scholarly journals Integrating Extracellular Flux Measurements and Genome-Scale Modeling Reveals Differences between Brown and White Adipocytes

Cell Reports ◽  
2017 ◽  
Vol 21 (11) ◽  
pp. 3040-3048 ◽  
Author(s):  
Alfred K. Ramirez ◽  
Matthew D. Lynes ◽  
Farnaz Shamsi ◽  
Ruidan Xue ◽  
Yu-Hua Tseng ◽  
...  
Keyword(s):  
Extracellular Flux ◽  
Scale Modeling ◽  
White Adipocytes ◽  
Flux Measurements ◽  
Genome Scale

Genome-scale Modeling of Metabolism and Macromolecular Expression and Their Applications

2020 ◽  
Vol 25 (6) ◽  
pp. 931-943
Author(s):  
Sanjeev Dahal ◽  
Jiao Zhao ◽  
Laurence Yang
Keyword(s):  
Scale Modeling ◽  
Genome Scale

A Genome-Scale Modeling Approach to Investigate the Antibiotics-Triggered Perturbation in the Metabolism of Pseudomonas aeruginosa

2016 ◽  
Vol 2 (3) ◽  
pp. 39-42 ◽  
Author(s):  
Zhaobin Xu ◽  
Nicholas Ribaudo ◽  
Xianhua Li ◽  
Thomas K. Wood ◽  
Zuyi Huang
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Modeling Approach ◽  
Scale Modeling ◽  
A Genome ◽  
Genome Scale

scholarly journals Cadmium-Related Effects on Cellular Immunity Comprises Altered Metabolism in Earthworm Coelomocytes

2020 ◽  
Vol 21 (2) ◽  
pp. 599 ◽  
Author(s):  
Martina Höckner ◽  
Claudio Adriano Piechnik ◽  
Birgit Fiechtner ◽  
Birgit Weinberger ◽  
Lars Tomanek
Keyword(s):  
Immune System ◽  
Energy Demand ◽  
Cell Protein ◽  
Metabolic Potential ◽  
Extracellular Flux ◽  
Potential Link ◽  
Flux Measurements ◽  
Acute Changes ◽  
Related Proteins ◽  
Cd Exposure

The heavy metal cadmium (Cd) is known to modulate the immune system, challenging soil-dwelling organisms where environmental Cd pollution is high. Since earthworms lack adaptive immunity, we determined Cd-related effects on coelomocytes, the cellular part of innate immunity, which is also the site of detoxification processes. A proteomics approach revealed a set of immunity-related proteins as well as gene products involved in energy metabolism changing in earthworms in response to Cd exposure. Based on these results, we conducted extracellular flux measurements of oxygen and acidification to reveal the effect of Cd on coelomocyte metabolism. We observed a significantly changing oxygen consumption rate, extracellular acidification, as well as metabolic potential, which can be defined as the response to an induced energy demand. Acute changes in intracellular calcium levels were also observed, indicating impaired coelomocyte activation. Lysosomes, the cell protein recycling center, and mitochondrial parameters did not change. Taken together, we were able to characterize coelomocyte metabolism to reveal a potential link to an impaired immune system upon Cd exposure.

scholarly journals Rhodosporidium toruloides - A potential red yeast chassis for lipids and beyond

2020 ◽  
Vol 20 (5) ◽  
Author(s):  
Zhiqiang Wen ◽  
Sufang Zhang ◽  
Chuks Kenneth Odoh ◽  
Mingjie Jin ◽  
Zongbao K Zhao
Keyword(s):  
Lipid Production ◽  
Rhodosporidium Toruloides ◽  
Biotechnological Applications ◽  
Future Directions ◽  
The Past ◽  
Enhanced Production ◽  
Scale Modeling ◽  
Red Yeast ◽  
Genome Scale ◽  
Made In

ABSTRACT The red yeast Rhodosporidium toruloides naturally produces microbial lipids and carotenoids. In the past decade or so, many studies demonstrated R. toruloides as a promising platform for lipid production owing to its diverse substrate appetites, robust stress resistance and other favorable features. Also, significant progresses have been made in genome sequencing, multi-omic analysis and genome-scale modeling, thus illuminating the molecular basis behind its physiology, metabolism and response to environmental stresses. At the same time, genetic parts and tools are continuously being developed to manipulate this distinctive organism. Engineered R. toruloides strains are emerging for enhanced production of conventional lipids, functional lipids as well as other interesting metabolites. This review updates those progresses and highlights future directions for advanced biotechnological applications.

scholarly journals Quantifying intracellular rates of glycolytic and oxidative ATP production and consumption using extracellular flux measurements

2017 ◽  
Vol 292 (17) ◽  
pp. 7189-7207 ◽  
Author(s):  
Shona A. Mookerjee ◽  
Akos A. Gerencser ◽  
David G. Nicholls ◽  
Martin D. Brand
Keyword(s):  
Atp Production ◽  
Extracellular Flux ◽  
Production And Consumption ◽  
Flux Measurements

scholarly journals Diagnostics for Stochastic Genome-Scale Modeling via Model Slicing and Debugging

PLoS ONE ◽  
2014 ◽  
Vol 9 (11) ◽  
pp. e110380
Author(s):  
Kevin J. Tsai ◽  
Chuan-Hsiung Chang
Keyword(s):  
Scale Modeling ◽  
Genome Scale

scholarly journals Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142

2012 ◽  
Vol 8 (4) ◽  
pp. e1002460 ◽  
Author(s):  
Trang T. Vu ◽  
Sergey M. Stolyar ◽  
Grigoriy E. Pinchuk ◽  
Eric A. Hill ◽  
Leo A. Kucek ◽  
...  
Keyword(s):  
Carbon Fluxes ◽  
Unicellular Cyanobacterium ◽  
Scale Modeling ◽  
Genome Scale
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