Article
Biochemical Research Methods
Kerian Thuillier, Caroline Baroukh, Alexander Bockmayr, Ludovic Cottret, Loic Pauleve, Anne Siegel
Summary: This study presents a novel approach to infer Boolean rules for metabolic regulation from time-series data and a prior knowledge network (PKN). By combining answer set programming and linear programming, candidate Boolean regulations that can reproduce the given data are generated. The quality of predictions depends on the available time-series data, such as kinetic, fluxomics or transcriptomics data.
Article
Biotechnology & Applied Microbiology
Maciek R. Antoniewicz
Summary: Metabolic engineering aims to improve biological production by designing and optimizing metabolic pathways, quantifying metabolic fluxes, and analyzing metabolic network models; essential concepts include metabolic network models and metabolic fluxes; in recent years, advancements in technology and methods have allowed for a deeper understanding of the capabilities of biological systems.
METABOLIC ENGINEERING
(2021)
Article
Engineering, Environmental
Shoji D. Thottathil, Paula C. J. Reis, Yves T. Prairie
Summary: Recent evidence suggests that methanogenesis in oxic conditions can contribute significantly to methane oversaturation and emissions in freshwater lakes. The oxic CH4 production (OMP) is linked to chlorophyll-a, total phosphorus, and dissolved organic carbon concentrations, and is influenced by the ratio of sediment area to surface mixed layer volume in lakes.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Review
Engineering, Chemical
Philippe Bogaerts, Alain Vande Wouwer
Summary: Metabolic flux analysis is often faced with system underdeterminacy, with various methods proposed to tackle this issue, including flux pathway analysis, flux balance analysis, flux variability analysis, and sampling.
Editorial Material
Plant Sciences
Nicholas J. Kruger, R. George Ratcliffe
Summary: Stable isotope labeling experiments provide opportunities for probing metabolic pathways, and metabolic flux analysis (MFA) is commonly used in prokaryotes but more challenging in plants. Constrains-based modeling for simulating network fluxes offers a versatile approach for exploring network capabilities, while MFA can be best utilized to probe interesting features revealed by simulation.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Review
Microbiology
Jack Jansma, Sahar El Aidy
Summary: Through in silico simulation methods based on flux balance analysis, interactions within the complex microbiota community in the human gut can be better investigated, aiding in understanding the intricate relationship between microbiota and the host. This approach can help researchers study the effects of various perturbations on different bacterial species in a shared metabolic environment, ultimately leading to improvements in human health.
Article
Biochemistry & Molecular Biology
Markus A. Koebis, Alexander Bockmayr, Ralf Steuer
Summary: Analysis of metabolic models using constraint-based optimization is a significant computational technique for studying and predicting cellular metabolism and growth. This work introduces a new approach called time-optimal adaptation (TOA), which allows for evaluating the fastest possible adaptation to a predefined cellular state while fulfilling dynamic and static constraints. TOA falls into the class of time-optimal control problems and extends existing modeling frameworks. The study demonstrates the application of TOA using a self-replicator model and explains experimental phenomena that are difficult to explore with existing methods.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Daniel J. Lugar, Sean G. Mack, Ganesh Sriram
Summary: Flux balance analysis (FBA) is a powerful method for predicting cell-wide metabolic activity, but interpreting the resulting flux vector can be challenging. The NetRed algorithm systematically reduces a stoichiometric matrix and flux vector to a more easily interpretable form, providing transparent and lossless simplification for metabolic networks. This reduction allows users to quickly identify metabolites and reaction pathways of interest with simplified presentation.
METABOLIC ENGINEERING
(2021)
Article
Biochemistry & Molecular Biology
Daniel Rios Garza, Didier Gonze, Haris Zafeiropoulos, Bin Liu, Karoline Faust
Summary: The human gut is a complex ecosystem with hundreds of microbial species interacting with each other and the human host. Mathematical models of the gut microbiome have been used to explain observations, but the traditional Lotka-Volterra model lacks interaction mechanisms and metabolic flexibility. Recent models that describe gut microbial metabolite production and consumption have been used to study the factors shaping gut microbial composition and their impact on metabolite concentrations in diseases. This review discusses how these models are built, what we have learned so far, and the current challenges and future directions.
Article
Biochemistry & Molecular Biology
Blas Blazquez, David San Leon, Antonia Rojas, Marta Tortajada, Juan Nogales
Summary: In this study, a high-quality genome-scale model (iBB1018) was constructed for accurate prediction of metabolic capabilities in B. subtilis. The model showed great accuracy in predicting carbon source utilization and identified potential novel carbon sources. Furthermore, the model was used for constructing the panphenome of B. subtilis, revealing the large metabolic versatility of the species and the importance of accessory metabolism at a species level.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Juan C. Villada, Maria F. Duran, Chee Kent Lim, Lisa Y. Stein, Patrick K. H. Lee
Summary: The study constructed a genome-scale metabolic model for Methylomicrobium album BG8, highlighting the importance of the ratio between oxygen and methane uptake for optimal growth. The results revealed a coupling between biomass production and carbon dioxide excretion, as well as a trade-off between biomass and acetate production. The integrative model developed in this study will aid in metabolic engineering and the development of a methane bioconversion platform.
Article
Endocrinology & Metabolism
Younes Rouabhi, Deng-Fu Guo, Yuying Zhao, Kamal Rahmouni
Summary: The BBSome protein complex plays an important role in metabolic regulation, especially in skeletal muscle and liver. Disruption of the BBSome in skeletal muscle has minimal effects on body weight and glucose handling, but improves insulin sensitivity in female mice. On the other hand, loss of the BBSome in hepatocytes leads to increased body weight, impaired glucose handling, and insulin sensitivity due to attenuated insulin signaling and reduced insulin receptor levels in the plasma membrane caused by mitochondrial dysfunction.
AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM
(2023)
Article
Agronomy
Johannes Laubach, John E. Hunt, Scott L. Graham, Rowan P. Buxton, Graeme N. D. Rogers, Paul L. Mudge, Jordan P. Goodrich, David Whitehead
Summary: The study investigated whether planting more diverse species in grazed grasslands can reduce N2O emissions and benefit greenhouse gas reduction. The results showed that the annual N2O emissions from the mixed pasture were lower than those from the ryegrass-white clover pasture. Additionally, the ryegrass-white clover pasture had a significant advantage in net greenhouse gas balance compared to the mixed pasture.
AGRICULTURAL AND FOREST METEOROLOGY
(2023)
Article
Multidisciplinary Sciences
Cesar Ordonez, Tonya DelSontro, Timon Langenegger, Daphne Donis, Ena L. Suarez, Daniel F. McGinnis
Summary: Recent discoveries challenge the paradigm by showing that oxic methane production (OMP) occurs in oxygenated surface waters worldwide. This study determines the net methane production rates in oxic surface waters of four pre-alpine lakes and finds that OMP is often the dominant source of diffusive methane emissions. Correlations with photosynthesis provide an empirical upscaling approach. Understanding the extent and drivers of OMP is crucial for constraining the atmospheric methane contribution by inland waters.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Hao Luo, Peishun Li, Boyang Ji, Jens Nielsen
Summary: The hybrid cybernetic model (HCM) approach is a dynamic modeling framework that integrates enzyme synthesis and activity regulation. It has been widely used in bioreaction engineering, especially for simulating microbial growth in different carbon source mixtures. The HCM strategy presented in this study introduces an optimized yield analysis algorithm (opt-yield-FBA) to simulate metabolic dynamics at the genome scale without the need for elementary flux modes (EFMs) calculation. The opt-yield-FBA algorithm can calculate optimal yield solutions and yield space for genome-scale metabolic models (GEMs).
METABOLIC ENGINEERING
(2023)