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A review of the mammalian unfolded protein response
TLDR
Recent advances in understanding the molecular structure of UPR in mammalian cells, its functional role in cellular stress, and its pathophysiology are described. Expand
Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints.
TLDR
This work applied the optimization and risk analysis of complex living entities (ORACLE) framework and constructed a large-scale mechanistic kinetic model of optimally grown Escherichia coli to investigate the complex interplay between stoichiometry, thermodynamics, and kinetics in determining the flexibility and capabilities of metabolism. Expand
Multiscale Models of Breast Cancer Progression
TLDR
It is expected that multiscale modeling and bottom-up agent-based models in particular will become an increasingly important platform technology for basic scientific discovery, as well as the identification and validation of potentially novel therapeutic targets. Expand
Menstrual cycle rhythmicity: metabolic patterns in healthy women
TLDR
The reduced metabolite levels observed may represent a time of vulnerability to hormone related health issues such as PMS and PMDD, in the setting of a healthy, rhythmic state and may form the basis of novel nutrition strategies for women. Expand
Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models.
TLDR
The computational framework ORACLE (Optimization and Risk Analysis of Complex Living Entities) is used to analyze the physiology of recombinant Escherichia coli producing 1,4-butanediol (BDO) and to identify potential strategies for improved production of BDO and demonstrates the potential and effectiveness of ORacLE for the accelerated design of microbial cell factories. Expand
Computational Modeling and Analysis of Insulin Induced Eukaryotic Translation Initiation
TLDR
A family of mathematical models of insulin induced translation initiation was developed and interrogated, suggesting that without insulin, a balance between the pro-initiation activity of the GTP-binding protein Rheb and anti-initiated activity of PTEN controlled basal initiation, while in the presence of insulin a combination of PI3K and RheB activity controlled inducible initiation. Expand
Population Heterogeneity in the Epithelial to Mesenchymal Transition Is Controlled by NFAT and Phosphorylated Sp1
TLDR
An ensemble of dynamic mathematical models describing TGF-β induced EMT are created to better understand the operational hierarchy of this complex molecular program, and potentially reveal a novel signaling axis which regulates carcinoma progression through an EMT versus tubulogenesis response. Expand
Physicochemical regulation of endothelial sprouting in a 3D microfluidic angiogenesis model.
TLDR
This biomimetic vessel platform demonstrated utility for delineating hitherto underappreciated contributors of angiogenesis, and future studies may enable important new mechanistic insights that will inform anti-angiogenic cancer therapy. Expand
Aging and sarcopenia associate with specific interactions between gut microbes, serum biomarkers and host physiology in rats
TLDR
It is demonstrated that aging skews the composition of the gut microbiome, in particular by altering the Sutterella to Barneseilla ratio, and alters the metabolic potential of intestinal bacteria, and provides candidate microbial species to target physical and metabolic decline during aging by modulating gut microbial ecology. Expand
Differential Metabolism of Medium-Chain Fatty Acids in Differentiated Human-Induced Pluripotent Stem Cell-Derived Astrocytes
TLDR
The results provide insights into designing different MCT-based ketogenic diets to target specific health benefits, and reveal MCFA-specific ketogenic properties. Expand
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