hong yang

Abstract: The green picoalga Ostreococcus is emerging as a simple plant model organism, and two species, O. lucimarinus and O. tauri, have now been sequenced and annotated manually. To evaluate the completeness of the metabolic annotation of both species, metabolic networks of O. lucimarinus and O. tauri were reconstructed from the KEGG database, thermodynamically constrained, elementally balanced, and functionally evaluated. The draft networks contained extensive gaps and, in the case of O. tauri, no biomass components could be produced due to an incomplete Calvin cycle. To find and remove gaps from the networks, an extensive reference biochemical reaction database was assembled using a stepwise approach that minimized the inclusion of microbial reactions. Gaps were then removed from both Ostreococcus networks using two existing gap-filling methodologies. In the first method, a bottom-up approach, a minimal list of reactions was added to each model to enable the production of all metabolites included in our biomass equation. In the second method, a top-down approach, all reactions in the reference database were added to the target networks and subsequently trimmed away based on the sequence alignment scores of identified orthologues. Because current gap-filling methods do not produce unique solutions, a quality metric that includes a weighting for phylogenetic distance and sequence similarity was developed to distinguish between gap-filling results automatically. The draft O. lucimarinus and O. tauri networks required the addition of 56 and 70 reactions, respectively, in order to produce the same biomass precursor metabolites that were produced by our plant reference database.

Abstract: HepG2, hepatocellular carcinoma cells, are used in drug toxicity studies and have also been explored for bioartificial livers. For these applications, the cells are under variable levels of nutrients and hormones, the effects of which on metabolism are poorly understood. In this study, HepG2-C3A cells were cultured under varying levels of glucose (high, low, and glucose-free) and insulin (without and with physiological levels of insulin) for 5 days. Cell growth was found to be comparable between high and low glucose media and lowest for glucose-free medium. Several features of central metabolism were affected profoundly by the medium glucose levels. Glucose consumption was greater for low glucose medium compared to high glucose medium, consistent with known glucose feedback regulation mechanisms. Urea productivity was highest in glucose-free medium. Further, it was seen that lactate acted as an alternative carbon source in the absence of glucose, whereas it acted as a sink for the high and low glucose media. Using a metabolic network flexibility analysis (MNFA) framework with stoichiometric and thermodynamic constraints, intracellular fluxes under varying levels of glucose and insulin were evaluated. The analysis indicates that urea production in HepG2-C3A cells arises via the arginase II pathway rather than from ammonia detoxification. Further, involvement of the putrescine metabolism with glutamine metabolism caused higher urea production in glucose-free medium consistent with higher glutamine uptake. MNFA indicated that in high and low glucose media, glycolysis, glutaminolysis, and oxidative phosphorylation were the main sources of energy (NADH, NADPH, and ATP). In the glucose-free medium, due to very low glycolytic flux, higher malate to pyruvate glutaminolytic flux and TCA cycle contributed more significantly to energy metabolism. The presence of insulin lowered glycerol uptake and corresponding fluxes involved in lipid metabolism for all glucose levels but otherwise exerted negligible effect on metabolism. HepG2-C3A cells thus show distinct differences from primary hepatocytes in terms of energy metabolism and urea production. This knowledge can be used to design media supplements and metabolically engineer cells to restore necessary hepatic functions to HepG2-C3A cells for a range of applications.

Abstract: Amino acid supplementation has been shown to enhance the liver-specific functions of cultured hepatocytes during plasma exposure. However, their transport through the cell membrane may restrict their availability for hepatic metabolism. Here, we focus on transport constraints related to uptake of the neutral amino acids and their impact on hepatic metabolism and liver-specific functions. Under varying combinations of their medium concentrations, we found that transport competition exists among the three amino acids alanine, serine and glutamine and that the resulting capacity constraints affect the urea and albumin production of cultured hepatocytes. Regression equations were developed to quantify these constraints and were incorporated with other constraints (mass balance, measured flux data and reaction directionality) within a multi-objective flux balance framework to understand how amino acid transport constraints propagate through central hepatic metabolism and to predict refined amino acid supplementations for specific hepatocyte design objectives.

Abstract: When cultured hepatocytes are exposed to challenging environments such as plasma, they frequently suffer a decline in liver-specific functions. Media supplements are sought to reduce or eliminate this effect. A rational design approach for amino acid supplementation in hepatocyte culture has been developed in our prior work, and designed amino acid supplementation (DAA) was found to increase urea and albumin production. To fully characterize the metabolic state of hepatocytes under different amino acid supplementations, a number of metabolite measurements are performed in this work and used in a metabolic network flexibility analysis framework including thermodynamic constraints to determine the range of values for the intracellular fluxes. A metabolic objective prediction model is used to infer the metabolic objectives of the hepatocytes and to quantify the intracellular flux distribution for three different amino acid supplementations. The results illustrate that DAA leads to greater fluxes in the tricarboxylic acid cycle (TCA) cycle, urea cycle, and fatty acid oxidation concomitant with lower fluxes in intracellular lipid metabolism compared with empirical amino acid and no amino acid supplementation for hepatocytes during plasma exposure. It is also found that hepatocytes exhibit flexibility in their metabolic objectives depending on the composition of the amino acid supplementations. By incorporating both experimental data and thermodynamic constraints into the mathematical model, the proposed approach leads to identification of metabolic objectives and characterization of fluxes’ variability and pathway changes due to different cultured conditions.

Abstract: ABSTRACT: Improvement of culture media for mammalian cells is conducted via empirical adjustments, sometimes aided by statistical design methodologies. Here, we demonstrate a proof of principle for the use of constraints-based modeling to achieve enhanced performance of liver-specific functions of cultured hepatocytes during plasma exposure by adjusting amino acid supplementation and hormone levels in the medium. Flux balance analysis (FBA) is used to determine an amino acid flux profile consistent with a desired output; this is used to design an amino acid supplementation. Under conditions of no supplementation, empirical supplementation, and designed supplementation, hepatocytes were exposed to plasma and their morphology, specific cell functions (urea, albumin production) and lipid metabolism were measured. Urea production under the designed amino acid supplementation was found to be increased compared with previously reported (empirical) amino acid supplementation. Not surprisingly, the urea production attained was less than the theoretical value, indicating the existence of pathways or constraints not present in the current model. Although not an explicit design objective, albumin production was also increased by designed amino acid supplementation, suggesting a functional linkage between these outputs. In conjunction with traditional approaches to improving culture conditions, the rational design approach described herein provides a novel means to tune the metabolic outputs of cultured hepatocytes.

Abstract: Extracorporeal bioartificial liver (BAL) devices are the most promising technology for treatment of the liver failure. However, when exposed to plasma from the patient, hepatocytes are prone to accumulate intracellular lipids and exhibit poor liver-specific functions. Our work focuses on understanding the metabolism of cultured hepatocytes used for BAL. In this paper, a logic based programming is used to determine the important reactions in cultured hepatocytes by systemically analyzing the hepatic metabolic network, and investigating whether insulin, amino acid and hormone supplementations upregulate or downregulate certain pathways that control important liver specific functions, such as urea and albumin production. Using elementary mode analysis we were able to obtain 32 independent pathways, which are then used to analyze the results of the logic-based programming approach.

Abstract: