmed the conserved roles of Ywhae and its partners between human and mouse. Furthermore, comparison of microarray data between advanced-age mice treated with human umbilical cord blood plasma protein and the phosphate-buffered saline control showed that the genes that contribute to the revitalization of advanced-age mice are different from the genes induced by aging. These results implied that the revitalization of advanced-age mice is not a simple reverse process of normal aging progression. Our data assigned novel roles of genes during aging progression and provided further theoretic evidence for future studies exploring the underlying mechanisms of aging and anti-aging-related disease therapy.
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Affiliation(s)
- Jiao Wang
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
| | - Qian Li
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
| | - Yanyan Kong
- Position Emission Computed Tomography Center, Huashan Hospital, Fudan University, Shanghai, China
| | - Fangfang Zhou
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
| | - Jie Li
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
| | - Weihao Li
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
| | - Kai Wang
- Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ting Wu
- Shanghai Stem Cell Group, Shanghai, China
| | - Yihui Guan
- Position Emission Computed Tomography Center, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiang Xie
- School of Computer Engineering and Science, Shanghai University, Shanghai, China
| | - Tieqiao Wen
- Laboratory of Molecular Neural Biology, School of Life Sciences, Shanghai University, Shanghai, China
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Moreno L, Rose C, Mohanraj A, Allinquant B, Billard JM, Dutar P. sAβPPα Improves Hippocampal NMDA-Dependent Functional Alterations Linked to Healthy Aging. J Alzheimers Dis 2015; 48:927-35. [DOI: 10.3233/jad-150297] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Dimitrakopoulou K, Vrahatis AG, Bezerianos A. Integromics network meta-analysis on cardiac aging offers robust multi-layer modular signatures and reveals micronome synergism. BMC Genomics 2015; 16:147. [PMID: 25887273 PMCID: PMC4367845 DOI: 10.1186/s12864-015-1256-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/19/2015] [Indexed: 02/02/2023] Open
Abstract
Background The avalanche of integromics and panomics approaches shifted the deciphering of aging mechanisms from single molecular entities to communities of them. In this orientation, we explore the cardiac aging mechanisms – risk factor for multiple cardiovascular diseases - by capturing the micronome synergism and detecting longevity signatures in the form of communities (modules). For this, we developed a meta-analysis scheme that integrates transcriptome expression data from multiple cardiac-specific independent studies in mouse and human along with proteome and micronome interaction data in the form of multiple independent weighted networks. Modularization of each weighted network produced modules, which in turn were further analyzed so as to define consensus modules across datasets that change substantially during lifespan. Also, we established a metric that determines - from the modular perspective - the synergism of microRNA-microRNA interactions as defined by significantly functionally associated targets. Results The meta-analysis provided 40 consensus integromics modules across mouse datasets and revealed microRNA relations with substantial collective action during aging. Three modules were reproducible, based on homology, when mapped against human-derived modules. The respective homologs mainly represent NADH dehydrogenases, ATP synthases, cytochrome oxidases, Ras GTPases and ribosomal proteins. Among various observations, we corroborate to the involvement of miR-34a (included in consensus modules) as proposed recently; yet we report that has no synergistic effect. Moving forward, we determined its age-related neighborhood in which HCN3, a known heart pacemaker channel, was included. Also, miR-125a-5p/-351, miR-200c/-429, miR-106b/-17, miR-363/-92b, miR-181b/-181d, miR-19a/-19b, let-7d/-7f, miR-18a/-18b, miR-128/-27b and miR-106a/-291a-3p pairs exhibited significant synergy and their association to aging and/or cardiovascular diseases is supported in many cases by a disease database and previous studies. On the contrary, we suggest that miR-22 has not substantial impact on heart longevity as proposed recently. Conclusions We revised several proteins and microRNAs recently implicated in cardiac aging and proposed for the first time modules as signatures. The integromics meta-analysis approach can serve as an efficient subvening signature tool for more-oriented better-designed experiments. It can also promote the combinational multi-target microRNA therapy of age-related cardiovascular diseases along the continuum from prevention to detection, diagnosis, treatment and outcome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1256-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Aristidis G Vrahatis
- Department of Medical Physics, School of Medicine, University of Patras, Patras, 26500, Greece. .,Department of Computer Engineering and Informatics, University of Patras, Patras, 26500, Greece.
| | - Anastasios Bezerianos
- Department of Medical Physics, School of Medicine, University of Patras, Patras, 26500, Greece. .,Singapore Institute for Neurotechnology (SINAPSE), Center of Life Sciences, National University of Singapore, Singapore, 117456, Singapore.
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