Determining the Biomass Composition of a Sponge Holobiont for Flux Analysis

2014 ◽  
pp. 107-125 ◽  
Author(s):  
Jabin Watson ◽  
Bernard Degnan ◽  
Sandie Degnan ◽  
Jens O. Krömer
Keyword(s):  
Biomass Composition ◽  
Flux Analysis

Determination of Biomass Composition ofCatharanthusroseusHairy Roots for Metabolic Flux Analysis

2006 ◽  
Vol 22 (6) ◽  
pp. 1659-1663
Author(s):  
Ganesh Sriram ◽  
Omar González-Rivera ◽  
Jacqueline V. Shanks
Keyword(s):  
Metabolic Flux Analysis ◽  
Metabolic Flux ◽  
Biomass Composition ◽  
Flux Analysis

Determination of Biomass Composition of Catharanthus roseus Hairy Roots for Metabolic Flux Analysis

2006 ◽  
Vol 22 (6) ◽  
pp. 1659-1663 ◽  
Author(s):  
G. Sriram ◽  
O. Gonzalez-Rivera ◽  
J.V. Shanks
Keyword(s):  
Hairy Roots ◽  
Catharanthus Roseus ◽  
Metabolic Flux Analysis ◽  
Metabolic Flux ◽  
Biomass Composition ◽  
Flux Analysis

scholarly journals On the impact of biomass composition in constraint-based flux analysis

2019 ◽  
Author(s):  
Meiyappan Lakshmanan ◽  
Sichang Long ◽  
Kok Siong Ang ◽  
Nathan Lewis ◽  
Dong-Yup Lee
Keyword(s):  
In Silico ◽  
Relevant Information ◽  
Biomass Composition ◽  
Flux Analysis ◽  
Biomass Equation ◽  
Highly Sensitive ◽  
Biomass Components ◽  
Genome Scale ◽  
The Impact ◽  
Macromolecular Composition

ABSTRACTThe biomass equation is a critical component in genome-scale metabolic models (GEMs): It is one of most widely used objective functions within constraint-based flux analysis formulation, describing cellular driving force under the growth condition. The equation accounts for the quantities of all known biomass precursors that are required for cell growth. Most often than not, published GEMs have adopted relevant information from other species to derive the biomass equation when any of the macromolecular composition is unavailable. Thus, its validity is still questionable. Here, we investigated the qualitative and quantitative aspects of biomass equations from GEMs of eight different yeast species. Expectedly, most yeast GEMs borrowed macromolecular compositions from the model yeast, Saccharomyces cerevisiae. We further confirmed that the biomass compositions could be markedly different even between phylogenetically closer species and none of the high throughput omics data such as genome, transcriptome and proteome provided a good estimate of relative amino acid abundances. Upon varying the stoichiometric coefficients of biomass components, subsequent flux simulations demonstrated how predicted in silico growth rates change with the carbon substrates used. Furthermore, the internal fluxes through individual reactions are highly sensitive to all components in the biomass equation. Overall, the current analysis clearly highlight that biomass equation need to be carefully drafted from relevant experiments, and the in silico simulation results should be appropriately interpreted to avoid any inaccuracies.

scholarly journals Bioenergetic and Proteomic Profiling of Immune Cells in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Patients: An Exploratory Study

Biomolecules ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 961
Author(s):  
Paula Fernandez-Guerra ◽  
Ana C. Gonzalez-Ebsen ◽  
Susanne E. Boonen ◽  
Julie Courraud ◽  
Niels Gregersen ◽  
...  
Keyword(s):  
Chronic Fatigue Syndrome ◽  
Complex Disease ◽  
Mononuclear Cells ◽  
Coupling Efficiency ◽  
Well Being ◽  
Chronic Fatigue ◽  
Myalgic Encephalomyelitis ◽  
Flux Analysis ◽  
Proteomic Profiling ◽  
Fatigue Syndrome

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a heterogeneous, debilitating, and complex disease. Along with disabling fatigue, ME/CFS presents an array of other core symptoms, including autonomic nervous system (ANS) dysfunction, sustained inflammation, altered energy metabolism, and mitochondrial dysfunction. Here, we evaluated patients' symptomatology and the mitochondrial metabolic parameters in peripheral blood mononuclear cells (PBMCs) and plasma from a clinically well-characterised cohort of six ME/CFS patients compared to age- and gender-matched controls. We performed a comprehensive cellular assessment using bioenergetics (extracellular flux analysis) and protein profiles (quantitative mass spectrometry-based proteomics) together with self-reported symptom measures of fatigue, ANS dysfunction, and overall physical and mental well-being. This ME/CFS cohort presented with severe fatigue, which correlated with the severity of ANS dysfunction and overall physical well-being. PBMCs from ME/CFS patients showed significantly lower mitochondrial coupling efficiency. They exhibited proteome alterations, including altered mitochondrial metabolism, centred on pyruvate dehydrogenase and coenzyme A metabolism, leading to a decreased capacity to provide adequate intracellular ATP levels. Overall, these results indicate that PBMCs from ME/CFS patients have a decreased ability to fulfill their cellular energy demands.

scholarly journals Renewable Biomass Utilization: A Way Forward to Establish Sustainable Chemical and Processing Industries

2021 ◽  
Vol 3 (1) ◽  
pp. 243-259
Author(s):  
Yadhu N. Guragain ◽  
Praveen V. Vadlani
Keyword(s):  
Fossil Fuels ◽  
Process Intensification ◽  
Raw Material ◽  
Biomass Composition ◽  
Biomass Feedstocks ◽  
Renewable Biomass ◽  
Sustainability Criteria ◽  
Biomass Component ◽  
Biomass Resources ◽  
Multiple Challenges

Lignocellulosic biomass feedstocks are promising alternatives to fossil fuels for meeting raw material needs of processing industries and helping transit from a linear to a circular economy and thereby meet the global sustainability criteria. The sugar platform route in the biochemical conversion process is one of the promising and extensively studied methods, which consists of four major conversion steps: pretreatment, hydrolysis, fermentation, and product purification. Each of these conversion steps has multiple challenges. Among them, the challenges associated with the pretreatment are the most significant for the overall process because this is the most expensive step in the sugar platform route and it significantly affects the efficiency of all subsequent steps on the sustainable valorization of each biomass component. However, the development of a universal pretreatment method to cater to all types of feedstock is nearly impossible due to the substantial variations in compositions and structures of biopolymers among these feedstocks. In this review, we have discussed some promising pretreatment methods, their processing and chemicals requirements, and the effect of biomass composition on deconstruction efficiencies. In addition, the global biomass resources availability and process intensification ideas for the lignocellulosic-based chemical industry have been discussed from a circularity and sustainability standpoint.

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