Article
Gastroenterology & Hepatology
Genta Kakiyama, Kei Minowa, Daniel Rodriguez-Agudo, Rebecca Martin, Hajime Takei, Kuniko Mitamura, Shigeo Ikegawa, Mitsuyoshi Suzuki, Hiroshi Nittono, Michael Fuchs, Douglas M. Heuman, Huiping Zhou, William M. Pandak
Summary: This study demonstrated that dietary coffee can prevent the accumulation of hepatic oxysterols by maintaining the expression of Cyp7b1/Sult2b1 genes in a diet-induced NAFLD mice model. Lowering liver oxysterols markedly reduced inflammation in the coffee-ingested mice. Caffeine is not fundamental to this effect. In addition, this study showed that the responses of Cyp7b1/Sult2b1 genes to insulin signaling can be mediated through a transcriptional factor, HNF4 alpha. The insulin-HNF4 alpha-Cyp7b1/Sult2b1 signaling pathway, which directly correlates to the onset of NASH triggered by insulin resistance, offers insight into approaches for NAFLD treatment.
AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Arokia Vijaya Anand Mariadoss, SeonJu Park, Kandasamy Saravanakumar, Anbazhagan Sathiyaseelan, Myeong-Hyeon Wang
Summary: The study investigated the antioxidant and anti-diabetic activities of Helianthus tuberosus, with the ethyl acetate fraction showing the highest activity. The phytochemical analysis identified various phenolic compounds which were found to interact with alpha-amylase and alpha-glucosidase, suggesting their potential as inhibitors for these enzymes.
Article
Biochemistry & Molecular Biology
Ye Tian, Wei Lu, Ruicheng Shi, Reagan Mcguffee, Richard Lee, David A. Ford, Bo Wang
Summary: The study reveals that targeting LPCAT3 could be a novel therapy for insulin resistance, as suppression of Lpcat3 expression improves insulin sensitivity and metabolic issues in diabetic mice.
Article
Multidisciplinary Sciences
Minxuan Xu, Jun Tan, Wei Dong, Benkui Zou, Xuepeng Teng, Liancai Zhu, Chenxu Ge, Xianling Dai, Qin Kuang, Shaoyu Zhong, Lili Lai, Chao Yi, Tingting Tang, Junjie Zhao, Longyan Wang, Jin Liu, Hao Wei, Yan Sun, Qiufeng Yang, Qiang Li, Deshuai Lou, Linfeng Hu, Xi Liu, Gang Kuang, Jing Luo, Mingxin Xiong, Jing Feng, Chufeng Zhang, Bochu Wang
Summary: This study reveals that Trim31 acts as an endogenous inhibitor of Rhbdf2 in mice, mitigating the development of NASH and potentially serving as a therapeutic target for treating NAFLD/NASH and associated metabolic disorders.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Sonia Mirjam Rizzo, Giulia Alessandri, Gabriele Andrea Lugli, Federico Fontana, Chiara Tarracchini, Leonardo Mancabelli, Alice Viappiani, Massimiliano G. G. Bianchi, Ovidio Bussolati, Douwe van Sinderen, Marco Ventura, Francesca Turroni
Summary: Breast milk is crucial for modulating the composition of the infant's intestinal microbiota, and besides the interaction with human milk sugars, other bioactive compounds like hormones, particularly insulin, may also influence the gut microbiota. This study explores the molecular interaction between insulin and bifidobacterial communities in the early stages of the human gut, revealing that insulin may enhance the presence of Bifidobacterium bifidum in the infant gut environment compared to other typical infant-associated bifidobacterial species.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Zunli Ke, Si Tan, Haiyang Li, Shanshan Jiang, Yuping Li, Rui Chen, Mingxia Li
Summary: Nonalcoholic liver disease (NAFLD) is a liver condition associated with excessive fat deposition and is closely related to obesity or metabolic syndrome. Oxidative stress plays an important role in the progression of NAFLD, and reducing oxidative stress may improve the condition. Tangeretin, a natural compound with antioxidant and hepatoprotective properties, has shown promise in ameliorating NAFLD. This study found that tangeretin supplementation slowed down NAFLD progression by improving metabolic indexes, reducing hepatic oxidative stress, and reducing fat accumulation in the liver. The study also identified the Nrf2 pathway as a potential mechanism through which tangeretin exerts its effects. These findings suggest that tangeretin could be used as a dietary therapy for obesity-related NAFLD or metabolic syndrome.
Article
Nutrition & Dietetics
Wiktor Bzdega, Piotr Franciszek Kurzyna, Ewa Harasim-Symbor, Adam Holownia, Adrian Chabowski, Karolina Konstantynowicz-Nowicka
Summary: CBG treatment may modulate sphingolipid metabolism, protecting the liver against the development of metabolic disorders.
Article
Physics, Multidisciplinary
Jun Qian, Xiao Sun, Tongda Zhang, Yueting Chai
Summary: Game theory is a powerful tool to study human cooperation and understand cooperation-facilitating mechanisms. This paper introduces a risk-resistant model to investigate whether punishment still promotes collaboration when people resist risk.
Article
Plant Sciences
Yujie Ma, Jinmei Li, Zhengcai Ju, Wendong Huang, Zhengtao Wang, Li Yang, Lili Ding
Summary: This study aimed to evaluate the effects and potential pharmacological mechanisms of Danning tablets against high fat diet-induced obesity, fatty liver, and related metabolic disorders. The results showed that Danning tablets could improve obesity-induced metabolic associated fatty liver disease (MAFLD) and related metabolic disorders, possibly through regulating the SREBP pathway.
JOURNAL OF ETHNOPHARMACOLOGY
(2021)
Article
Gastroenterology & Hepatology
Martin Karl, Solveig Hasselwander, Yawen Zhou, Gisela Reifenberg, Yong Ook Kim, Kyoung-Sook Park, Dirk A. Ridder, Xiaoyu Wang, Eric Seidel, Nadine Hoevelmeyer, Beate K. Straub, Huige Li, Detlef Schuppan, Ning Xia
Summary: This study suggests that B lymphocytes play both detrimental and protective roles in the development of non-alcoholic fatty liver disease (NAFLD). The lack of secretion of pathogenic antibodies partially protects from NAFLD, while certain subsets of B cells provide additional protection. Regulatory B cells producing IL-10 may represent a protective subset of B cells.
Article
Medicine, Research & Experimental
Stephania Guzman, Magdalena Dragan, Hyokjoon Kwon, Vanessa de Oliveira, Shivani Rao, Vrushank Bhatt, Katarzyna M. Kalemba, Ankit Shah, Vinod K. Rustgi, He Wang, Paul R. Bech, Ali Abbara, Chioma Izzi-Engbeaya, Pinelopi Manousou, Jessie Y. Guo, Grace L. Guo, Sally Radovick, Waljit S. Dhillo, Fredric E. Wondisford, Andy Babwah, Moshmi Bhattacharya
Summary: Nonalcoholic fatty liver disease (NAFLD) is a common liver disease associated with obesity, diabetes, and metabolic syndrome. Activation of the kisspeptin 1 receptor (KISS1R) signaling pathway has therapeutic effects in treating NAFLD.
JOURNAL OF CLINICAL INVESTIGATION
(2022)
Article
Multidisciplinary Sciences
Cong-Min Tang, Zhen Zhang, Yan Sun, Wen-Jing Ding, Xue-Chun Yang, Yi-Ping Song, Ming-Ying Ling, Xue-Hui Li, Rong Yan, Yu-Jing Zheng, Na Yu, Wen-Hua Zhang, Yong Wang, Shao-Peng Wang, Hai-Qing Gao, Chuan-Li Zhao, Yan-Qiu Xing
Summary: Aging is associated with structural changes, altered metabolites, and physiological/pathological changes in liver cells. This study applied metabolomics and phosphoproteomics to identify changes in metabolites and phosphorylated proteins in the liver of aging mice, revealing new biomarkers and pathways associated with aging and cancer.
Article
Medicine, General & Internal
Mona Synnove Bjune, Laurence Lawrence-Archer, Johnny Laupsa-Borge, Cathrine Horn Sommersten, Adrian McCann, Robert Clay Glastad, Iain George Johnston, Matthias Kern, Matthias Blueher, Gunnar Mellgren, Simon N. Dankel
Summary: The hepatic valine/3-HIB pathway plays an important role in the mechanism of fatty liver and may be a potential target for therapeutic intervention.
Article
Integrative & Complementary Medicine
You Wu, Boju Sun, Xiaoyuan Guo, Lili Wu, Yaomu Hu, Lingling Qin, Tao Yang, Mei Li, Tianyu Qin, Miao Jiang, Tonghua Liu
Summary: ZSP treatment significantly improved glucose metabolism and weight gain in db/db mice by enhancing the PI3K/AKT signaling pathway, increasing the expression of genes related to glycogen synthesis and glycolysis, and reducing gluconeogenesis.
Article
Biochemistry & Molecular Biology
Runhua Du, Guobin Liu, He Huang
Summary: This study expands the known Khib sites and provides the deepest Khib proteome in mammalian cells through proteomics analysis. 2-hydroxyisobutyrylated proteins have diverse subcellular localizations and participate in various molecular functions and cellular processes, including metabolic processes and disease-related pathways. In addition, elevated Khib levels in HeLa cells result in the up-regulation and down-regulation of genes associated with human papillomavirus infection, protein digestion and absorption, as well as multiple diseases and Glycolysis/Gluconeogenesis processes.
BIOORGANIC & MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Laurent A. Winckers, Chris T. Evelo, Egon L. Willighagen, Martina Kutmon
Summary: Research has shown that engineered nanomaterials can induce toxic effects related to gene expression and biological processes, and a targeted filtering approach can identify toxicity focus, highlighting differences in affected processes among different cell lines. Colorectal adenocarcinoma cells exhibit high resilience to different concentrations, while small airway epithelial cells show cytotoxic response to high concentration.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Amadeo Munoz Garcia, Emma L. Bishop, Danyang Li, Louisa E. Jeffery, Antje Garten, Alpesh Thakker, Michelangelo Certo, Claudio Mauro, Daniel A. Tennant, Sarah Dimeloe, Chris T. Evelo, Susan L. Coort, Martin Hewison
Summary: The active form of vitamin D, 1,25-dihydroxyvitamin D, plays a role in regulating immune function by modulating antigen presentation by dendritic cells. Research shows that 1,25D promotes fatty acid synthesis in tolerogenic dendritic cells, leading to metabolic remodeling.
JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2021)
Editorial Material
Biochemical Research Methods
Kristina Hanspers, Martina Kutmon, Susan L. Coort, Daniela Digles, Lauren J. Dupuis, Friederike Ehrhart, Finterly Hu, Elisson N. Lopes, Marvin Martens, Nhung Pham, Woosub Shin, Denise N. Slenter, Andra Waagmeester, Egon L. Willighagen, Laurent A. Winckers, Chris T. Evelo, Alexander R. Pico
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Food Science & Technology
Dieuwertje E. Kok, Rebecca C. Richmond, Michiel Adriaens, Chris T. Evelo, Dianne Ford, John C. Mathers, Natassia Robinson, Jill A. McKay
Summary: This study investigates the effects of early nutritional exposure on offspring health. Mouse models show that folate depletion-induced methylation changes are mirrored in humans. The findings suggest that the eight genes affected by global changes may impact neurocognitive function.
MOLECULAR NUTRITION & FOOD RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Ilona T. Liesenborghs, Johannes S. A. G. Schouten, Martina Kutmon, Theo G. M. F. Gorgels, Chris T. Evelo, Wouter H. G. Hubens, Henny J. M. Beckers, Carroll A. B. Webers, Lars M. T. Eijssen
Summary: This study integrated gene expression data of healthy trabecular meshwork (TM) to identify its signature genes and pathways, providing a reference for the study of molecular disease processes and the selection of candidate target genes for new treatments. The study identified non-ubiquitous genes and pathways as the signature of the functioning of the healthy TM, and also identified candidate TM-specific genes. This method can be applied to study other tissues that are difficult to obtain.
Article
Multidisciplinary Sciences
Ryan A. Miller, Martina Kutmon, Anwesha Bohler, Andra Waagmeester, Chris T. Evelo, Egon L. Willighagen
Summary: Biological knowledge can be translated into diagrams for machine readable formats; WikiPathways supports multiple drawing styles which need harmonizing; Study finds that graphically modelled biological knowledge can be translated into a semantic model.
Article
Chemistry, Multidisciplinary
Ammar Ammar, Rachel Cavill, Chris Evelo, Egon Willighagen
Summary: A large database of 0.6 million mutated binding site protein-ligand complexes, called PSnpBind, has been constructed to provide a reference dataset for studying the effects of natural variants on drug targets. This database is important for developing machine learning algorithms and studying protein-ligand affinity.
JOURNAL OF CHEMINFORMATICS
(2022)
Article
Oncology
Marvin Martens, Franziska Kreidl, Friederike Ehrhart, Didier Jean, Merlin Mei, Holly M. Mortensen, Alistair Nash, Penny Nymark, Chris T. Evelo, Ferdinando Cerciello
Summary: Malignant pleural mesothelioma (MPM) is a highly aggressive malignancy mainly triggered by exposure to asbestos and characterized by complex biology. The research community has generated a significant body of knowledge over the decades to improve understanding of the disease for prevention, diagnostics, and new treatments. Developing integrated tools for accessing and analyzing data can aid scientists in studying and comprehending MPM more effectively.
FRONTIERS IN ONCOLOGY
(2022)
Article
Genetics & Heredity
Denise N. Slenter, Irene M. G. M. Hemel, Chris T. Evelo, Joergen Bierau, Egon L. Willighagen, Laura K. M. Steinbusch
Summary: This study aims to integrate metabolic interaction knowledge with clinical data in a visualization, to assist in the diagnosis of difficult-to-understand inherited metabolic disorders (IMDs). By visualizing the interactions between urine biomarkers and enzymes, this approach can help doctors make more accurate diagnoses. The study demonstrates the feasibility of this method and identifies some challenges that need to be addressed.
ORPHANET JOURNAL OF RARE DISEASES
(2023)
Article
Chemistry, Multidisciplinary
Ammar Ammar, Rachel Cavill, Chris Evelo, Egon Willighagen
Summary: Protein mutations, especially in the binding site, can impact drug response. Experimental screening is time-consuming and expensive, so computational approaches are valuable in guiding these experiments.
JOURNAL OF CHEMINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Philippe Rocca-Serra, Wei Gu, Vassilios Ioannidis, Tooba Abbassi-Daloii, Salvador Capella-Gutierrez, Ishwar Chandramouliswaran, Andrea Splendiani, Tony Burdett, Robert Giessmann, David Henderson, Dominique Batista, Ibrahim Emam, Yojana Gadiya, Lucas Giovanni, Egon Willighagen, Chris Evelo, Alasdair J. G. Gray, Philip Gribbon, Nick Juty, Danielle Welter, Karsten Quast, Paul Peeters, Tom Plasterer, Colin Wood, Eelke van der Horst, Dorothy Reilly, Herman van Vlijmen, Serena Scollen, Allyson Lister, Milo Thurston, Ramon Granell, FAIR Cookbook Contributors, Susanna-Assunta Sanson
Summary: The FAIR Principles, which emphasize the Findability, Accessibility, Interoperability, and Reusability of data, are widely recognized as essential for good data stewardship and reproducibility. However, practical implementation guidance is lacking. To address this gap, we have created the FAIR Cookbook, an open online resource providing hands-on recipes for implementing FAIR principles in the Life Sciences.
Article
Environmental Sciences
Irini Furxhi, Egon Willighagen, Chris Evelo, Anna Costa, Davide Gardini, Ammar Ammar
Summary: The current effort towards digital transformation in scientific domains requires FAIR data, but there is a lack of FAIR metadata in the nanosafety domain. This study utilized the NSDRA framework to address this challenge and tested different QSAR models and machine learning algorithms. The results showed the importance of FAIR data practices and the potential for increasing transparency and trustworthiness in computational studies.
Article
Immunology
Nhung Pham, Finterly Hu, Chris T. Evelo, Martina Kutmon
Summary: This study mapped proteomics data to pathway models and revealed the impact of COVID-19 on pathway activities in different tissues. The results indicate that COVID-19 affects not only the lung but also other tissues systemically.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Mathematical & Computational Biology
Nicolas Matentzoglu, James P. Balhoff, Susan M. Bello, Chris Bizon, Matthew Brush, Tiffany J. Callahan, Christopher G. Chute, William D. Duncan, Chris T. Evelo, Davera Gabriel, John Graybeal, Alasdair Gray, Benjamin M. Gyori, Melissa Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad B. Hegde, Amelia L. Hoyt, Charles T. Hoyt, Dazhi Jiao, Ernesto Jimenez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Koehler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim Putman, Nuria Queralt-Rosinach, Kent Shefchek, Harold Solbrig, Anne Thessen, Tania Tudorache, Nicole Vasilevsky, Alex H. Wagner, Christopher J. Mungall
Summary: This paper introduces the "Simple Standard for Sharing Ontological Mappings (SSSOM)" standard, which addresses issues in mapping different representations of objects in different databases by enhancing readability of metadata, defining an easy-to-use table-based format, and implementing open collaborative workflows. The standard provides reference tools and software libraries for handling mappings.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)
Article
Toxicology
Holly M. Mortensen, Marvin Martens, Jonathan Senn, Trevor Levey, Chris T. Evelo, Egon L. Willighagen, Thomas Exner
Summary: Computational toxicology plays a central role in the current transformation in toxicology and chemical risk assessment. The Adverse Outcome Pathway (AOP) framework assists in organizing mechanistic information and contributes to New Approach Methodologies (NAMs). The AOP-DB database provides a comprehensive overview of the biological context of AOPs and facilitates integration with other relevant datasets.
FRONTIERS IN TOXICOLOGY
(2022)