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Helmy M, Elhalis H, Rashid MM, Selvarajoo K. Can digital twin efforts shape microorganism-based alternative food? Curr Opin Biotechnol 2024; 87:103115. [PMID: 38547588 DOI: 10.1016/j.copbio.2024.103115] [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: 11/29/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 06/09/2024]
Abstract
With the continuous increment in global population growth, compounded by post-pandemic food security challenges due to labor shortages, effects of climate change, political conflicts, limited land for agriculture, and carbon emissions control, addressing food production in a sustainable manner for future generations is critical. Microorganisms are potential alternative food sources that can help close the gap in food production. For the development of more efficient and yield-enhancing products, it is necessary to have a better understanding on the underlying regulatory molecular pathways of microbial growth. Nevertheless, as microbes are regulated at multiomics scales, current research focusing on single omics (genomics, proteomics, or metabolomics) independently is inadequate for optimizing growth and product output. Here, we discuss digital twin (DT) approaches that integrate systems biology and artificial intelligence in analyzing multiomics datasets to yield a microbial replica model for in silico testing before production. DT models can thus provide a holistic understanding of microbial growth, metabolite biosynthesis mechanisms, as well as identifying crucial production bottlenecks. Our argument, therefore, is to support the development of novel DT models that can potentially revolutionize microorganism-based alternative food production efficiency.
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Affiliation(s)
- Mohamed Helmy
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, SK, Canada; Department of Computer Science, Lakehead University, ON, Canada; Department of Computer Science, College of Science and Engineering, Idaho State University, ID, USA; Bioinformatics Institute (BII), Agency for Science, Technology and Research (A⁎STAR), Singapore 138671, Singapore
| | - Hosam Elhalis
- Research School of Biology, Australian National University, Canberra, Australia
| | - Md Mamunur Rashid
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A⁎STAR), Singapore 138671, Singapore
| | - Kumar Selvarajoo
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A⁎STAR), Singapore 138671, Singapore; Synthetic Biology Translational Research Program and SynCTI, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117456, Singapore; School of Biological Sciences, Nanyang Technological University (NTU), Singapore 637551, Singapore.
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de Souza DM, Cavalcante HC, Dos Santos Lima M, Alves AF, da Veiga Dutra ML, D'Oliveira AB, Vasconcelos de Araújo AN, Gomes Dutra LM, Batista KS, de Souza Aquino J. Intermittent fasting associated with coconut oil (Cocos nucifera L.) alters gut-liver axis parameters in diet-induced obese rats. Nutrition 2024; 121:112370. [PMID: 38401196 DOI: 10.1016/j.nut.2024.112370] [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: 08/01/2023] [Revised: 11/15/2023] [Accepted: 01/24/2024] [Indexed: 02/26/2024]
Abstract
OBJECTIVE The aim of this article is to investigate the effect of intermittent fasting, associated or not with coconut oil intake, on the gut-liver axis of obese rats. METHODS A total of 50 rats were divided into five groups: control, obese, obese with intermittent fasting, obese with intermittent fasting plus coconut oil, and obese with caloric restriction. The rats were induced to obesity with a high-sugar diet for 17 wk. The respective interventions were carried out in the last 4 wk. RESULTS The groups with intermittent fasting protocols had reduced total cholesterol (on average 54.31%), low-density lipoprotein (on average 53.39%), and triacylglycerols (on average 23.94%) versus the obese group; and the obese with intermittent fasting plus coconut oil group had the highest high-density lipoprotein compared with all groups. The obese with intermittent fasting plus coconut oil and obese with caloric restriction groups had lower metabolic load compared with the other groups. The obese group had high citric and succinic acid concentrations, which affected the hepatic tricarboxylic acid cycle, while all the interventions had reduced concentrations of these acids. No histologic changes were observed in the intestine or liver of the groups. CONCLUSION Intermittent fasting, especially when associated with coconut oil, had effects comparable with caloric restriction in modulating the parameters of the gut-liver axis.
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Affiliation(s)
- Danielle Melo de Souza
- Laboratory of Experimental Nutrition, Department of Nutrition, Federal University of Paraíba, João Pessoa, Brazil; Postgraduate Program in Nutrition Sciences, Federal University of Paraíba, João Pessoa, Brazil
| | - Hassler Clementino Cavalcante
- Laboratory of Experimental Nutrition, Department of Nutrition, Federal University of Paraíba, João Pessoa, Brazil; Postgraduate Program in Nutrition Sciences, Federal University of Paraíba, João Pessoa, Brazil
| | - Marcos Dos Santos Lima
- Postgraduate Program in Food Science and Technology, Federal University of Paraíba, João Pessoa, Brazil; Food and Beverage Analysis Laboratory, Department of Food Technology, Instituto Federal do Sertão Pernambucano, Petrolina, Brazil
| | - Adriano Francisco Alves
- Pathology Laboratory, Department of Physiology and Pathology, Federal University of Paraíba, João Pessoa, Brazil
| | - Maria Letícia da Veiga Dutra
- Laboratory of Experimental Nutrition, Department of Nutrition, Federal University of Paraíba, João Pessoa, Brazil; Postgraduate Program in Nutrition Sciences, Federal University of Paraíba, João Pessoa, Brazil
| | - Aline Barbosa D'Oliveira
- Laboratory of Experimental Nutrition, Department of Nutrition, Federal University of Paraíba, João Pessoa, Brazil
| | - Alana Natalícia Vasconcelos de Araújo
- Laboratory of Experimental Nutrition, Department of Nutrition, Federal University of Paraíba, João Pessoa, Brazil; Postgraduate Program in Nutrition Sciences, Federal University of Paraíba, João Pessoa, Brazil
| | - Larissa Maria Gomes Dutra
- Postgraduate Program in Food Science and Technology, Federal University of Paraíba, João Pessoa, Brazil
| | - Kamila Sabino Batista
- Semiarid National Institute (Instituto Nacional do Semiárido - INSA), Campina Grande, Brazil
| | - Jailane de Souza Aquino
- Laboratory of Experimental Nutrition, Department of Nutrition, Federal University of Paraíba, João Pessoa, Brazil; Postgraduate Program in Nutrition Sciences, Federal University of Paraíba, João Pessoa, Brazil; Postgraduate Program in Food Science and Technology, Federal University of Paraíba, João Pessoa, Brazil.
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Nemoto S, Kubota T, Ishikura T, Nakayama M, Kobayashi A, Yazaki J, Uchida K, Matsuda M, Kondo T, Ohara O, Koseki H, Koyasu S, Ohno H. Characterization of metabolic phenotypes and distinctive genes in mice with low-weight gain. FASEB J 2024; 38:e23339. [PMID: 38069905 DOI: 10.1096/fj.202301565r] [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: 08/03/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023]
Abstract
Being overweight exacerbates various metabolic diseases, necessitating the identification of target molecules for obesity control. In the current study, we investigated common physiological features related to metabolism in mice with low weight gain: (1) G protein-coupled receptor, family C, group 5, member B-knockout; (2) gastric inhibitory polypeptide receptor-knockout; and (3) Iroquois-related homeobox 3-knockout. Moreover, we explored genes involved in metabolism by analyzing differentially expressed genes (DEGs) between low-weight gain mice and the respective wild-type control mice. The common characteristics of the low-weight gain mice were low inguinal white adipose tissue (iWAT) and liver weight despite similar food intake along with lower blood leptin levels and high energy expenditure. The DEGs of iWAT, epididymal (gonadal) WAT, brown adipose tissue, muscle, liver, hypothalamus, and hippocampus common to these low-weight gain mice were designated as candidate genes associated with metabolism. One such gene tetraspanin 7 (Tspan7) from the iWAT was validated using knockout and overexpressing mouse models. Mice with low Tspan7 expression gained more weight, while those with high Tspan7 expression gained less weight, confirming the involvement of the Tspan7 gene in weight regulation. Collectively, these findings suggest that the candidate gene list generated in this study contains potential target molecules for obesity regulation. Further validation and additional data from low-weight gain mice will aid in understanding the molecular mechanisms associated with obesity.
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Affiliation(s)
- Shino Nemoto
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tetsuya Kubota
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Division of Diabetes and Metabolism, The Institute of Medical Science, Asahi Life Foundation, Tokyo, Japan
- Division of Cardiovascular Medicine, Toho University Ohashi Medical Center, Tokyo, Japan
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoyuki Ishikura
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Manabu Nakayama
- Laboratory of Medical Omics Research, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Atsuo Kobayashi
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Junshi Yazaki
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kazuyo Uchida
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masashi Matsuda
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Takashi Kondo
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shigeo Koyasu
- Laboratory for Immune Cell Systems, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroshi Ohno
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory for Immune Regulation, Graduate School of Medical and Pharmaceutical Sciences, Chiba University, Chiba, Japan
- Immunobiology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
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Avtanski D, Hadzi-Petrushev N, Josifovska S, Mladenov M, Reddy V. Emerging technologies in adipose tissue research. Adipocyte 2023; 12:2248673. [PMID: 37599422 PMCID: PMC10443968 DOI: 10.1080/21623945.2023.2248673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023] Open
Abstract
Technologies are transforming the understanding of adipose tissue as a complex and dynamic tissue that plays a critical role in energy homoeostasis and metabolic health. This mini-review provides a brief overview of the potential impact of novel technologies in biomedical research and aims to identify areas where these technologies can make the most significant contribution to adipose tissue research. It discusses the impact of cutting-edge technologies such as single-cell sequencing, multi-omics analyses, spatial transcriptomics, live imaging, 3D tissue engineering, microbiome analysis, in vivo imaging, and artificial intelligence/machine learning. As these technologies continue to evolve, we can expect them to play an increasingly important role in advancing our understanding of adipose tissue and improving the treatment of related diseases.
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Affiliation(s)
- Dimiter Avtanski
- Friedman Diabetes Institute, Lenox Hill Hospital, New York, NY, USA
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Nikola Hadzi-Petrushev
- Faculty of Natural Sciences and Mathematics, Institute of Biology, “Ss. Cyril and Methodius” University, Skopje, North Macedonia
| | - Slavica Josifovska
- Faculty of Natural Sciences and Mathematics, Institute of Biology, “Ss. Cyril and Methodius” University, Skopje, North Macedonia
| | - Mitko Mladenov
- Faculty of Natural Sciences and Mathematics, Institute of Biology, “Ss. Cyril and Methodius” University, Skopje, North Macedonia
| | - Varun Reddy
- New York Institute of Technology College of Osteopathic Medicine, Old Westbury, NY, USA
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5
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Ji T, Fang B, Zhang M, Liu Y. Succinate Enhances Lipolysis and Decreases Adipocytes Size in Both Subcutaneous and Visceral Adipose Tissue from High-Fat-Diet-Fed Obese Mice. Foods 2023; 12:4285. [PMID: 38231706 DOI: 10.3390/foods12234285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/15/2023] [Accepted: 11/22/2023] [Indexed: 01/19/2024] Open
Abstract
Obesity is a risk factor for many chronic diseases related to the overexpansion of adipose tissue during obesity, leading to metabolic dysfunction and ectopic lipids. Previous studies reported a close relationship between succinate and obesity and its co-morbidities, and studies have also reported on its anti-obesity potential. To confirm its efficacy in obesity interventions, we supplemented mice with obesity induced by a high-fat diet with succinate (1.5% m/v in drinking water) for 11 weeks without changing the diet. After succinate supplementation, the changes in body weight, adipose tissue deposition, glucose tolerance, energy expenditure and lipid metabolism were evaluated. It was found that succinate supplementation significantly decreased subcutaneous adipose tissue (HFD: 4239.3 ± 211.2 mg; HFD-SA: 3268.9 ± 265.7 mg. p < 0.05), triglyceride contents (decreased by 1.53 mmol/g and 0.39 mmol/g in eWAT and ingWAT, respectively, p < 0.05) and NEFA (decreased by 1.41 μmol/g and 1.31 μmol/g in eWAT and ingWAT, respectively, p < 0.05). The adipocytes' sizes all significantly decreased in both subcutaneous and visceral adipose tissue (the proportion of adipocytes with diameters larger than 100 μm in eWAT and ingWAT decreased by 16.83% and 11.96%, respectively. p < 0.05). Succinate significantly enhanced lipolysis in adipose tissue (eWAT: Adrb3, Hsl and Plin1; ingWAT: Hsl and CPT1a; p < 0.05), whereas the expression of lipogenesis-related genes remained unchanged (p > 0.05). Succinate supplementation also enhanced the activity of BAT by stimulating the expression of Ucp1 and Cidea (p < 0.05). Our results reported that succinate has a potential beneficial effect on obesity pathogenesis but cannot efficiently decrease bodyweight.
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Affiliation(s)
- Tengteng Ji
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Bing Fang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Ming Zhang
- School of Food Science and Chemical Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Yaqiong Liu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
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Zhang Y, Shi J, Tan C, Liu Y, Xu YJ. Oilomics: An important branch of foodomics dealing with oil science and technology. Food Res Int 2023; 173:113301. [PMID: 37803609 DOI: 10.1016/j.foodres.2023.113301] [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: 05/08/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 10/08/2023]
Abstract
Oil is one of three nutritious elements. The application of omics techniques in the field of oil science and technology is attracted increasing attention. Oilomics, which emerged as an important branch of foodomics, has been widely used in various aspects of oil science and technology. However, there are currently no articles systematically reviewing the application of oilomics. This paper aims to provide a critical overview of the advantages and value of oilomics technology compared to traditional techniques in various aspects of oil science and technology, including oil nutrition, oil processing, oil quality, safety, and traceability. Moreover, this article intends to review major issues in oilomics and give a comprehensive, critical overview of the current state of the art, future challenges and trends in oilomics, with a view to promoting the optimal application and development of oilomics technology in oil science and technology.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, No. 1800, Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Jiachen Shi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, No. 1800, Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Chinping Tan
- Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra Malaysia, UPM, 43400 Serdang, Selangor, Malaysia
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, No. 1800, Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Reacher Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, No. 1800, Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China.
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Amin AM, Mostafa H, Khojah HMJ. Insulin resistance in Alzheimer's disease: The genetics and metabolomics links. Clin Chim Acta 2023; 539:215-236. [PMID: 36566957 DOI: 10.1016/j.cca.2022.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease with significant socioeconomic burden worldwide. Although genetics and environmental factors play a role, AD is highly associated with insulin resistance (IR) disorders such as metabolic syndrome (MS), obesity, and type two diabetes mellitus (T2DM). These findings highlight a shared pathogenesis. The use of metabolomics as a downstream systems' biology (omics) approach can help to identify these shared metabolic traits and assist in the early identification of at-risk groups and potentially guide therapy. Targeting the shared AD-IR metabolic trait with lifestyle interventions and pharmacological treatments may offer promising AD therapeutic approach. In this narrative review, we reviewed the literature on the AD-IR pathogenic link, the shared genetics and metabolomics biomarkers between AD and IR disorders, as well as the lifestyle interventions and pharmacological treatments which target this pathogenic link.
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Affiliation(s)
- Arwa M Amin
- Department of Clinical and Hospital Pharmacy, College of Pharmacy, Taibah University, Madinah, Saudi Arabia.
| | - Hamza Mostafa
- Biomarkers and Nutrimetabolomics Laboratory, Department of Nutrition, Food Sciences and Gastronomy, Food Innovation Network (XIA), Nutrition and Food Safety Research Institute (INSA), Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Hani M J Khojah
- Department of Clinical and Hospital Pharmacy, College of Pharmacy, Taibah University, Madinah, Saudi Arabia
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Chromatographic-Based Platforms as New Avenues for Scientific Progress and Sustainability. Molecules 2022; 27:molecules27165267. [PMID: 36014506 PMCID: PMC9412595 DOI: 10.3390/molecules27165267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/29/2022] [Accepted: 08/15/2022] [Indexed: 11/29/2022] Open
Abstract
Chromatography was born approximately one century ago and has undergone outstanding technological improvements in innovation, research, and development since then that has made it fundamental to advances in knowledge at different levels, with a relevant impact on the well-being and health of individuals. Chromatography boosted a comprehensive and deeper understanding of the complexity and diversity of human–environment interactions and systems, how these interactions affect our life, and the several societal challenges we are currently facing, namely those related to the sustainability of our planet and the future generations. From the life sciences, which allowed us to identify endogenous metabolites relevant to disease mechanisms, to the OMICS field, nanotechnology, clinical and forensic analysis, drug discovery, environment, and “foodprint”, among others, the wide range of applications of today’s chromatographic techniques is impressive. This is fueled by a great variability of powerful chromatographic instruments currently available, with very high sensitivity, resolution, and identification capacity, that provide a strong basis for an analytical platform able to support the challenging demands of the postgenomic and post COVID-19 eras. Within this context, this review aims to address the great utility of chromatography in helping to cope with several societal-based challenges, such as the characterization of disease and/or physiological status, and the response to current agri-food industry challenges of food safety and sustainability, or the monitoring of environmental contamination. These are increasingly important challenges considering the climate changes, the tons of food waste produced every day, and the exponential growth of the human population. In this context, the principles governing the separation mechanisms in chromatography as well the different types and chromatographic techniques will be described. In addition, the major achievements and the most important technological advances will be also highlighted. Finally, a set of studies was selected in order to evince the importance of different chromatographic analyses to understand processes or create fundamental information in the response to current societal challenges.
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Abstract
We have developed the underrepresented post-translational modification (PTM) database (urPTMdb), a PTM gene set database to accelerate the discovery of enriched protein modifications in experimental data. urPTMdb provides curated lists of proteins reported to be substrates of underrepresented modifications. Their enrichment in proteomics datasets can reveal unexpected PTM regulations. urPTMdb can be implemented in existing workflows, or used in TeaProt, an online Shiny tool that integrates upstream transcription factor enrichment analysis with downstream pathway analysis through an easy-to-use interactive interface. TeaProt annotates user-uploaded data with drug-gene interactions, subcellular localizations, phenotypic functions, gene-disease associations, and enzyme-gene interactions. TeaProt enables gene set enrichment analysis (GSEA) to discover enrichments in gene sets from various resources, including MSigDB, CHEA, and urPTMdb. We demonstrate the utility of urPTMdb and TeaProt through the analysis of a previously published Western diet-induced remodeling of the tongue proteome, which revealed altered cellular processes associated with energy metabolism, interferon alpha/gamma response, adipogenesis, HMGylation substrate enrichment, and transcription regulation through PPARG and CEBPA. Additionally, we analyzed the interactome of ADP-ribose glycohydrolase TARG1, a key enzyme that removes mono-ADP-ribosylation. This analysis identified an enrichment of ADP-ribosylation, ribosomal proteins, and proteins localized in the nucleoli and endoplasmic reticulum. TeaProt and urPTMdb are accessible at https://tea.coffeeprot.com/.
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Affiliation(s)
- Jeffrey Molendijk
- Department
of Anatomy and Physiology, University of
Melbourne, Melbourne, VIC 3010, Australia,. Phone: +61 401 758 489
| | - Rui Yip
- Department
of Anatomy and Physiology, University of
Melbourne, Melbourne, VIC 3010, Australia
| | - Benjamin L. Parker
- Department
of Anatomy and Physiology, University of
Melbourne, Melbourne, VIC 3010, Australia
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Gut microbiota mediates the alleviative effect of polar lipids-enriched milk fat globule membrane on obesity-induced glucose metabolism disorders in peripheral tissues in rat dams. Int J Obes (Lond) 2022; 46:793-801. [PMID: 35091670 DOI: 10.1038/s41366-021-01029-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 10/25/2021] [Accepted: 11/17/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Obesity during pregnancy and lactation not only increases the incidence of metabolic disorders and gestational diabetes in mothers, but also programs adiposity and related metabolic diseases in offspring. The aim of this study was to investigate the effects of milk polar lipids on gut microbiota and glucose metabolism in high-fat diet (HFD)-fed rat dams. METHODS Sprague Dawley (SD) female rats were fed a HFD for 8 weeks to induce obesity, followed by HFD with or without oral administration of polar lipids-enriched milk fat globule membrane (MFGM-PL) at 400 mg/kg BW during pregnancy and lactation. At the end of lactation, fresh fecal samples of dams were collected, the gut microbiota was assessed, and the insulin-signaling protein expression in peripheral tissues (adipose tissue, liver and skeletal muscle) were measured. RESULTS MFGM-PL supplementation attenuated body weight gain, ameliorated serum lipid profiles and improved insulin sensitivity in obese dams at the end of lactation. 16 S rDNA sequencing revealed that MFGM-PL increased the community richness and diversity of gut microbiota. The composition of gut microbiota was also changed after MFGM-PL supplementation as shown by an increase in the ratio of Bacteroidetes/Firmicutes and the relative abundance of Akkermansia, as well as a decrease in the relative abundance of Ruminococcaceae. The functional prediction of microbial communities by PICRUSt analysis showed that there were 7 KEGG pathways related to carbohydrate metabolism changed after MFGM-PL supplementation to HFD dams, including glycolysis/gluconeogenesis and insulin signaling pathway. Furthermore, MFGM-PL improved insulin signaling in the peripheral tissues including liver, adipose tissue and skeletal muscle. CONCLUSIONS MFGM-PL supplementation during pregnancy and lactation improves the glucose metabolism disorders in HFD-induced obese dams, which may be linked to the regulation of gut microbiota induced by MFGM-PL.
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Ochin CC, Wilson T, Garelnabi M. Dietary Oxidized Linoleic Acids Modulate Fatty Acids in Mice. J Lipid Atheroscler 2022; 11:197-210. [PMID: 35656146 PMCID: PMC9133782 DOI: 10.12997/jla.2022.11.2.197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 11/11/2022] Open
Abstract
Objective An elevated concentration of oxidized lipids along with the abnormal accumulation of lipids has been linked to the formation of atheromatous plaque and the development of cardiovascular diseases. This study aims to investigate if consumption of different concentrations of dietary oxidized linoleic acid alters the distribution of long chain fatty acids (LCFAs) within the liver relative to plasma in mice. Methods C57BL/6 male mice (n = 40) were divided into 4 groups: Standard chow as plain control (P group, n =10), Chow supplemented with linoleic acid 9 mg/mouse/day, linoleic control (C group, n=0), oxidized linoleic acid; 9 mg/mouse/day (A group, n=10) and oxidized linoleic acid 18 mg/mouse/day diet (B group, n=10). Liver and plasma samples were extracted, trans-esterified and subsequently analyzed using gas chromatography mass spectrometry (GC-MS) for LCFAs; palmitic acid, stearic acid, oleic acid, linoleic acid and arachidonic acid. Results LCFA methyl esters were eluted and identified based on their respective physiochemical characteristics of GCMS assay with inter assay coefficient of variation percentage (CV%, 1.81–5.28%), limits of quantification and limit of detection values (2.021–11.402 mg/mL and 1.016–4.430 mg/mL) respectively. Correlation analysis of liver and plasma lipids of the mice groups yielded coefficients (r=0.96, 0.6, 0.8 and 0.33) with fatty acid percentage total of (16%, 10%, 16% and 58%) for the P, C, A and B groups respectively. Conclusion The sustained consumption of a diet rich in oxidized linoleic acid disrupted fatty acid metabolism. The intake also resulted in elevated concentration of LCFAs that are precursors of bioactive metabolite molecule.
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Affiliation(s)
- Chinedu C. Ochin
- Department of Biomedical and Nutritional Sciences, University of Massachusetts, Lowell, MA, USA
| | - Thomas Wilson
- Department of Biomedical and Nutritional Sciences, University of Massachusetts, Lowell, MA, USA
| | - Mahdi Garelnabi
- Department of Biomedical and Nutritional Sciences, University of Massachusetts, Lowell, MA, USA
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Gutiérrez Y, Fresch M, Hellmann SL, Hankeln T, Scherber C, Brockmeyer J. A multifactorial proteomics approach to sex‐specific effects of diet composition and social environment in an omnivorous insect. Ecol Evol 2021. [DOI: 10.1002/ece3.7676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Yeisson Gutiérrez
- Centro de Bioinformática y Biología Computacional de Colombia – BIOS Manizales Colombia
| | - Marion Fresch
- Department Food Chemistry Institute for Biochemistry and Technical Biochemistry University of Stuttgart Stuttgart Germany
| | - Sören L. Hellmann
- Institute of Organismic and Molecular Evolutionary Biology University of Mainz Mainz Germany
| | - Thomas Hankeln
- Institute of Organismic and Molecular Evolutionary Biology University of Mainz Mainz Germany
| | - Christoph Scherber
- Institute of Landscape Ecology University of Münster Münster Germany
- Centre for Biodiversity Monitoring Zoological Research Museum Alexander Koenig Bonn Germany
| | - Jens Brockmeyer
- Department Food Chemistry Institute for Biochemistry and Technical Biochemistry University of Stuttgart Stuttgart Germany
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Dutt M, Ng YK, Molendijk J, Karimkhanloo H, Liao L, Blazev R, Montgomery MK, Watt MJ, Parker BL. Western Diet Induced Remodelling of the Tongue Proteome. Proteomes 2021; 9:proteomes9020022. [PMID: 34066295 PMCID: PMC8163156 DOI: 10.3390/proteomes9020022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/03/2021] [Accepted: 05/08/2021] [Indexed: 12/14/2022] Open
Abstract
The tongue is a heavily innervated and vascularized striated muscle that plays an important role in vocalization, swallowing and digestion. The surface of the tongue is lined with papillae which contain gustatory cells expressing various taste receptors. There is growing evidence to suggest that our perceptions of taste and food preference are remodelled following chronic consumption of Western diets rich in carbohydrate and fats. Our sensitivity to taste and also to metabolising Western diets may be a key factor in the rising prevalence of obesity; however, a systems-wide analysis of the tongue is lacking. Here, we defined the proteomic landscape of the mouse tongue and quantified changes following chronic consumption of a chow or Western diet enriched in lipid, fructose and cholesterol for 7 months. We observed a dramatic remodelling of the tongue proteome including proteins that regulate fatty acid and mitochondrial metabolism. Furthermore, the expressions of several receptors, metabolic enzymes and hormones were differentially regulated, and are likely to provide novel therapeutic targets to alter taste perception and food preference to combat obesity.
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Dietary obesity in mice is associated with lipid deposition and metabolic shifts in the lungs sharing features with the liver. Sci Rep 2021; 11:8712. [PMID: 33888788 PMCID: PMC8062462 DOI: 10.1038/s41598-021-88097-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/18/2021] [Indexed: 12/20/2022] Open
Abstract
Obesity is associated with both chronic and acute respiratory illnesses, such as asthma, chronic obstructive pulmonary disease (COPD) or increased susceptibility to infectious diseases. Anatomical but also systemic and local metabolic alterations are proposed contributors to the pathophysiology of lung diseases in the context of obesity. To bring perspective to this discussion, we used NMR to compare the obesity-associated metabolomic profiles of the lung with those of the liver, heart, skeletal muscles, kidneys, brain and serum from male C57Bl/6J mice fed with a high-fat and high-sucrose (HFHSD) diet vs. standard (SD) chow for 14 weeks. Our results showed that the lung was the second most affected organ after the liver, and that the two organs shared reduced one-carbon (1C) metabolism and increased lipid accumulation. Altered 1C metabolism was found in all organs and in the serum, but serine levels were increased only in the lung of HFHSD compared to SD. Lastly, tricarboxylic acid (TCA)-derived metabolites were specifically and oppositely regulated in the serum and kidneys but not in other organs. Collectively, our data highlighted that HFHSD induced specific metabolic changes in all organs, the lung being the second most affected organ, the main alterations affecting metabolite concentrations of the 1C pathway and, to a minor extend, TCA. The absolute metabolite quantification performed in this study reveals some metabolic specificities affecting both the liver and the lung, that may reveal common metabolic determinants to the ongoing pathological process.
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Statistical and Machine-Learning Analyses in Nutritional Genomics Studies. Nutrients 2020; 12:nu12103140. [PMID: 33066636 PMCID: PMC7602401 DOI: 10.3390/nu12103140] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/08/2020] [Accepted: 10/10/2020] [Indexed: 12/18/2022] Open
Abstract
Nutritional compounds may have an influence on different OMICs levels, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, and metagenomics. The integration of OMICs data is challenging but may provide new knowledge to explain the mechanisms involved in the metabolism of nutrients and diseases. Traditional statistical analyses play an important role in description and data association; however, these statistical procedures are not sufficiently enough powered to interpret the large integrated multiple OMICs (multi-OMICS) datasets. Machine learning (ML) approaches can play a major role in the interpretation of multi-OMICS in nutrition research. Specifically, ML can be used for data mining, sample clustering, and classification to produce predictive models and algorithms for integration of multi-OMICs in response to dietary intake. The objective of this review was to investigate the strategies used for the analysis of multi-OMICs data in nutrition studies. Sixteen recent studies aimed to understand the association between dietary intake and multi-OMICs data are summarized. Multivariate analysis in multi-OMICs nutrition studies is used more commonly for analyses. Overall, as nutrition research incorporated multi-OMICs data, the use of novel approaches of analysis such as ML needs to complement the traditional statistical analyses to fully explain the impact of nutrition on health and disease.
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Yu J, Xiang JY, Xiang H, Xie Q. Cecal Butyrate (Not Propionate) Was Connected with Metabolism-Related Chemicals of Mice, Based on the Different Effects of the Two Inonotus obliquus Extracts on Obesity and Their Mechanisms. ACS OMEGA 2020; 5:16690-16700. [PMID: 32685836 PMCID: PMC7364710 DOI: 10.1021/acsomega.0c01566] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/18/2020] [Indexed: 05/05/2023]
Abstract
Obesity is a metabolic disease and causes significant changes in host and gut microbial metabolite levels. However, little research has been done on the relationship between host and gut microbial metabolites. Thus, this study investigated the connection of the chemicals, based on the different effects of two Inonotus obliquus extracts on high-fat-diet-induced mice and their mechanisms. In this study, C57BL6/J mice fed with a high-fat diet were given I. obliquus ethanol extract (IOE) and polysaccharide (IOP). 1H NMR-based metabolomics, 16S rRNA sequencing, and real-time reverse transcription polymerase chain reaction (RT-PCR) were used to detect metabolites, cecal microbes, and expressions of genes in liver. IOE and IOP effectively improved the obesity of mice, including the adjustment of body weight gain, energy intake, energy efficiency, liver glucose metabolism and triglyceride metabolism, tricarboxylic acid (TCA) cycle, and degradation of three major nutrients (carbohydrate, lipid, and protein). IOE significantly increased cecal propionate based on Bacteroides and Akkermansia, thereby inhibiting energy intake and fat accumulation in mice. IOP remarkably improved the level of cecal butyrate by Lactobacillus and the Bacteroidales S24-7 group, resulting in increased energy consumption, and fat degradation by regulating the TCA cycle of the host. Two extracts containing different bioactive substances of I. obliquus improved obesity in mice through different effects on production of cecal microbial metabolites. Moreover, cecal butyrate (not propionate) was connected with chemicals of mice, including four metabolites of the TCA cycle and other metabolism-related chemicals.
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Affiliation(s)
- Jian Yu
- School
of Life Sciences, Jilin University, Changchun, Jilin 130012, People’s Republic
of China
| | - Jun-Yan Xiang
- School
of Life Sciences, Jilin University, Changchun, Jilin 130012, People’s Republic
of China
| | - Hongyu Xiang
- Key
Laboratory for Molecular Enzymology and Engineering of Ministry of
Education, School of Life Sciences, Jilin
University, Changchun, Jilin 130012, People’s Republic of China
- National
Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin 130012, People’s Republic of China
- School
of Life Sciences, Jilin University, Changchun, Jilin 130012, People’s Republic
of China
| | - Qiuhong Xie
- Key
Laboratory for Molecular Enzymology and Engineering of Ministry of
Education, School of Life Sciences, Jilin
University, Changchun, Jilin 130012, People’s Republic of China
- National
Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin 130012, People’s Republic of China
- School
of Life Sciences, Jilin University, Changchun, Jilin 130012, People’s Republic
of China
- , Tel/Fax: +86-431-85153832
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