Results 1 to 10 of about 450,259 (150)

Metabolic modeling links gut microbiota to metabolic markers of Parkinson’s disease [PDF]

Gut Microbes
Human gut microbiota have been implicated in metabolic disruptions in Parkinson’s disease (PD). However, the underlying mechanisms linking gut microbiota to these disease-related metabolic changes remain largely unknown.
Tim Hensen, Ines Thiele
doaj   +2 more sources

MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models [PDF]

Frontiers in Physiology, 2016
Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Previous work, by us and others, revealed the potential of analyzing extracellular metabolomic data in the context of the
Maike Kathrin Aurich, Ronan Fleming, Ines Thiele   +2 more
doaj   +4 more sources

Investigating the Chemolithoautotrophic and Formate Metabolism of Nitrospira moscoviensis by Constraint-Based Metabolic Modeling and 13C-Tracer Analysis

mSystems, 2021
Nitrite-oxidizing bacteria belonging to the genus Nitrospira mediate a key step in nitrification and play important roles in the biogeochemical nitrogen cycle and wastewater treatment.
Christopher E. Lawson, Aniela B. Mundinger, Hanna Koch, Tyler B. Jacobson, Coty A. Weathersby, Mike S. M. Jetten, Martin Pabst, Daniel Amador-Noguez, Daniel R. Noguera, Katherine McMahon, Sebastian Lücker   +10 more
doaj   +1 more source

Genome-Scale Modeling Specifies the Metabolic Capabilities of Rhizophagus irregularis

mSystems, 2022
Rhizophagus irregularis is one of the most extensively studied arbuscular mycorrhizal fungi (AMF) that forms symbioses with and improves the performance of many crops. Lack of transformation protocol for R.
Philipp Wendering, Zoran Nikoloski
doaj   +1 more source

Predicting Microbiome Metabolism and Interactions through Integrating Multidisciplinary Principles

mSystems, 2021
In this Commentary, we will discuss some of the current trends and challenges in modeling microbiome metabolism. A focus will be the state of the art in the integration of metabolic networks, ecological and evolutionary principles, and spatiotemporal ...
Caleb M. Schmidt, Parsa Ghadermazi, Siu Hung Joshua Chan   +2 more
doaj   +1 more source

Current Status and Future Prospects of Genome-Scale Metabolic Modeling to Optimize the Use of Mesenchymal Stem Cells in Regenerative Medicine

Frontiers in Bioengineering and Biotechnology, 2020
Mesenchymal stem cells are a promising source for externally grown tissue replacements and patient-specific immunomodulatory treatments. This promise has not yet been fulfilled in part due to production scaling issues and the need to maintain the correct
Þóra Sigmarsdóttir, Þóra Sigmarsdóttir, Sarah McGarrity, Sarah McGarrity, Óttar Rolfsson, James T. Yurkovich, Ólafur E. Sigurjónsson, Ólafur E. Sigurjónsson   +7 more
doaj   +1 more source

The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases

Metabolites, 2021
Genome-scale metabolic models are of high interest in a number of different research fields. Flux balance analysis (FBA) and other mathematical methods allow the prediction of the steady-state behavior of metabolic networks under different environmental ...
Julia Koblitz, Sabine Eva Will, S. Alexander Riemer, Thomas Ulas, Meina Neumann-Schaal, Dietmar Schomburg   +5 more
doaj   +1 more source

Death by a thousand cuts: the challenges and diverse landscape of lignocellulosic hydrolysate inhibitors

Frontiers in Microbiology, 2014
Lignocellulosic hydrolysate (LCH) inhibitors are a large class of bioactive molecules that arise from pretreatment, hydrolysis, and fermentation of plant biomass.
Jeff Scott Piotrowski, Yaoping eZhang, Trey eSato, Irene eOng, David eKeating, Donna eBates, Robert eLandick   +6 more
doaj   +1 more source

Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor [PDF]

, 2010
Background The transition from exponential to stationary phase in Streptomyces coelicolor is accompanied by a major metabolic switch and results in a strong activation of secondary metabolism.
Alam, Mohammad T., Breitling, Rainer, HASH(0x55aa09327868), Hodgson, D. A., Merlo, Maria E., Takano, Eriko, Wellington, E. M. H.   +6 more
core   +10 more sources

Metabolic Network Analysis of Microbial Methane Utilization for Biomass Formation and Upgrading to Bio-Fuels

Frontiers in Energy Research, 2018
The potent greenhouse gas methane presents a widely accessible resource, being the primary component in natural gas as well as in bio-gas from anaerobic digesters.
Nils J. H. Averesch, Frauke Kracke
doaj   +1 more source