scholarly journals SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

2018 ◽  
Author(s):  
Benjamín J. Sánchez ◽  
Feiran Li ◽  
Eduard J. Kerkhoven ◽  
Jens Nielsen
Keyword(s):  
Experimental Data ◽  
Saccharomyces Cerevisiae ◽  
Lipid Metabolism ◽  
Acyl Chain ◽  
Energy Costs ◽  
Detailed Data ◽  
Modeling Framework ◽  
Lipid Species ◽  
Constraint Based Modeling ◽  
Genome Scale

SummaryA recurrent problem in genome-scale metabolic models (GEMs) is to correctly represent lipids as biomass requirements, due to the numerous of possible combinations of individual lipid species and the corresponding lack of fully detailed data. In this study we present SLIMEr, a formalism for correctly representing lipid requirements in GEMs using commonly available experimental data. SLIMEr enhances a GEM with mathematical constructs where we Split Lipids Into Measurable Entities (SLIME reactions), in addition to constraints on both the lipid classes and the acyl chain distribution. By implementing SLIMEr on the consensus GEM of Saccharomyces cerevisiae, we can predict accurate amounts of lipid species, analyze the flexibility of the resulting distribution, and compute the energy costs of moving from one metabolic state to another. The approach shows potential for better understanding lipid metabolism in yeast under different conditions. SLIMEr is freely available at https://github.com/SysBioChalmers/SLIMEr.

scholarly journals The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism

2008 ◽  
Vol 2 (1) ◽  
pp. 71 ◽  
Author(s):  
Intawat Nookaew ◽  
Michael C Jewett ◽  
Asawin Meechai ◽  
Chinae Thammarongtham ◽  
Kobkul Laoteng ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Lipid Metabolism ◽  
Metabolic Model ◽  
Genome Scale

scholarly journals SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

2019 ◽  
Vol 13 (1) ◽  
Author(s):  
Benjamín J. Sánchez ◽  
Feiran Li ◽  
Eduard J. Kerkhoven ◽  
Jens Nielsen
Keyword(s):  
Lipid Metabolism ◽  
Modeling Framework ◽  
Constraint Based Modeling

scholarly journals Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Marie Schöpping ◽  
Paula Gaspar ◽  
Ana Rute Neves ◽  
Carl Johan Franzén ◽  
Ahmad A. Zeidan
Keyword(s):  
Bifidobacterium Longum ◽  
Defined Medium ◽  
Nutritional Requirements ◽  
Modeling Framework ◽  
Carbohydrate Utilization ◽  
Bifidobacterium Animalis ◽  
Manual Curation ◽  
Constraint Based Modeling ◽  
Complex Culture ◽  
Genome Scale

AbstractAlthough bifidobacteria are widely used as probiotics, their metabolism and physiology remain to be explored in depth. In this work, strain-specific genome-scale metabolic models were developed for two industrially and clinically relevant bifidobacteria, Bifidobacterium animalis subsp. lactis BB-12® and B. longum subsp. longum BB-46, and subjected to iterative cycles of manual curation and experimental validation. A constraint-based modeling framework was used to probe the metabolic landscape of the strains and identify their essential nutritional requirements. Both strains showed an absolute requirement for pantethine as a precursor for coenzyme A biosynthesis. Menaquinone-4 was found to be essential only for BB-46 growth, whereas nicotinic acid was only required by BB-12®. The model-generated insights were used to formulate a chemically defined medium that supports the growth of both strains to the same extent as a complex culture medium. Carbohydrate utilization profiles predicted by the models were experimentally validated. Furthermore, model predictions were quantitatively validated in the newly formulated medium in lab-scale batch fermentations. The models and the formulated medium represent valuable tools to further explore the metabolism and physiology of the two species, investigate the mechanisms underlying their health-promoting effects and guide the optimization of their industrial production processes.

Microstructural morphology of sphingolipid dispersions as investigated by freeze-fracture EM

1995 ◽  
Vol 53 ◽  
pp. 944-945
Author(s):  
Vitthal S. Kulkarni ◽  
Wayne H. Anderson ◽  
Rhoderick E. Brown
Keyword(s):  
Acyl Chain ◽  
Biological Significance ◽  
Freeze Fracture ◽  
Fatty Acyl ◽  
Fatty Acyl Moiety ◽  
Aqueous Dispersions ◽  
Head Groups ◽  
Lipid Species ◽  
Microstructural Morphology ◽  
Layer Chromatography

The biological significance of the sphingomyelins (SM) and monoglycosylated sphingolipids like galactosylceramides (GalCer) are well documented Our recent investigation showed tubular bilayers in the aqueous dispersions of N-nervonoyl GalCer [N-(24:lΔ15,cls) GalCer] (a major fatty acyl moiety of natural GalCer). To determine the influence of lipid head groups on the resulting mesophasic morphology, we investigated microstructural self-assemblies of N-nervonoyl-SM [N-(24:1 Δ15,cls) SM; the second most abundant sphingomyelin in mammalian cell membranes], 1- palmitoyl-2-nervonoyl phosphatidylcholine [PNPC] (the lipid species with the same acyl chain configuration as in N-(24: 1) GalCer) and also compared it with egg-SM by freeze-fracture EM.Procedures for synthesizing and purifying N-(24:1) GalCer, N-(24:1) SM, and PNPC have been reported . Egg-SM was purchased from Avanti Polar Lipids, Alabaster AL. All lipids were >99% pure as checked by thin layer chromatography. Lipid dispersions were prepared by hydrating dry lipid with phosphate buffer (pH 6.6) at 80-90°C (3-5 min), vigorously vortexing (1 min) and repeating this procedure for three times prior to three freeze-thaw cycles.

Achieving Procedure of a Kinetic Model to Predict the Influence of the Process Global Temperature on a Technological Alcoholic Fermentation II. An Arrhenius type Kinetic Model

2008 ◽  
Vol 59 (4) ◽  
Author(s):  
Neculai Catalin Lungu ◽  
Maria Alexandroaei
Keyword(s):  
Experimental Data ◽  
Saccharomyces Cerevisiae ◽  
Kinetic Model ◽  
Economic Efficiency ◽  
Fermentation Process ◽  
Alcoholic Fermentation ◽  
Global Temperature ◽  
Medium Temperature ◽  
Biotechnological Process

The aim of the present work is to offer a practical methodology to realise an Arrhenius type kinetic model for a biotechnological process of alcoholic fermentation based on the Saccharomyces cerevisiae yeast. Using the experimental data we can correlate the medium temperature of fermentation with the time needed for a fermentation process under imposed conditions of economic efficiency.

scholarly journals How does hepatic lipid accumulation lead to lipotoxicity in non-alcoholic fatty liver disease?

2021 ◽  
Vol 15 (1) ◽  
pp. 21-35
Author(s):  
Yana Geng ◽  
Klaas Nico Faber ◽  
Vincent E. de Meijer ◽  
Hans Blokzijl ◽  
Han Moshage
Keyword(s):  
Lipid Metabolism ◽  
Liver Disease ◽  
Fatty Liver ◽  
Lipid Accumulation ◽  
Fatty Liver Disease ◽  
Lipid Uptake ◽  
Cellular Mechanisms ◽  
Alcoholic Fatty Liver ◽  
Lipid Species ◽  
Alcoholic Fatty Liver Disease

Abstract Background Non-alcoholic fatty liver disease (NAFLD), characterized as excess lipid accumulation in the liver which is not due to alcohol use, has emerged as one of the major health problems around the world. The dysregulated lipid metabolism creates a lipotoxic environment which promotes the development of NAFLD, especially the progression from simple steatosis (NAFL) to non-alcoholic steatohepatitis (NASH). Purposeand Aim This review focuses on the mechanisms of lipid accumulation in the liver, with an emphasis on the metabolic fate of free fatty acids (FFAs) in NAFLD and presents an update on the relevant cellular processes/mechanisms that are involved in lipotoxicity. The changes in the levels of various lipid species that result from the imbalance between lipolysis/lipid uptake/lipogenesis and lipid oxidation/secretion can cause organellar dysfunction, e.g. ER stress, mitochondrial dysfunction, lysosomal dysfunction, JNK activation, secretion of extracellular vesicles (EVs) and aggravate (or be exacerbated by) hypoxia which ultimately lead to cell death. The aim of this review is to provide an overview of how abnormal lipid metabolism leads to lipotoxicity and the cellular mechanisms of lipotoxicity in the context of NAFLD.

Comparison of soot models for reacting sprays in diesel engine-like conditions

2021 ◽  
pp. 095440702110154
Author(s):  
Pavan Prakash Duvvuri ◽  
Rajesh Kumar Shrivastava ◽  
Sheshadri Sreedhara
Keyword(s):  
Experimental Data ◽  
Volume Fraction ◽  
Soot Volume Fraction ◽  
Modeling Framework ◽  
Aerosol Dynamics ◽  
Significant Difference ◽  
Polycyclic Aromatic ◽  
Order Of Magnitude ◽  
Detailed Kinetics ◽  
Soot Model

Stringent emission legislations and growing health concerns have contributed to the evolution of soot modeling in diesel engines from simple empirical relations to methods involving detailed kinetics and complex aerosol dynamics. In this paper, four different soot models have been evaluated for the high temperature, high pressure combusting dodecane spray cases of engine combustion network (ECN) spray A which mimics engine-relevant conditions. The soot models considered include an empirical, a multistep, a method of moments based, and a discrete sectional method soot model. Two experimental cases with ambient oxygen volume of 21% and 15% have been modeled. A good agreement between simulations and experiments for vapor penetration and heat release rate has been obtained. Quasi-steady soot volume fraction contours for the four soot models have been compared with experiments. Contours of the species and source terms involved in soot modeling have also been compared for a better understanding of soot processes. The empirical soot model results in higher magnitude and spread of soot due to a lack of modeling framework for oxidation through OH species. Among the four models studied, the multistep soot model has been observed to provide the most promising agreement with the experimental data in terms of distribution of soot and location of peak soot volume fraction. Due to a two-way coupling of soot models, the detailed models predict an upstream location for soot as compared to the multi-step soot model which is one way coupled. A significant difference (of an order of magnitude) in the concentration of PAH (polycyclic aromatic hydrocarbons) precursor between multistep and detailed soot models has been observed because of precursor consumption due to the coupling of detailed soot models with chemical kinetics. It is recommended that kinetic schemes, especially those concerning PAH, be validated with experimental data with a kinetics-coupled soot model.

scholarly journals Genome-Scale Metabolic Network Analysis of the Opportunistic Pathogen Pseudomonas aeruginosa PAO1

2008 ◽  
Vol 190 (8) ◽  
pp. 2790-2803 ◽  
Author(s):  
Matthew A. Oberhardt ◽  
Jacek Puchałka ◽  
Kimberly E. Fryer ◽  
Vítor A. P. Martins dos Santos ◽  
Jason A. Papin
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Metabolic Network ◽  
Opportunistic Pathogen ◽  
Scale Model ◽  
Modeling Framework ◽  
Major Life ◽  
Metabolic Versatility ◽  
A Genome ◽  
Scale Properties ◽  
Genome Scale

ABSTRACT Pseudomonas aeruginosa is a major life-threatening opportunistic pathogen that commonly infects immunocompromised patients. This bacterium owes its success as a pathogen largely to its metabolic versatility and flexibility. A thorough understanding of P. aeruginosa's metabolism is thus pivotal for the design of effective intervention strategies. Here we aim to provide, through systems analysis, a basis for the characterization of the genome-scale properties of this pathogen's versatile metabolic network. To this end, we reconstructed a genome-scale metabolic network of Pseudomonas aeruginosa PAO1. This reconstruction accounts for 1,056 genes (19% of the genome), 1,030 proteins, and 883 reactions. Flux balance analysis was used to identify key features of P. aeruginosa metabolism, such as growth yield, under defined conditions and with defined knowledge gaps within the network. BIOLOG substrate oxidation data were used in model expansion, and a genome-scale transposon knockout set was compared against in silico knockout predictions to validate the model. Ultimately, this genome-scale model provides a basic modeling framework with which to explore the metabolism of P. aeruginosa in the context of its environmental and genetic constraints, thereby contributing to a more thorough understanding of the genotype-phenotype relationships in this resourceful and dangerous pathogen.

scholarly journals Lipid Remodeling Confers Osmotic Stress Tolerance to Embryogenic Cells during Cryopreservation

2021 ◽  
Vol 22 (4) ◽  
pp. 2174
Author(s):  
Liang Lin ◽  
Junchao Ma ◽  
Qin Ai ◽  
Hugh W. Pritchard ◽  
Weiqi Li ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Technology Development ◽  
Membrane Lipids ◽  
Species Conservation ◽  
Membrane Lipid ◽  
Cell Integrity ◽  
Embryogenic Cells ◽  
Osmotic Stress Tolerance ◽  
Lipid Species ◽  
Magnolia Officinalis

Plant species conservation through cryopreservation using plant vitrification solutions (PVS) is based in empiricism and the mechanisms that confer cell integrity are not well understood. Using ESI-MS/MS analysis and quantification, we generated 12 comparative lipidomics datasets for membranes of embryogenic cells (ECs) of Magnolia officinalis during cryogenic treatments. Each step of the complex PVS-based cryoprotocol had a profoundly different impact on membrane lipid composition. Loading treatment (osmoprotection) remodeled the cell membrane by lipid turnover, between increased phosphatidic acid (PA) and phosphatidylglycerol (PG) and decreased phosphatidylcholine (PC) and phosphatidylethanolamine (PE). The PA increase likely serves as an intermediate for adjustments in lipid metabolism to desiccation stress. Following PVS treatment, lipid levels increased, including PC and PE, and this effectively counteracted the potential for massive loss of lipid species when cryopreservation was implemented in the absence of cryoprotection. The present detailed cryobiotechnology findings suggest that the remodeling of membrane lipids and attenuation of lipid degradation are critical for the successful use of PVS. As lipid metabolism and composition varies with species, these new insights provide a framework for technology development for the preservation of other species at increasing risk of extinction.

scholarly journals A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Omid Oftadeh ◽  
Pierre Salvy ◽  
Maria Masid ◽  
Maxime Curvat ◽  
Ljubisa Miskovic ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Expression System ◽  
Biomass Composition ◽  
Industrial Biotechnology ◽  
Overflow Metabolism ◽  
Cellular Expression ◽  
A Genome ◽  
Wide Range ◽  
Eukaryotic Organisms ◽  
Genome Scale

AbstractEukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of multiple biological networks into a single model for cell analysis and engineering. One of the most accurate models of biological systems include Expression and Thermodynamics FLux (ETFL), which efficiently integrates RNA and protein synthesis with traditional genome-scale metabolic models. However, ETFL is so far only applicable for E. coli. To adapt this model for Saccharomyces cerevisiae, we developed yETFL, in which we augmented the original formulation with additional considerations for biomass composition, the compartmentalized cellular expression system, and the energetic costs of biological processes. We demonstrated the ability of yETFL to predict maximum growth rate, essential genes, and the phenotype of overflow metabolism. We envision that the presented formulation can be extended to a wide range of eukaryotic organisms to the benefit of academic and industrial research.

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