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Kaput J, Monteiro JP. Human Nutrition Research in the Data Era: Results of 11 Reports on the Effects of a Multiple-Micronutrient-Intervention Study. Nutrients 2024; 16:188. [PMID: 38257081 PMCID: PMC10819666 DOI: 10.3390/nu16020188] [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: 11/17/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Large datasets have been used in molecular and genetic research for decades, but only a few studies have included nutrition and lifestyle factors. Our team conducted an n-of-1 intervention with 12 vitamins and five minerals in 9- to 13-year-old Brazilian children and teens with poor healthy-eating indices. A unique feature of the experimental design was the inclusion of a replication arm. Twenty-six types of data were acquired including clinical measures, whole-genome mapping, whole-exome sequencing, and proteomic and a variety of metabolomic measurements over two years. A goal of this study was to use these diverse data sets to discover previously undetected physiological effects associated with a poor diet that include a more complete micronutrient composition. We summarize the key findings of 11 reports from this study that (i) found that LDL and total cholesterol and fasting glucose decreased in the population after the intervention but with inter-individual variation; (ii) associated a polygenic risk score that predicted baseline vitamin B12 levels; (iii) identified metabotypes linking diet intake, genetic makeup, and metabolic physiology; (iv) found multiple biomarkers for nutrient and food groups; and (v) discovered metabolites and proteins that are associated with DNA damage. This summary also highlights the limitations and lessons in analyzing diverse omic data.
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Affiliation(s)
| | - Jacqueline Pontes Monteiro
- Faculty of Medicine of Ribeirão Preto, Department of Pediatrics, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil;
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2
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White M, Arif‐Pardy J, Van Mieghem T, Connor KL. Fetal spina bifida associates with dysregulation in nutrient-sensitive placental gene networks: Findings from a matched case-control study. Clin Transl Sci 2024; 17:e13710. [PMID: 38226444 PMCID: PMC10804907 DOI: 10.1111/cts.13710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/17/2023] [Accepted: 12/06/2023] [Indexed: 01/17/2024] Open
Abstract
To improve outcomes in fetuses with spina bifida (SB), better understanding is needed of the molecular drivers of SB and its comorbidities. Pregnant people carrying a fetus with isolated SB (cases; n = 12) or a fetus with no congenital anomalies (controls; n = 21) were recruited at Mount Sinai Hospital, Toronto, Ontario, Canada. Clinical data and placental samples were collected. Placental transcriptome was sequenced (Clariom D microarray) and a nutrient-focused gene expression analysis pipeline was applied to determine whether fetal SB associates with placental dysfunction. Of the 391 differentially expressed genes (DEGs) in cases, 11% (n = 42) had at least one nutrient cofactor, including B vitamins (n = 7 genes), iron/heme (n = 6), and zinc (n = 11). Cases had dysregulation in genes not previously known to associate with SB, and in placental genes that have known links to SB but have not been previously identified in the placenta. Cases also had downregulated nutrient transport and upregulated branching angiogenesis and immune/inflammatory processes. Five nutrient-dependent transcription regulators, collectively predicted to target 46% of DEGs in cases, were identified and were most commonly dependent on B vitamins (n = 3) and zinc (n = 2). Placental gene expression changes were most acute in cases with poor growth. Placentae from fetuses with SB have dysregulation in several gene networks, including those that are sensitive to multiple micronutrients beyond the well-known folic acid. An improved understanding of placental phenotype in fetuses with SB may help identify novel mechanisms associated with comorbidities in fetuses with SB, and reveal new targets to improve fetal outcomes in this population.
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Affiliation(s)
- Marina White
- Health SciencesCarleton UniversityOttawaOntarioCanada
| | | | - Tim Van Mieghem
- Department of Obstetrics and GynaecologyMount Sinai HospitalTorontoOntarioCanada
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3
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Rajaratnam S, Pradhan SS, Naik AA, Sivaramakrishnan V. Integrated Multi-Omics Analysis and Validation in Yeast Model of Amyotrophic Lateral Sclerosis. Methods Mol Biol 2024; 2761:397-419. [PMID: 38427252 DOI: 10.1007/978-1-0716-3662-6_28] [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] [Indexed: 03/02/2024]
Abstract
Transcriptomics is a complex process that involves raw data extraction, normalization, differential gene expression, and analysis. The Gene Expression Omnibus (GEO) database at the National Center for Biotechnology Information (NCBI) is a repository of experimental datasets. Amyotrophic lateral sclerosis (ALS) datasets are deposited by various scientists and research investigators to expand the horizon of scientific knowledge. R-statistical tools are the most common ways for conducting these kinds of studies. The first step is the identification of appropriate datasets. Since the raw data is available in a variety of formats, a large array of software is used for extraction and analysis. Normalization is conducted for the datasets using NetworkAnalyst. Differential analysis is further conducted on the normalized data to identify significantly enriched genes. The significant genes are then grouped into pathways. The results were validated using yeast model of ALS in which the yeast is transformed with ALS plasmids encoding genes associated with ALS. The resulting GFP-tagged protein aggregates are imaged using fluorescence microscopy and subsequently validated using filter retardation assay and quantified using ImageJ software. Functional role of different genes is studied using metabolite treatment and knockout studies.
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Affiliation(s)
- Saiswaroop Rajaratnam
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, Andhra Pradesh, India
| | - Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, Andhra Pradesh, India
| | - Ashwin Ashok Naik
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, Andhra Pradesh, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, Andhra Pradesh, India.
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Kodam P, Sai Swaroop R, Pradhan SS, Sivaramakrishnan V, Vadrevu R. Integrated multi-omics analysis of Alzheimer's disease shows molecular signatures associated with disease progression and potential therapeutic targets. Sci Rep 2023; 13:3695. [PMID: 36879094 PMCID: PMC9986671 DOI: 10.1038/s41598-023-30892-6] [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] [Received: 10/20/2022] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by the formation of amyloid plaques implicated in neuronal death. Genetics, age, and sex are the risk factors attributed to AD. Though omics studies have helped to identify pathways associated with AD, an integrated systems analysis with the available data could help to understand mechanisms, potential biomarkers, and therapeutic targets. Analysis of transcriptomic data sets from the GEO database, and proteomic and metabolomic data sets from literature was performed to identify deregulated pathways and commonality analysis identified overlapping pathways among the data sets. The deregulated pathways included those of neurotransmitter synapses, oxidative stress, inflammation, vitamins, complement, and coagulation pathways. Cell type analysis of GEO data sets showed microglia, endothelial, myeloid, and lymphoid cells are affected. Microglia are associated with inflammation and pruning of synapses with implications for memory and cognition. Analysis of the protein-cofactor network of B2, B6, and pantothenate shows metabolic pathways modulated by these vitamins which overlap with the deregulated pathways from the multi-omics analysis. Overall, the integrated analysis identified the molecular signature associated with AD. Treatment with anti-oxidants, B2, B6, and pantothenate in genetically susceptible individuals in the pre-symptomatic stage might help in better management of the disease.
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Affiliation(s)
- Pradeep Kodam
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Jawahar Nagar, Hyderabad, Telangana, 500078, India
| | - R Sai Swaroop
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, 515134, India
| | - Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, 515134, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, 515134, India.
| | - Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Jawahar Nagar, Hyderabad, Telangana, 500078, India.
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White M, Arif-Pardy J, Connor KL. Identification of novel nutrient-sensitive gene regulatory networks in amniocytes from fetuses with spina bifida. Reprod Toxicol 2023; 116:108333. [PMID: 36584796 DOI: 10.1016/j.reprotox.2022.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/14/2022] [Accepted: 12/26/2022] [Indexed: 12/28/2022]
Abstract
Neural tube defects (NTDs) remain among the most common congenital anomalies. Contributing risk factors include genetics and nutrient deficiencies, however, a comprehensive assessment of nutrient-gene interactions in NTDs is lacking. We applied a nutrient-focused gene expression analysis pipeline to identify nutrient-sensitive gene regulatory networks in amniocyte gene expression data (GSE4182) from fetuses with NTDs (cases; n = 3) and fetuses with no congenital anomalies (controls; n = 5). Differentially expressed genes (DEGs) were screened for having nutrient cofactors. Nutrient-dependent transcriptional regulators (TRs) that regulated DEGs, and nutrient-sensitive miRNAs with a previous link to NTDs, were identified. Of the 880 DEGs in cases, 10% had at least one nutrient cofactor. DEG regulatory network analysis revealed that 39% and 52% of DEGs in cases were regulated by 22 nutrient-sensitive miRNAs and 10 nutrient-dependent TRs, respectively. Zinc- and B vitamin-dependent gene regulatory networks (Zinc: 10 TRs targeting 50.6% of DEGs; B vitamins: 4 TRs targeting 37.7% of DEGs, 9 miRNAs targeting 17.6% of DEGs) were dysregulated in cases. We identified novel, nutrient-sensitive gene regulatory networks not previously linked to NTDs, which may indicate new targets to explore for NTD prevention or to optimise fetal development.
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Affiliation(s)
- Marina White
- Health Sciences, Carleton University, 1125 Colonel By Dr, Ottawa K1S 5B6, ON, Canada
| | - Jayden Arif-Pardy
- Health Sciences, Carleton University, 1125 Colonel By Dr, Ottawa K1S 5B6, ON, Canada
| | - Kristin L Connor
- Health Sciences, Carleton University, 1125 Colonel By Dr, Ottawa K1S 5B6, ON, Canada.
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Pradhan SS, Rao KR, Manjunath M, Saiswaroop R, Patnana DP, Phalguna KS, Choudhary B, Sivaramakrishnan V. Vitamin B 6, B 12 and folate modulate deregulated pathways and protein aggregation in yeast model of Huntington disease. 3 Biotech 2023; 13:96. [PMID: 36852176 PMCID: PMC9958225 DOI: 10.1007/s13205-023-03525-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
Huntington's disease (HD) is an incurable and progressive neurodegenerative disease affecting the basal ganglia of the brain. HD is caused due to expansion of the polyglutamine tract in the protein Huntingtin resulting in aggregates. The increased PolyQ length results in aggregation of protein Huntingtin leading to neuronal cell death. Vitamin B6, B12 and folate are deficient in many neurodegenerative diseases. We performed an integrated analysis of transcriptomic, metabolomic and cofactor-protein network of vitamin B6, B12 and folate was performed. Our results show considerable overlap of pathways modulated by Vitamin B6, B12 and folate with those obtained from transcriptomic and metabolomic data of HD patients and model systems. Further, in yeast model of HD we showed treatment of B6, B12 or folate either alone or in combination showed impaired aggregate formation. Transcriptomic analysis of yeast model treated with B6, B12 and folate showed upregulation of pathways like ubiquitin mediated proteolysis, autophagy, peroxisome, fatty acid, lipid and nitrogen metabolism. Metabolomic analysis of yeast model shows deregulation of pathways like aminoacyl-tRNA biosynthesis, metabolism of various amino acids, nitrogen metabolism and glutathione metabolism. Integrated transcriptomic and metabolomic analysis of yeast model showed concordance in the pathways obtained. Knockout of Peroxisomal (PXP1 and PEX7) and Autophagy (ATG5) genes in yeast increased aggregates which is mitigated by vitamin B6, B12 and folate treatment. Taken together our results show a role for Vitamin B6, B12 and folate mediated modulation of pathways important for preventing protein aggregation with potential implications for HD. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03525-y.
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Affiliation(s)
- Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - K. Raksha Rao
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka 560100 India
| | - Meghana Manjunath
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka 560100 India
| | - R. Saiswaroop
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - Durga Prasad Patnana
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - Kanikaram Sai Phalguna
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka 560100 India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
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7
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Naik AA, Sivaramakrishnan V. Systems analysis of steroid induced osteonecrosis shows role for heme and vitamin D in pathogenesis. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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8
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Kaput J. Developing the Pathway to Personalized Health: The Potential of N-of-1 Studies for Personalizing Nutrition. J Nutr 2021; 151:2863-2864. [PMID: 34293136 DOI: 10.1093/jn/nxab243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Chen X, Xu M, An Y. Identifying the essential nodes in network pharmacology based on multilayer network combined with random walk algorithm. J Biomed Inform 2020; 114:103666. [PMID: 33352331 DOI: 10.1016/j.jbi.2020.103666] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 11/15/2022]
Abstract
Compared with the general complex network, the multilayer network is more suitable for the description of reality. It can be used as a tool of network pharmacology to analyze the mechanism of drug action from an overall perspective. Combined with random walk algorithm, it measures the importance of nodes from the entire network rather than a single layer. Here a four-layer network was constructed based on the data about the action process of prescriptions, consisting of ingredients, target proteins, metabolic pathways and diseases. The random walk algorithm was used to calculate the betweenness centrality of the protein layer nodes to get the rank of their importance. According to above method, we screened out the top 10% proteins that play a key role in treatment. Prescriptions Xiaochaihu Decoction was taken as example to prove our method. The selected proteins were measured with the ones that have been validated to be associated with the treated diseases. The results showed that its accuracy was no less than the topology-based method of single-layer network. The applicability of our method was proved by another prescription Yupingfeng Decoction. Our study demonstrated that multilayer network combined with random walk algorithm was an effective method for pre-screening vital target proteins related to prescriptions.
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Affiliation(s)
- Xianlai Chen
- Big Data Institute, Central South University, Changsha, Hunan, China.
| | - Mingyue Xu
- Big Data Institute, Central South University, Changsha, Hunan, China.
| | - Ying An
- Big Data Institute, Central South University, Changsha, Hunan, China.
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10
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Nijhout HF, Kudla AM, Hazelwood CC. Genetic assimilation and accommodation: Models and mechanisms. Curr Top Dev Biol 2020; 141:337-369. [PMID: 33602492 DOI: 10.1016/bs.ctdb.2020.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genetic assimilation and genetic accommodation are mechanisms by which novel phenotypes are produced and become established in a population. Novel characters may be fixed and canalized so they are insensitive to environmental variation, or can be plastic and adaptively responsive to environmental variation. In this review we explore the various theories that have been proposed to explain the developmental origin and evolution of novel phenotypes and the mechanisms by which canalization and phenotypic plasticity evolve. These theories and models range from conceptual to mathematical and have taken different views of how genes and environment contribute to the development and evolution of the properties of phenotypes. We will argue that a deeper and more nuanced understanding of genetic accommodation requires a recognition that phenotypes are not static entities but are dynamic system properties with no fixed deterministic relationship between genotype and phenotype. We suggest a mechanistic systems-view of development that allows one to incorporate both genes and environment in a common model, and that enables both quantitative analysis and visualization of the evolution of canalization and phenotypic plasticity.
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Affiliation(s)
| | - Anna M Kudla
- Department of Biology, Duke University, Durham, NC, United States
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11
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Naik AA, Narayanan A, Khanchandani P, Sridharan D, Sukumar P, Srimadh Bhagavatam SK, Seshagiri PB, Sivaramakrishnan V. Systems analysis of avascular necrosis of femoral head using integrative data analysis and literature mining delineates pathways associated with disease. Sci Rep 2020; 10:18099. [PMID: 33093559 PMCID: PMC7581770 DOI: 10.1038/s41598-020-75197-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/13/2020] [Indexed: 12/19/2022] Open
Abstract
Avascular necrosis of femoral head (AVNFH) is a debilitating disease, which affects the middle aged population. Though the disease is managed using bisphosphonate, it eventually leads to total hip replacement due to collapse of femoral head. Studies regarding the association of single nucleotide polymorphisms with AVNFH, transcriptomics, proteomics, metabolomics, biophysical, ultrastructural and histopathology have been carried out. Functional validation of SNPs was carried out using literature. An integrated systems analysis using the available datasets might help to gain further insights into the disease process. We have carried out an analysis of transcriptomic data from GEO-database, SNPs associated with AVNFH, proteomic and metabolomic data collected from literature. Based on deficiency of vitamins in AVNFH, an enzyme-cofactor network was generated. The datasets are analyzed using ClueGO and the genes are binned into pathways. Metabolomic datasets are analyzed using MetaboAnalyst. Centrality analysis using CytoNCA on the data sets showed cystathionine beta synthase and methylmalonyl-CoA-mutase to be common to 3 out of 4 datasets. Further, the genes common to at least two data sets were analyzed using DisGeNET, which showed their involvement with various diseases, most of which were risk factors associated with AVNFH. Our analysis shows elevated homocysteine, hypoxia, coagulation, Osteoclast differentiation and endochondral ossification as the major pathways associated with disease which correlated with histopathology, IHC, MRI, Micro-Raman spectroscopy etc. The analysis shows AVNFH to be a multi-systemic disease and provides molecular signatures that are characteristic to the disease process.
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Affiliation(s)
- Ashwin Ashok Naik
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthinilayam, Andhra Pradesh, 515 134, India
| | - Aswath Narayanan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthinilayam, Andhra Pradesh, 515 134, India
| | - Prakash Khanchandani
- Department of Orthopedics, Sri Sathya Sai Institute of Higher Medical Sciences, Prasanthigram, Andhra Pradesh, 515 134, India.
| | - Divya Sridharan
- Molecular Reproduction and Developmental Genetics, Indian Institute of Science, Bangalore, Bangalore, India
| | - Piruthivi Sukumar
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Sai Krishna Srimadh Bhagavatam
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthinilayam, Andhra Pradesh, 515 134, India
| | - Polani B Seshagiri
- Molecular Reproduction and Developmental Genetics, Indian Institute of Science, Bangalore, Bangalore, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthinilayam, Andhra Pradesh, 515 134, India.
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12
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Abstract
It is proposed that proteins/enzymes be classified into two classes according to their essentiality for immediate survival/reproduction and their function in long-term health: that is, survival proteins versus longevity proteins. As proposed by the triage theory, a modest deficiency of one of the nutrients/cofactors triggers a built-in rationing mechanism that favors the proteins needed for immediate survival and reproduction (survival proteins) while sacrificing those needed to protect against future damage (longevity proteins). Impairment of the function of longevity proteins results in an insidious acceleration of the risk of diseases associated with aging. I also propose that nutrients required for the function of longevity proteins constitute a class of vitamins that are here named "longevity vitamins." I suggest that many such nutrients play a dual role for both survival and longevity. The evidence for classifying taurine as a conditional vitamin, and the following 10 compounds as putative longevity vitamins, is reviewed: the fungal antioxidant ergothioneine; the bacterial metabolites pyrroloquinoline quinone (PQQ) and queuine; and the plant antioxidant carotenoids lutein, zeaxanthin, lycopene, α- and β-carotene, β-cryptoxanthin, and the marine carotenoid astaxanthin. Because nutrient deficiencies are highly prevalent in the United States (and elsewhere), appropriate supplementation and/or an improved diet could reduce much of the consequent risk of chronic disease and premature aging.
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Affiliation(s)
- Bruce N Ames
- Nutrition and Metabolism Center, Children's Hospital Oakland Research Institute (CHORI), Oakland, CA 94609-1809
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Gosak M, Markovič R, Dolenšek J, Slak Rupnik M, Marhl M, Stožer A, Perc M. Network science of biological systems at different scales: A review. Phys Life Rev 2018; 24:118-135. [DOI: 10.1016/j.plrev.2017.11.003] [Citation(s) in RCA: 174] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/13/2017] [Accepted: 10/15/2017] [Indexed: 12/20/2022]
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Mathias MG, Coelho‐Landell CDA, Scott‐Boyer M, Lacroix S, Morine MJ, Salomão RG, Toffano RBD, Almada MORDV, Camarneiro JM, Hillesheim E, de Barros TT, Camelo‐Junior JS, Campos Giménez E, Redeuil K, Goyon A, Bertschy E, Lévêques A, Oberson J, Giménez C, Carayol J, Kussmann M, Descombes P, Métairon S, Draper CF, Conus N, Mottaz SC, Corsini GZ, Myoshi SKB, Muniz MM, Hernandes LC, Venâncio VP, Antunes LMG, da Silva RQ, Laurito TF, Rossi IR, Ricci R, Jorge JR, Fagá ML, Quinhoneiro DCG, Reche MC, Silva PVS, Falquetti LL, da Cunha THA, Deminice TMM, Tambellini TH, de Souza GCA, de Oliveira MM, Nogueira‐Pileggi V, Matsumoto MT, Priami C, Kaput J, Monteiro JP. Clinical and Vitamin Response to a Short-Term Multi-Micronutrient Intervention in Brazilian Children and Teens: From Population Data to Interindividual Responses. Mol Nutr Food Res 2018; 62:e1700613. [PMID: 29368422 PMCID: PMC6120145 DOI: 10.1002/mnfr.201700613] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 12/02/2017] [Indexed: 12/11/2022]
Abstract
SCOPE Micronutrients are in small amounts in foods, act in concert, and require variable amounts of time to see changes in health and risk for disease. These first principles are incorporated into an intervention study designed to develop new experimental strategies for setting target recommendations for food bioactives for populations and individuals. METHODS AND RESULTS A 6-week multivitamin/mineral intervention is conducted in 9-13 year olds. Participants (136) are (i) their own control (n-of-1); (ii) monitored for compliance; (iii) measured for 36 circulating vitamin forms, 30 clinical, anthropometric, and food intake parameters at baseline, post intervention, and following a 6-week washout; and (iv) had their ancestry accounted for as modifier of vitamin baseline or response. The same intervention is repeated the following year (135 participants). Most vitamins respond positively and many clinical parameters change in directions consistent with improved metabolic health to the intervention. Baseline levels of any metabolite predict its own response to the intervention. Elastic net penalized regression models are identified, and significantly predict response to intervention on the basis of multiple vitamin/clinical baseline measures. CONCLUSIONS The study design, computational methods, and results are a step toward developing recommendations for optimizing vitamin levels and health parameters for individuals.
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Affiliation(s)
| | | | - Marie‐Pier Scott‐Boyer
- The Microsoft Research, Centre for Computational and Systems Biology (COSBI)University of TrentoRoveretoItaly
| | - Sébastien Lacroix
- The Microsoft Research, Centre for Computational and Systems Biology (COSBI)University of TrentoRoveretoItaly
| | - Melissa J. Morine
- The Microsoft Research, Centre for Computational and Systems Biology (COSBI)University of TrentoRoveretoItaly
- Department of MathematicsUniversity of TrentoTrentoItaly
| | - Roberta Garcia Salomão
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | | | | | | | - Elaine Hillesheim
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Nelly Conus
- Nestlé Institute of Health SciencesLausanneSwitzerland
| | | | | | | | - Mariana Mendes Muniz
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | | | - Vinícius Paula Venâncio
- School of Pharmaceutical Science of Ribeirao PretoUniversity of São PauloRibeirao PretoBrazil
| | | | | | - Taís Fontellas Laurito
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | - Isabela Ribeiro Rossi
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | - Raquel Ricci
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | - Jéssica Ré Jorge
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | - Mayara Leite Fagá
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | | | | | | | - Letícia Lima Falquetti
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | | | | | | | | | | | - Vicky Nogueira‐Pileggi
- Department of PediatricsFaculty of MedicineNutrition and MetabolismUniversity of São Paulo
| | | | - Corrado Priami
- The Microsoft Research, Centre for Computational and Systems Biology (COSBI)University of TrentoRoveretoItaly
- Department of MathematicsUniversity of TrentoTrentoItaly
| | - Jim Kaput
- Nestlé Institute of Health SciencesLausanneSwitzerland
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Lacroix S, Klicic Badoux J, Scott-Boyer MP, Parolo S, Matone A, Priami C, Morine MJ, Kaput J, Moco S. A computationally driven analysis of the polyphenol-protein interactome. Sci Rep 2018; 8:2232. [PMID: 29396566 PMCID: PMC5797150 DOI: 10.1038/s41598-018-20625-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/22/2018] [Indexed: 01/08/2023] Open
Abstract
Polyphenol-rich foods are part of many nutritional interventions aimed at improving health and preventing cardiometabolic diseases (CMDs). Polyphenols have oxidative, inflammatory, and/or metabolic effects. Research into the chemistry and biology of polyphenol bioactives is prolific but knowledge of their molecular interactions with proteins is limited. We mined public data to (i) identify proteins that interact with or metabolize polyphenols, (ii) mapped these proteins to pathways and networks, and (iii) annotated functions enriched within the resulting polyphenol-protein interactome. A total of 1,395 polyphenols and their metabolites were retrieved (using Phenol-Explorer and Dictionary of Natural Products) of which 369 polyphenols interacted with 5,699 unique proteins in 11,987 interactions as annotated in STITCH, Pathway Commons, and BindingDB. Pathway enrichment analysis using the KEGG repository identified a broad coverage of significant pathways of low specificity to particular polyphenol (sub)classes. When compared to drugs or micronutrients, polyphenols have pleiotropic effects across many biological processes related to metabolism and CMDs. These systems-wide effects were also found in the protein interactome of the polyphenol-rich citrus fruits, used as a case study. In sum, these findings provide a knowledgebase for identifying polyphenol classes (and polyphenol-rich foods) that individually or in combination influence metabolism.
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Affiliation(s)
- Sébastien Lacroix
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
- Institute of Nutrition and Functional Foods (INAF), Québec, Canada
| | | | - Marie-Pier Scott-Boyer
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
- Centre de Recherche du Centre Hospitalier Universitaire de Québec (CRCHUQ), Québec, Canada
| | - Silvia Parolo
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
| | - Alice Matone
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
| | - Corrado Priami
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
- Department of Computer Science, University of Pisa, Pisa (PI), Italy
| | - Melissa J Morine
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto (TN), Italy
| | - Jim Kaput
- Nestle Institute of Health Sciences, Lausanne, Switzerland
| | - Sofia Moco
- Nestle Institute of Health Sciences, Lausanne, Switzerland.
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Patients' osteometabolic control improves the management of medication-related osteonecrosis of the jaw. Oral Surg Oral Med Oral Pathol Oral Radiol 2018; 125:147-156. [DOI: 10.1016/j.oooo.2017.10.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 09/03/2017] [Accepted: 10/18/2017] [Indexed: 12/18/2022]
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Parolo S, Lacroix S, Kaput J, Scott-Boyer MP. Ancestors' dietary patterns and environments could drive positive selection in genes involved in micronutrient metabolism-the case of cofactor transporters. GENES AND NUTRITION 2017; 12:28. [PMID: 29043008 PMCID: PMC5628472 DOI: 10.1186/s12263-017-0579-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 09/19/2017] [Indexed: 02/06/2023]
Abstract
Background During evolution, humans colonized different ecological niches and adopted a variety of subsistence strategies that gave rise to diverse selective pressures acting across the genome. Environmentally induced selection of vitamin, mineral, or other cofactor transporters could influence micronutrient-requiring molecular reactions and contribute to inter-individual variability in response to foods and nutritional interventions. Methods A comprehensive list of genes coding for transporters of cofactors or their precursors was built using data mining procedures from the HGDP dataset and then explored to detect evidence of positive genetic selection. This dataset was chosen since it comprises several genetically diverse worldwide populations whom ancestries have evolved in different environments and thus lived following various nutritional habits and lifestyles. Results We identified 312 cofactor transporter (CT) genes involved in between-cell or sub-cellular compartment distribution of 28 cofactors derived from dietary intake. Twenty-four SNPs distributed across 14 CT genes separated populations into continental and intra-continental groups such as African hunter-gatherers and farmers, and between Native American sub-populations. Notably, four SNPs were located in SLC24A3 with one being a known eQTL of the NCKX3 protein. Conclusions These findings could support the importance of considering individual’s genetic makeup along with their metabolic profile when tailoring personalized dietary interventions for optimizing health. Electronic supplementary material The online version of this article (10.1186/s12263-017-0579-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Silvia Parolo
- The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), piazza Manifattura 1, 38068 Rovereto, TN Italy
| | - Sébastien Lacroix
- The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), piazza Manifattura 1, 38068 Rovereto, TN Italy
| | | | - Marie-Pier Scott-Boyer
- The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), piazza Manifattura 1, 38068 Rovereto, TN Italy
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van Ommen B, van den Broek T, de Hoogh I, van Erk M, van Someren E, Rouhani-Rankouhi T, Anthony JC, Hogenelst K, Pasman W, Boorsma A, Wopereis S. Systems biology of personalized nutrition. Nutr Rev 2017; 75:579-599. [PMID: 28969366 PMCID: PMC5914356 DOI: 10.1093/nutrit/nux029] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Personalized nutrition is fast becoming a reality due to a number of technological, scientific, and societal developments that complement and extend current public health nutrition recommendations. Personalized nutrition tailors dietary recommendations to specific biological requirements on the basis of a person's health status and goals. The biology underpinning these recommendations is complex, and thus any recommendations must account for multiple biological processes and subprocesses occurring in various tissues and must be formed with an appreciation for how these processes interact with dietary nutrients and environmental factors. Therefore, a systems biology-based approach that considers the most relevant interacting biological mechanisms is necessary to formulate the best recommendations to help people meet their wellness goals. Here, the concept of "systems flexibility" is introduced to personalized nutrition biology. Systems flexibility allows the real-time evaluation of metabolism and other processes that maintain homeostasis following an environmental challenge, thereby enabling the formulation of personalized recommendations. Examples in the area of macro- and micronutrients are reviewed. Genetic variations and performance goals are integrated into this systems approach to provide a strategy for a balanced evaluation and an introduction to personalized nutrition. Finally, modeling approaches that combine personalized diagnosis and nutritional intervention into practice are reviewed.
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Affiliation(s)
- Ben van Ommen
- TNO (The Netherlands Organization for Applied Scientific Research), Zeist, the Netherlands
| | - Tim van den Broek
- TNO (The Netherlands Organization for Applied Scientific Research), Zeist, the Netherlands
| | - Iris de Hoogh
- TNO (The Netherlands Organization for Applied Scientific Research), Zeist, the Netherlands
| | - Marjan van Erk
- TNO (The Netherlands Organization for Applied Scientific Research), Zeist, the Netherlands
| | - Eugene van Someren
- TNO (The Netherlands Organization for Applied Scientific Research), Zeist, the Netherlands
| | - Tanja Rouhani-Rankouhi
- TNO (The Netherlands Organization for Applied Scientific Research), Zeist, the Netherlands
| | | | - Koen Hogenelst
- TNO (The Netherlands Organization for Applied Scientific Research), Zeist, the Netherlands
| | - Wilrike Pasman
- TNO (The Netherlands Organization for Applied Scientific Research), Zeist, the Netherlands
| | - André Boorsma
- TNO (The Netherlands Organization for Applied Scientific Research), Zeist, the Netherlands
| | - Suzan Wopereis
- TNO (The Netherlands Organization for Applied Scientific Research), Zeist, the Netherlands
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Kaput J, Perozzi G, Radonjic M, Virgili F. Propelling the paradigm shift from reductionism to systems nutrition. GENES & NUTRITION 2017; 12:3. [PMID: 28138347 PMCID: PMC5264346 DOI: 10.1186/s12263-016-0549-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 12/13/2016] [Indexed: 12/14/2022]
Abstract
The complex physiology of living organisms represents a challenge for mechanistic understanding of the action of dietary bioactives in the human body and of their possible role in health and disease. Animal, cell, and microbial models have been extensively used to address questions that could not be pursued experimentally in humans, posing an additional level of complexity in translation of the results to healthy and diseased metabolism. The past few decades have witnessed a surge in development of increasingly sensitive molecular techniques and bioinformatic tools for storing, managing, and analyzing increasingly large datasets. Application of such powerful means to molecular nutrition research led to a major leap in study designs and experimental approaches yielding experimental data connecting dietary components to human health. Scientific journals bear major responsibilities in the advancement of science. As primary actors of dissemination to the scientific community, journals can impose rigid criteria for publishing only sound, reliable, and reproducible data. Journal policies are meant to guide potential authors to adopt the most updated standardization guidelines and shared best practices. Such policies evolve in parallel with the evolution of novel approaches and emerging challenges and therefore require constant updating. We highlight in this manuscript the major scientific issues that led to formulating new, updated journal policies for Genes & Nutrition, a journal which targets the growing field of nutritional systems biology interfacing personalized nutrition and preventive medicine, with the ultimate goal of promoting health and preventing or treating disease. We focus here on relevant issues requiring standardization in nutrition research. We also introduce new sections on human genetic variation and nutritional bioinformatics which follow the evolution of nutritional science into the twenty-first century.
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Affiliation(s)
- Jim Kaput
- Nestle Institute of Health Sciences, Lausanne, Switzerland
| | | | | | - Fabio Virgili
- CREA-NUT, Food & Nutrition Research Centre, Rome, Italy
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Gharsallah C, Ben Abdelkrim A, Fakhfakh H, Salhi-Hannachi A, Gorsane F. SSR marker-assisted screening of commercial tomato genotypes under salt stress. BREEDING SCIENCE 2016; 66:823-830. [PMID: 28163598 PMCID: PMC5282763 DOI: 10.1270/jsbbs.16112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/14/2016] [Indexed: 06/02/2023]
Abstract
Salt stress was applied to tomato commercial genotypes to study adverse effects on their phenotypic traits. Three were saline tolerant (San Miguel, Romelia and Llanero), two were mildly tolerant (Perfect peel HF1 and Heinz 1350) whereas the remaining were sensitive. Genotyping cultivars using 19 polymorphic SSRs out of 25 tested produced a total of 70 alleles with an average of 3.68 alleles per locus and PIC values ranging from 0.22 (SSR 26, 92, 66 and TG35) to 0.82 (SSR 356). Principal component analysis (PCA) showed two contrasting panels discriminating tolerant and sensitive groups and one panel with scattered genotypes. STRUCTURE analysis clustered genotypes within three groups in accordance with their salt stress behavior. The success of tomato salt-tolerance breeding programs can be enhanced through molecular characterization of diversity within commercial cultivars that adapt differently to stress conditions. To this end, we combined phenotypes and SSR marker-genotypes to seek sources of salt tolerance that might be tomato species-specific. We integrated and represented genotype-phenotype associations from multiple loci into a multi-layer network representation. It is a systemic view linking discriminating genotypes to salt stress phenotypes, which may guide strategies for the introgression of valuable traits in target tomato varieties to overcome salinity.
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Affiliation(s)
- Charfeddine Gharsallah
- Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of Tunis, University of Tunis El Manar,
2092, Tunis,
Tunisia
| | - Ahmed Ben Abdelkrim
- Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of Tunis, University of Tunis El Manar,
2092, Tunis,
Tunisia
| | - Hatem Fakhfakh
- Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of Tunis, University of Tunis El Manar,
2092, Tunis,
Tunisia
- Faculty of Sciences of Bizerte, University of Carthage,
7021 Zarzouna,
Tunisia
| | - Amel Salhi-Hannachi
- Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of Tunis, University of Tunis El Manar,
2092, Tunis,
Tunisia
| | - Faten Gorsane
- Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of Tunis, University of Tunis El Manar,
2092, Tunis,
Tunisia
- Faculty of Sciences of Bizerte, University of Carthage,
7021 Zarzouna,
Tunisia
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Maher M, Pooler AM, Kaput J, Kussmann M. A systems approach to personalised nutrition: Report on the Keystone Symposium "Human Nutrition, Environment and Health". Appl Transl Genom 2016; 10:16-8. [PMID: 27668171 PMCID: PMC5025480 DOI: 10.1016/j.atg.2016.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Michael Maher
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Amy M Pooler
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - James Kaput
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
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