scholarly journals Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis

2011 ◽  
Vol 7 (3) ◽  
pp. e1001116 ◽  
Author(s):  
Matthew A. Oberhardt ◽  
Jacek Puchałka ◽  
Vítor A. P. Martins dos Santos ◽  
Jason A. Papin
2021 ◽  
Author(s):  
Hong Yang ◽  
Jordi Mayneris-Perxachs ◽  
Noemí Boqué ◽  
Josep M del Bas ◽  
Lluís Arola ◽  
...  

AbstractThe prevalence of non-alcohol fatty liver disease (NAFLD), defined as the liver’s excessive fat accumulation, continues to increase dramatically. We have recently revealed the molecular mechanism underlying NAFLD using in-depth multi-omics profiling and identified that combined metabolic activators (CMA) could be administered to decrease the amount of hepatic steatosis (HS) in mouse model and NAFLD patients based on systems analysis. Here, we investigated the effects of a CMA including L-carnitine, N-acetyl-l-cysteine, nicotinamide riboside and betaine on a Golden Syrian hamster NAFLD model fed with HFD, and found that HS was decreased with the administration of CMA. To explore the mechanisms involved in the clearance HS, we generated liver transcriptomics data before and after CMA administration, and integrated these data using liver-specific genome-scale metabolic model of liver tissue. We systemically determined the molecular changes after the supplementation of CMAs and found that it activates mitochondria in the liver tissue by modulating the global fatty acid, amino acids, antioxidant and folate metabolism.


Biomedicines ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1310
Author(s):  
Simon Lam ◽  
Nils Hartmann ◽  
Rui Benfeitas ◽  
Cheng Zhang ◽  
Muhammad Arif ◽  
...  

Neurodegenerative diseases, including Alzheimer’s (AD) and Parkinson’s diseases (PD), are complex heterogeneous diseases with highly variable patient responses to treatment. Due to the growing evidence for ageing-related clinical and pathological commonalities between AD and PD, these diseases have recently been studied in tandem. In this study, we analysed transcriptomic data from AD and PD patients, and stratified these patients into three subclasses with distinct gene expression and metabolic profiles. Through integrating transcriptomic data with a genome-scale metabolic model and validating our findings by network exploration and co-analysis using a zebrafish ageing model, we identified retinoids as a key ageing-related feature in all subclasses of AD and PD. We also demonstrated that the dysregulation of androgen metabolism by three different independent mechanisms is a source of heterogeneity in AD and PD. Taken together, our work highlights the need for stratification of AD/PD patients and development of personalised and precision medicine approaches based on the detailed characterisation of these subclasses.


2021 ◽  
Author(s):  
Simon Lam ◽  
Nils Hartmann ◽  
Rui Benfeitas ◽  
Cheng Zhang ◽  
Muhammad Arif ◽  
...  

Neurodegenerative diseases (NDDs), including Alzheimer's (AD) and Parkinson's diseases (PD), are complex heterogeneous diseases with highly variable patient responses to treatment. Due to the growing evidence for ageing-related clinical and pathological commonalities between AD and PD, these diseases have recently been studied in tandem. In this study, we analyse transcriptomic data from AD and PD patients, and stratify these patients into three subclasses with distinct gene expression and metabolic profiles. Through integrating transcriptomic data with a genome-scale metabolic model and validating our findings by network exploration and co-analysis using a zebrafish ageing model, we identify retinoids as a key ageing-related feature in all subclasses of AD and PD. We also demonstrate that the dysregulation of androgen metabolism by three different independent mechanisms is a source of heterogeneity in AD and PD. Taken together, our work highlights the need for stratification of AD/PD patients and development of personalised and precision medicine approaches based on the detailed characterisation of these subclasses.


2013 ◽  
Vol 91 (2) ◽  
pp. 275-299 ◽  
Author(s):  
J. Philipp Benz ◽  
Bryant H. Chau ◽  
Diana Zheng ◽  
Stefan Bauer ◽  
N. Louise Glass ◽  
...  

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
R. P. Vivek-Ananth ◽  
Karthikeyan Mohanraj ◽  
Muralidharan Vandanashree ◽  
Anupam Jhingran ◽  
James P. Craig ◽  
...  

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