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de Freitas-Marchi BL, Dos Santos JF, Reigado GR, Fernandes MTP, Alcalde FSC, de Oliveira Carvalho CR, Nunes VA. Effect of Uncaria tomentosa aqueous extract on the response to palmitate-induced lipotoxicity in cultured skeletal muscle cells. BMC Complement Med Ther 2023; 23:412. [PMID: 37968654 PMCID: PMC10647034 DOI: 10.1186/s12906-023-04204-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/06/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Type 2 diabetes mellitus (T2DM) is frequently associated with dyslipidemia, which corresponds to the increase in the triglycerides and fatty acid concentrations in tissues, such as the skeletal muscle. Also, T2DM molecular mechanism involves increasing in reactive oxygen species (ROS) production and oxidative stress. The use of herbal medicines such as Uncaria tomentosa (Ut) has been proposed as an auxiliary treatment for patients with T2DM. In this study, it was evaluated the effect of Ut aqueous extract on cell viability and ROS production, in skeletal myoblasts from C2C12 lineage exposed to the free fatty acid palmitate (PA). METHODS Cells were incubated with PA in different concentrations ranging from 10 to 1000 μM, for 24 or 48 h, for cytotoxicity assay. Cell death, DNA fragmentation and ROS production assays were performed in cell cultures incubated with PA for 24 h, in the pre (preventive condition) or post treatment (therapeutic condition) with 250 μg/ml Ut aqueous extract, for 2 or 6 h. Cell death was evaluated by MTT method or flow cytometry. ROS generation was measured by fluorescence spectroscopy using the DCFDA probe. RESULTS Cell viability was reduced to approximately 44% after the incubation with PA for 24 h from the concentration of 500 µM. In the incubation of cells with 500 μM PA and Ut extract for 6 h, in both conditions (preventive or therapeutic), it was observed an increase of 27 and 70% in cell viability respectively, in comparison to the cultures incubated with only PA. Also, the incubation of cultures with 500 μM PA, for 24 h, increased 20-fold the ROS formation, while the treatment with Ut extract, for 6 h, both in the preventive or therapeutic conditions, promoted decrease of 21 and 55%, respectively. CONCLUSION The Ut extract was efficient in promoting cell protection against PA lipotoxicity and ROS generation, potentially preventing oxidative stress in C2C12 skeletal muscle cells. Since T2DM molecular mechanism involves oxidative stress condition and it is often associated with dyslipidemia and fatty acid accumulation in muscle tissue, these results open perspectives for the use of Ut as an auxiliary strategy for T2DM management.
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Affiliation(s)
- Bruna Leticia de Freitas-Marchi
- Laboratory of Skin Physiology and Tissue Bioengineering, School of Arts, Sciences and Humanities, University of Sao Paulo (EACH-USP), São Paulo, SP, Brazil
| | - Jeniffer Farias Dos Santos
- Laboratory of Skin Physiology and Tissue Bioengineering, School of Arts, Sciences and Humanities, University of Sao Paulo (EACH-USP), São Paulo, SP, Brazil
| | - Gustavo Roncoli Reigado
- Laboratory of Skin Physiology and Tissue Bioengineering, School of Arts, Sciences and Humanities, University of Sao Paulo (EACH-USP), São Paulo, SP, Brazil
| | - Myrian Thiago Pruschinski Fernandes
- Laboratory of Skin Physiology and Tissue Bioengineering, School of Arts, Sciences and Humanities, University of Sao Paulo (EACH-USP), São Paulo, SP, Brazil
| | - Felipe Santiago Chambergo Alcalde
- Laboratory of Skin Physiology and Tissue Bioengineering, School of Arts, Sciences and Humanities, University of Sao Paulo (EACH-USP), São Paulo, SP, Brazil
| | | | - Viviane Abreu Nunes
- Laboratory of Skin Physiology and Tissue Bioengineering, School of Arts, Sciences and Humanities, University of Sao Paulo (EACH-USP), São Paulo, SP, Brazil.
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Sawicki C, Haslam D, Bhupathiraju S. Utilising the precision nutrition toolkit in the path towards precision medicine. Proc Nutr Soc 2023; 82:359-369. [PMID: 37475596 DOI: 10.1017/s0029665123003038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
The overall aim of precision nutrition is to replace the 'one size fits all' approach to dietary advice with recommendations that are more specific to the individual in order to improve the prevention or management of chronic disease. Interest in precision nutrition has grown with advancements in technologies such as genomics, proteomics, metabolomics and measurement of the gut microbiome. Precision nutrition initiatives have three major applications in precision medicine. First, they aim to provide more 'precision' dietary assessments through artificial intelligence, wearable devices or by employing omic technologies to characterise diet more precisely. Secondly, precision nutrition allows us to understand the underlying mechanisms of how diet influences disease risk and identify individuals who are more susceptible to disease due to gene-diet or microbiota-diet interactions. Third, precision nutrition can be used for 'personalised nutrition' advice where machine-learning algorithms can integrate data from omic profiles with other personal and clinical measures to improve disease risk. Proteomics and metabolomics especially provide the ability to discover new biomarkers of food or nutrient intake, proteomic or metabolomic signatures of diet and disease, and discover potential mechanisms of diet-disease interactions. Although there are several challenges that must be overcome to improve the reproducibility, cost-effectiveness and efficacy of these approaches, precision nutrition methodologies have great potential for nutrition research and clinical application.
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Affiliation(s)
- Caleigh Sawicki
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Danielle Haslam
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Shilpa Bhupathiraju
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
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Hoch M, Ehlers L, Bannert K, Stanke C, Brauer D, Caton V, Lamprecht G, Wolkenhauer O, Jaster R, Wolfien M. In silico investigation of molecular networks linking gastrointestinal diseases, malnutrition, and sarcopenia. Front Nutr 2022; 9:989453. [DOI: 10.3389/fnut.2022.989453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022] Open
Abstract
Malnutrition (MN) is a common primary or secondary complication in gastrointestinal diseases. The patient’s nutritional status also influences muscle mass and function, which can be impaired up to the degree of sarcopenia. The molecular interactions in diseases leading to sarcopenia are complex and multifaceted, affecting muscle physiology, the intestine (nutrition), and the liver at different levels. Although extensive knowledge of individual molecular factors is available, their regulatory interplay is not yet fully understood. A comprehensive overall picture of pathological mechanisms and resulting phenotypes is lacking. In silico approaches that convert existing knowledge into computationally readable formats can help unravel mechanisms, underlying such complex molecular processes. From public literature, we manually compiled experimental evidence for molecular interactions involved in the development of sarcopenia into a knowledge base, referred to as the Sarcopenia Map. We integrated two diseases, namely liver cirrhosis (LC), and intestinal dysfunction, by considering their effects on nutrition and blood secretome. We demonstrate the performance of our model by successfully simulating the impact of changing dietary frequency, glycogen storage capacity, and disease severity on the carbohydrate and muscle systems. We present the Sarcopenia Map as a publicly available, open-source, and interactive online resource, that links gastrointestinal diseases, MN, and sarcopenia. The map provides tools that allow users to explore the information on the map and perform in silico simulations.
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Nanomaterial-Based Electrochemical Nanodiagnostics for Human and Gut Metabolites Diagnostics: Recent Advances and Challenges. BIOSENSORS 2022; 12:bios12090733. [PMID: 36140118 PMCID: PMC9496054 DOI: 10.3390/bios12090733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/27/2022] [Accepted: 08/31/2022] [Indexed: 11/29/2022]
Abstract
Metabolites are the intermediatory products of metabolic processes catalyzed by numerous enzymes found inside the cells. Detecting clinically relevant metabolites is important to understand their physiological and biological functions along with the evolving medical diagnostics. Rapid advances in detecting the tiny metabolites such as biomarkers that signify disease hallmarks have an immense need for high-performance identifying techniques. Low concentrations are found in biological fluids because the metabolites are difficult to dissolve in an aqueous medium. Therefore, the selective and sensitive study of metabolites as biomarkers in biological fluids is problematic. The different non-electrochemical and conventional methods need a long time of analysis, long sampling, high maintenance costs, and costly instrumentation. Hence, employing electrochemical techniques in clinical examination could efficiently meet the requirements of fully automated, inexpensive, specific, and quick means of biomarker detection. The electrochemical methods are broadly utilized in several emerging and established technologies, and electrochemical biosensors are employed to detect different metabolites. This review describes the advancement in electrochemical sensors developed for clinically associated human metabolites, including glucose, lactose, uric acid, urea, cholesterol, etc., and gut metabolites such as TMAO, TMA, and indole derivatives. Different sensing techniques are evaluated for their potential to achieve relevant degrees of multiplexing, specificity, and sensitivity limits. Moreover, we have also focused on the opportunities and remaining challenges for integrating the electrochemical sensor into the point-of-care (POC) devices.
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Blencowe M, Karunanayake T, Wier J, Hsu N, Yang X. Network Modeling Approaches and Applications to Unravelling Non-Alcoholic Fatty Liver Disease. Genes (Basel) 2019; 10:E966. [PMID: 31771247 PMCID: PMC6947017 DOI: 10.3390/genes10120966] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/18/2019] [Accepted: 11/22/2019] [Indexed: 12/12/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a progressive condition of the liver encompassing a range of pathologies including steatosis, non-alcoholic steatohepatitis (NASH), cirrhosis, and hepatocellular carcinoma. Research into this disease is imperative due to its rapid growth in prevalence, economic burden, and current lack of FDA approved therapies. NAFLD involves a highly complex etiology that calls for multi-tissue multi-omics network approaches to uncover the pathogenic genes and processes, diagnostic biomarkers, and potential therapeutic strategies. In this review, we first present a basic overview of disease pathogenesis, risk factors, and remaining knowledge gaps, followed by discussions of the need and concepts of multi-tissue multi-omics approaches, various network methodologies and application examples in NAFLD research. We highlight the findings that have been uncovered thus far including novel biomarkers, genes, and biological pathways involved in different stages of NAFLD, molecular connections between NAFLD and its comorbidities, mechanisms underpinning sex differences, and druggable targets. Lastly, we outline the future directions of implementing network approaches to further improve our understanding of NAFLD in order to guide diagnosis and therapeutics.
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Affiliation(s)
- Montgomery Blencowe
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA; (M.B.); (T.K.); (J.W.); (N.H.)
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Tilan Karunanayake
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA; (M.B.); (T.K.); (J.W.); (N.H.)
| | - Julian Wier
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA; (M.B.); (T.K.); (J.W.); (N.H.)
| | - Neil Hsu
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA; (M.B.); (T.K.); (J.W.); (N.H.)
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA; (M.B.); (T.K.); (J.W.); (N.H.)
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Interdepartmental Program of Bioinformatics, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
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Reddy BM, Pranavchand R, Latheef SAA. Overview of genomics and post-genomics research on type 2 diabetes mellitus: Future perspectives and a framework for further studies. J Biosci 2019; 44:21. [PMID: 30837372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this review, we briefly outlined salient features of pathophysiology and results of the genetic association studies hitherto conducted on type 2 diabetes. Primarily focusing on the current status of genomic research, we briefly discussed the limited progress made during the post-genomic era and tried to identify the limitations of the post-genomic research strategies. We suggested reanalysis of the existing genomic data through advanced statistical and computational methods and recommended integrated genomics-metabolomics approaches for future studies to facilitate understanding of the gene-environment interactions in the manifestation of the disease. We also propose a framework for research that may be apt for determining the effects of urbanization and changing lifestyles in the manifestation of complex genetic disorders like type 2 diabetes in the Indian populations and offset the confounding effects of both genetic and environmental factors in the natural way.
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Overview of genomics and post-genomics research on type 2 diabetes mellitus: Future perspectives and a framework for further studies. J Biosci 2019. [DOI: 10.1007/s12038-018-9818-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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8
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Gomez-Pinilla F, Yang X. System biology approach intersecting diet and cell metabolism with pathogenesis of brain disorders. Prog Neurobiol 2018; 169:76-90. [PMID: 30059718 PMCID: PMC6231047 DOI: 10.1016/j.pneurobio.2018.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 07/15/2018] [Indexed: 12/21/2022]
Abstract
The surge in meals high in calories has prompted an epidemic of metabolic disorders around the world such that the elevated incidence of obese and diabetic individuals is alarming. New research indicates that metabolic disorders pose a risk for neurological and psychiatric conditions including stroke, Alzheimer's disease, Huntington's disease, and depression, all of which have a metabolic component. These relationships are rooted to a dysfunctional interaction between molecular processes that regulate energy metabolism and synaptic plasticity. The strong adaptive force of dietary factors on shaping the brain during evolution can be manipulated to transform the interaction between cell bioenergetics and epigenome with the aptitude to promote long-lasting brain healthiness. A thorough understanding of the association between the broad action of nutrients and brain fitness requires high level data processing empowered with the capacity to integrate information from a multitude of molecular entities and pathways. Nutritional systems biology is emerging as a viable approach to elucidate the multiple molecular layers involved in information processing in cells, tissues, and organ systems in response to diet. Information about the wide range of cellular and molecular interactions elicited by foods on the brain and cognitive plasticity is crucial for the design of public health initiatives for curtailing the epidemic of metabolic and brain disorders.
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Affiliation(s)
- Fernando Gomez-Pinilla
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA; Department of Neurosurgery, UCLA Brain Injury Research Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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9
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Hepatic Dysfunction Caused by Consumption of a High-Fat Diet. Cell Rep 2018; 21:3317-3328. [PMID: 29241556 DOI: 10.1016/j.celrep.2017.11.059] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 11/11/2017] [Accepted: 11/16/2017] [Indexed: 12/16/2022] Open
Abstract
Obesity is a major human health crisis that promotes insulin resistance and, ultimately, type 2 diabetes. The molecular mechanisms that mediate this response occur across many highly complex biological regulatory levels that are incompletely understood. Here, we present a comprehensive molecular systems biology study of hepatic responses to high-fat feeding in mice. We interrogated diet-induced epigenomic, transcriptomic, proteomic, and metabolomic alterations using high-throughput omic methods and used a network modeling approach to integrate these diverse molecular signals. Our model indicated that disruption of hepatic architecture and enhanced hepatocyte apoptosis are among the numerous biological processes that contribute to early liver dysfunction and low-grade inflammation during the development of diet-induced metabolic syndrome. We validated these model findings with additional experiments on mouse liver sections. In total, we present an integrative systems biology study of diet-induced hepatic insulin resistance that uncovered molecular features promoting the development and maintenance of metabolic disease.
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10
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Abstract
PURPOSE Cardiovascular disease (CVD) is the leading cause of death in the United States and globally. There is significant evidence implicating genetic and dietary factors in the development and progression of CVD and its risk factors. Nutritional genomics is a comparatively new field of science that focuses on the relationship of individual genetic variation with response to nutrition. The purpose of this review is to summarize recent progress, in the field of nutritional genomics as it relates to cardiovascular disease. RECENT FINDINGS Evidence from recent studies has shown significant effects of gene-diet interactions on CVD biomarkers and the development and progression of CVD. The cardiovascular effects of gene-nutrient interactions with respect to macronutrients and genes such as FTO, ACE, PPARs, TCF7L2, BDNF, MC4R, APOAs, FADS, etc. have shown consistent results across age groups and populations whereas gene-nutrient interaction effects of other genes have only been limited to specific ages, genders or populations and need to validated and confirmed. SUMMARY The identification of individual genetic variation influencing diet-related CVD risk is important and may inform future nutritional intervention studies. Although there is ample scientific evidence indicating that the genetic susceptibility to CVD can be modified by diet, we are still not at a stage where this information is easily translated into dietary plans. Thus, there is a need for better approaches to achieve precision in dietary data collection and streamline computational approaches for meaningful and effective nutritional interventions.
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Affiliation(s)
- V Saroja Voruganti
- Department of Nutrition and UNC Nutrition Research Institute, University of North Carolina at Chapel Hill, 500 Laureate Way, Suite 3150, Kannapolis, NC 28081
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11
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Zhang Y, Qin C, Yang L, Lu R, Zhao X, Nie G. A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals. BMC Genomics 2018; 19:246. [PMID: 29642853 PMCID: PMC5896114 DOI: 10.1186/s12864-018-4647-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 04/03/2018] [Indexed: 12/31/2022] Open
Abstract
Background Glucose plays a key role as an energy source in most mammals, but its importance in fish appears to be limited that so far seemed to belong to diabetic humans only. Several laboratories worldwide have made important efforts in order to better understand this strange phenotype observed in fish. However, the mechanism of carbohydrate/glucose metabolism is astonishingly complex. Why basal glycaemia is different between fish and mammals and how carbohydrate metabolism is different amongst organisms is largely uncharted territory. The utilization of comparative systems biology with model vertebrates to explore fish metabolism has become an essential approach to unravelling hidden in vivo mechanisms. Results In this study, we first built a database containing 791, 593, 523, 666 and 698 carbohydrate/glucose metabolic genes from the genomes of Danio rerio, Xenopus tropicalis, Gallus gallus, Mus musculus and Homo sapiens, respectively, and most of these genes in our database are predicted to encode specific enzymes that play roles in defined reactions; over 57% of these genes are related to human type 2 diabetes. Then, we systematically compared these genes and found that more than 70% of the carbohydrate/glucose metabolic genes are conserved in the five species. Interestingly, there are 4 zebrafish-specific genes (si:ch211-167b20.8, CABZ01043017.1, socs9 and eif4e1c) and 1 human-specific gene (CALML6) that may alter glucose utilization in their corresponding species. Interestingly, these 5 genes are all carbohydrate regulation factors, but the enzymes themselves are involved in insulin regulation pathways. Lastly, in order to facilitate the use of our data sets, we constructed a glucose metabolism database platform (http://101.200.43.1:10000/). Conclusions This study provides the first systematic genomic insights into carbohydrate/glucose metabolism. After exhaustive analysis, we found that most metabolic genes are conserved in vertebrates. This work may resolve some of the complexities of carbohydrate/glucose metabolic heterogeneity amongst different vertebrates and may provide a reference for the treatment of diabetes and for applications in the aquaculture industry. Electronic supplementary material The online version of this article (10.1186/s12864-018-4647-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuru Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China.,College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Chaobin Qin
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China.,College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Liping Yang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China.,College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Ronghua Lu
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China.,College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Xiaoyan Zhao
- School of Computer and Information Engineering, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Guoxing Nie
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China. .,College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, 453007, People's Republic of China.
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Alkhatib A, Tsang C, Tiss A, Bahorun T, Arefanian H, Barake R, Khadir A, Tuomilehto J. Functional Foods and Lifestyle Approaches for Diabetes Prevention and Management. Nutrients 2017; 9:E1310. [PMID: 29194424 PMCID: PMC5748760 DOI: 10.3390/nu9121310] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/26/2017] [Accepted: 11/27/2017] [Indexed: 02/07/2023] Open
Abstract
Functional foods contain biologically active ingredients associated with physiological health benefits for preventing and managing chronic diseases, such as type 2 diabetes mellitus (T2DM). A regular consumption of functional foods may be associated with enhanced anti-oxidant, anti-inflammatory, insulin sensitivity, and anti-cholesterol functions, which are considered integral to prevent and manage T2DM. Components of the Mediterranean diet (MD)-such as fruits, vegetables, oily fish, olive oil, and tree nuts-serve as a model for functional foods based on their natural contents of nutraceuticals, including polyphenols, terpenoids, flavonoids, alkaloids, sterols, pigments, and unsaturated fatty acids. Polyphenols within MD and polyphenol-rich herbs-such as coffee, green tea, black tea, and yerba maté-have shown clinically-meaningful benefits on metabolic and microvascular activities, cholesterol and fasting glucose lowering, and anti-inflammation and anti-oxidation in high-risk and T2DM patients. However, combining exercise with functional food consumption can trigger and augment several metabolic and cardiovascular protective benefits, but it is under-investigated in people with T2DM and bariatric surgery patients. Detecting functional food benefits can now rely on an "omics" biological profiling of individuals' molecular, genetics, transcriptomics, proteomics, and metabolomics, but is under-investigated in multi-component interventions. A personalized approach for preventing and managing T2DM should consider biological and behavioral models, and embed nutrition education as part of lifestyle diabetes prevention studies. Functional foods may provide additional benefits in such an approach.
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Affiliation(s)
- Ahmad Alkhatib
- Dasman Diabetes Institute, P.O. Box 1180, Dasman 15462, Kuwait.
| | - Catherine Tsang
- Faculty of Health and Social Care, Edge Hill University, St. Helens Road, Ormskirk, Lancashire L39 4QP, UK.
| | - Ali Tiss
- Dasman Diabetes Institute, P.O. Box 1180, Dasman 15462, Kuwait.
| | - Theeshan Bahorun
- ANDI Centre of Excellence for Biomedical and Biomaterials Research, University of Mauritius, MSIRI Building, Réduit 80837, Mauritius.
| | | | - Roula Barake
- Dasman Diabetes Institute, P.O. Box 1180, Dasman 15462, Kuwait.
| | | | - Jaakko Tuomilehto
- Dasman Diabetes Institute, P.O. Box 1180, Dasman 15462, Kuwait.
- Diabetes Research Group, King Abdulaziz University, P.O. Box 80200, Jeddah 21589, Saudi Arabia.
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Ke M, Wu H, Zhu Z, Zhang C, Zhang Y, Deng Y. Differential proteomic analysis of white adipose tissues from T2D KKAy mice by LC-ESI-QTOF. Proteomics 2017; 17. [PMID: 27995753 DOI: 10.1002/pmic.201600219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 11/28/2016] [Accepted: 12/13/2016] [Indexed: 12/14/2022]
Abstract
Type 2 diabetes (T2D) has become a worldwide increasingly social health burden for its high morbidity and heightened prevalence. As one of the main tissues involved in uptake of glucose under the stimulation of insulin, WAT plays very important role in metabolic and homeostasis regulation. We performed a differential proteomics study to investigate alterations in epididymis fat pad of high fat diet fed T2D KKAy mice compared to normal fed C57BL/6J mice, by 18 O-labeling relative quantitative technique. Among 329 confidently identified proteins, 121 proteins showed significant changes with CV ≤ 20% (fold changes of >2 or <0.5 as threshold). According to GO classification, we found that altered proteins contained members of biological processes of metabolic process, oxidative stress, ion homeostasis, apoptosis and cell division. In metabolic, proteins assigned to fatty acid biosynthesis (FAS etc.) were decreased, the key enzyme (ACOX3) in β-oxidation process was increased. Increased glycolysis enzymes (ENOB etc.) and decreased TCA cycle related enzymes (SCOT1 etc.) suggested that glucose metabolism in mitochondria of T2D mice might be impaired. Elevated oxidative stress was observed with alterations of a series of oxidordeuctase (QSOX1 etc.). Besides, alterations of ion homeostasis (AT2C1 etc.) proteins were also observed. The enhancement of cell proliferation associated proteins (ELYS etc.) and inhibition of apoptosis associated proteins (RASF6 etc.) in WAT might contributed to the fat pad and body weight gain. Overall, these changes in WAT may serve as a reference for understanding the functional mechanism of T2D.
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Affiliation(s)
- Ming Ke
- Beijing Institute of Technology, School of life science, Haidian, Beijing, P. R. China
| | - Hanyan Wu
- Beijing Institute of Technology, School of life science, Haidian, Beijing, P. R. China
| | - Zhaoyang Zhu
- Beijing Institute of Technology, School of life science, Haidian, Beijing, P. R. China
| | - Chi Zhang
- Beijing Institute of Technology, School of life science, Haidian, Beijing, P. R. China
| | - Yongqian Zhang
- Beijing Institute of Technology, School of life science, Haidian, Beijing, P. R. China
| | - Yunlin Deng
- Beijing Institute of Technology, School of life science, Haidian, Beijing, P. R. China
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Arneson D, Shu L, Tsai B, Barrere-Cain R, Sun C, Yang X. Multidimensional Integrative Genomics Approaches to Dissecting Cardiovascular Disease. Front Cardiovasc Med 2017; 4:8. [PMID: 28289683 PMCID: PMC5327355 DOI: 10.3389/fcvm.2017.00008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/09/2017] [Indexed: 12/19/2022] Open
Abstract
Elucidating the mechanisms of complex diseases such as cardiovascular disease (CVD) remains a significant challenge due to multidimensional alterations at molecular, cellular, tissue, and organ levels. To better understand CVD and offer insights into the underlying mechanisms and potential therapeutic strategies, data from multiple omics types (genomics, epigenomics, transcriptomics, metabolomics, proteomics, microbiomics) from both humans and model organisms have become available. However, individual omics data types capture only a fraction of the molecular mechanisms. To address this challenge, there have been numerous efforts to develop integrative genomics methods that can leverage multidimensional information from diverse data types to derive comprehensive molecular insights. In this review, we summarize recent methodological advances in multidimensional omics integration, exemplify their applications in cardiovascular research, and pinpoint challenges and future directions in this incipient field.
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Affiliation(s)
- Douglas Arneson
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, USA; Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Le Shu
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, USA; Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Brandon Tsai
- Department of Integrative Biology and Physiology, University of California Los Angeles , Los Angeles, CA , USA
| | - Rio Barrere-Cain
- Department of Integrative Biology and Physiology, University of California Los Angeles , Los Angeles, CA , USA
| | - Christine Sun
- Department of Integrative Biology and Physiology, University of California Los Angeles , Los Angeles, CA , USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA, USA; Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA; Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA; Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
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15
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Najafi A, Ghanei M, Jamalkandi SA. Airway remodeling: Systems biology approach, from bench to bedside. Technol Health Care 2016; 24:811-819. [PMID: 27315153 DOI: 10.3233/thc-161228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Airway Remodeling, a patho-physiologic process, is considered as a key feature of chronic airway diseases. In recent years, our understanding of the complex diseases has increased significantly by the use of combined approaches, including systems biology, which may contribute to the development of personalized and predictive medicine approaches. Integrative analysis, along with the cooperation of clinicians, computer scientists, research scientists, and bench scientists, has become an important part of the experimental design and therapeutic strategies in the era of omics. The airway remodeling process is the result of the dysregulation of several signaling pathways that modulate the airway regeneration; therefore, high-throughput experiments and systems biology approach can help to understand this process better. The study reviews related literature and is consistent with the existing clinical evidence.
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Affiliation(s)
- Ali Najafi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mostafa Ghanei
- Chemical Injury Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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16
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Ewald DR, Sumner SCJ. Blood type biochemistry and human disease. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2016; 8:517-535. [PMID: 27599872 PMCID: PMC5061611 DOI: 10.1002/wsbm.1355] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/08/2016] [Accepted: 06/26/2016] [Indexed: 12/12/2022]
Abstract
Associations between blood type and disease have been studied since the early 1900s when researchers determined that antibodies and antigens are inherited. In the 1950s, the chemical identification of the carbohydrate structure of surface antigens led to the understanding of biosynthetic pathways. The blood type is defined by oligosaccharide structures, which are specific to the antigens, thus, blood group antigens are secondary gene products, while the primary gene products are various glycosyltransferase enzymes that attach the sugar molecules to the oligosaccharide chain. Blood group antigens are found on red blood cells, platelets, leukocytes, plasma proteins, certain tissues, and various cell surface enzymes, and also exist in soluble form in body secretions such as breast milk, seminal fluid, saliva, sweat, gastric secretions, urine, and amniotic fluid. Recent advances in technology, biochemistry, and genetics have clarified the functional classifications of human blood group antigens, the structure of the A, B, H, and Lewis determinants and the enzymes that produce them, and the association of blood group antigens with disease risks. Further research to identify differences in the biochemical composition of blood group antigens, and the relationship to risks for disease, can be important for the identification of targets for the development of nutritional intervention strategies, or the identification of druggable targets. WIREs Syst Biol Med 2016, 8:517-535. doi: 10.1002/wsbm.1355 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- D Rose Ewald
- Discovery Sciences, RTI International, Research Triangle Park, NC, USA
| | - Susan C J Sumner
- Discovery Sciences, RTI International, Research Triangle Park, NC, USA.
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17
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Meng Q, Ying Z, Noble E, Zhao Y, Agrawal R, Mikhail A, Zhuang Y, Tyagi E, Zhang Q, Lee JH, Morselli M, Orozco L, Guo W, Kilts TM, Zhu J, Zhang B, Pellegrini M, Xiao X, Young MF, Gomez-Pinilla F, Yang X. Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders. EBioMedicine 2016; 7:157-66. [PMID: 27322469 PMCID: PMC4909610 DOI: 10.1016/j.ebiom.2016.04.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/05/2016] [Accepted: 04/07/2016] [Indexed: 12/30/2022] Open
Abstract
Nutrition plays a significant role in the increasing prevalence of metabolic and brain disorders. Here we employ systems nutrigenomics to scrutinize the genomic bases of nutrient–host interaction underlying disease predisposition or therapeutic potential. We conducted transcriptome and epigenome sequencing of hypothalamus (metabolic control) and hippocampus (cognitive processing) from a rodent model of fructose consumption, and identified significant reprogramming of DNA methylation, transcript abundance, alternative splicing, and gene networks governing cell metabolism, cell communication, inflammation, and neuronal signaling. These signals converged with genetic causal risks of metabolic, neurological, and psychiatric disorders revealed in humans. Gene network modeling uncovered the extracellular matrix genes Bgn and Fmod as main orchestrators of the effects of fructose, as validated using two knockout mouse models. We further demonstrate that an omega-3 fatty acid, DHA, reverses the genomic and network perturbations elicited by fructose, providing molecular support for nutritional interventions to counteract diet-induced metabolic and brain disorders. Our integrative approach complementing rodent and human studies supports the applicability of nutrigenomics principles to predict disease susceptibility and to guide personalized medicine. Fructose promotes transcriptomic and epigenomic reprogramming to perturb brain networks linking metabolism and brain function. The extracellular matrix genes Bgn and Fmod emerge as key regulators of gene networks responsive to fructose. The omega-3 fatty acid DHA reverses fructose-induced genomic and network reprogramming.
Meng et al. report fructose as a powerful inducer of genomic and epigenomic variability with the capacity to reorganize gene networks critical for central metabolic regulation and neuronal processes in the brain; conversely, an omega-3 fatty acid, DHA, has the potential to normalize the genomic impact of fructose. Our findings help explain the pathogenic actions of fructose on prevalent metabolic and brain disorders and provide proof-of-concept for nutritional remedies supported by nutrigenomics evidence. Our integrative approach complementing rodent and human studies supports the applicability of nutrigenomics principles to predict disease susceptibility and to guide personalized medicine.
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Affiliation(s)
- Qingying Meng
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhe Ying
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Emily Noble
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yuqi Zhao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rahul Agrawal
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Andrew Mikhail
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yumei Zhuang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ethika Tyagi
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Qing Zhang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jae-Hyung Lee
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Maxillofacial Biomedical Engineering, School of Dentistry, Kyung Hee University, Seoul 130-701, Korea
| | - Marco Morselli
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Luz Orozco
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Weilong Guo
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Center for Synthetic & Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China
| | - Tina M Kilts
- Craniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marian F Young
- Craniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fernando Gomez-Pinilla
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Neurosurgery, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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18
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Zhao Y, Wang Y, Zou L, Huang J. Reconstruction and applications of consensus yeast metabolic network based on RNA sequencing. FEBS Open Bio 2016; 6:264-75. [PMID: 27239440 PMCID: PMC4821349 DOI: 10.1002/2211-5463.12033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/08/2016] [Accepted: 01/13/2016] [Indexed: 11/06/2022] Open
Abstract
One practical application of genome-scale metabolic reconstructions is to interrogate multispecies relationships. Here, we report a consensus metabolic model in four yeast species (Saccharomyces cerevisiae, S. paradoxus, S. mikatae, and S. bayanus) by integrating metabolic network simulations with RNA sequencing (RNA-seq) datasets. We generated high-resolution transcriptome maps of four yeast species through de novo assembly and genome-guided approaches. The transcriptomes were annotated and applied to build the consensus metabolic network, which was verified using independent RNA-seq experiments. The expression profiles reveal that the genes involved in amino acid and lipid metabolism are highly coexpressed. The diverse phenotypic characteristics, such as cellular growth and gene deletions, can be simulated using the metabolic model. We also explored the applications of the consensus model in metabolic engineering using yeast-specific reactions and biofuel production as examples. Similar strategies will benefit communities studying genome-scale metabolic networks of other organisms.
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Affiliation(s)
- Yuqi Zhao
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Yunnan China
| | - Yanjie Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province Kunming Institute of Zoology Chinese Academy of Sciences Yunnan China
| | - Lei Zou
- Department of General Surgery First People's Hospital of Yunnan Province Kunming China
| | - Jingfei Huang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Yunnan China; Collaborative Innovation Center for Natural Products and Biological Drugs of Yunnan Kunming Yunnan China
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19
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Kaput J, Kussmann M, Radonjic M, Virgili F, Perozzi G. Human nutrition, environment, and health. GENES AND NUTRITION 2015; 10:489. [PMID: 26319142 DOI: 10.1007/s12263-015-0489-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Jim Kaput
- Nestlé Institute of Health Sciences, Lausanne, Switzerland,
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