Metabolic flux analysis of hepatocyte function in hormone- and amino acid-supplemented plasma

Understanding the metabolic and regulatory pathways of hepatocytes is important for biotechnological applications involving liver cells. Previous attempts to culture hepatocytes in plasma yielded poor functional results. Recently we reported that hormone (insulin and hydrocortisone) and amino acid supplementation reduces intracellular lipid accumulation and restores liver-specific function in hepatocytes exposed to heparinized human plasma. In the current study, we performed metabolic flux analysis (MFA) using a simplified metabolic network model of cultured hepatocytes to quantitively estimate the changes in lipid metabolism and relevant intracellular pathways in response to hormone and amino acid supplementation. The model accounts for the majority of central carbon and nitrogen metabolism, and assumes pseudo-steady-state with no metabolic futile cycles. We found that beta-oxidation and tricarboxylic acid (TCA) cycle fluxes were upregulated by both hormone and amino acid supplementation, thus enhancing the rate of lipid oxidation. Concomitantly, hormone and amino acid supplementation increased gluconeogenic fluxes. This, together with an increased rate of glucose clearance, caused an increase in predicted glycogen synthesis. Urea synthesis was primarily derived from ammonia and aspartate generated through transamination reactions, while exogenous ammonia removal accounted for only 3-6% of the urea nitrogen. Amino acid supplementation increased the endogenous synthesis of oxaloacetate, and in turn that of aspartate, a necessary substrate for the urea cycle. These findings from MFA provide cues as to which genes/pathways relevant to fatty acid oxidation, urea production, and gluconeogenesis may be upregulated by plasma supplementation, and are consistent with current knowledge of hepatic amino acid metabolism, which provides further credence to this approach for evaluating the metabolic state of hepatocytes under various environmental conditions.     

Effect of amino acid supplementation on titer and glycosylation distribution in hybridoma cell cultures—Systems biology‐based interpretation using genome‐scale metabolic flux balance model and multivariate data analysis

Genome‐scale flux balance analysis (FBA) is a powerful systems biology tool to characterize intracellular reaction fluxes during cell cultures. FBA estimates intracellular reaction rates by optimizing an objective function, subject to the constraints of a metabolic model and media uptake/excretion rates. A dynamic extension to FBA, dynamic flux balance analysis (DFBA), can calculate intracellular reaction fluxes as they change during cell cultures. In a previous study by Read et al. (2013), a series of informed amino acid supplementation experiments were performed on twelve parallel murine hybridoma cell cultures, and this data was leveraged for further analysis (Read et al., Biotechnol Prog. 2013;29:745–753). In order to understand the effects of media changes on the model murine hybridoma cell line, a systems biology approach is applied in the current study. Dynamic flux balance analysis was performed using a genome‐scale mouse metabolic model, and multivariate data analysis was used for interpretation. The calculated reaction fluxes were examined using partial least squares and partial least squares discriminant analysis. The results indicate media supplementation increases product yield because it raises nutrient levels extending the growth phase, and the increased cell density allows for greater culture performance. At the same time, the directed supplementation does not change the overall metabolism of the cells. This supports the conclusion that product quality, as measured by glycoform assays, remains unchanged because the metabolism remains in a similar state. Additionally, the DFBA shows that metabolic state varies more at the beginning of the culture but less by the middle of the growth phase, possibly due to stress on the cells during inoculation. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1163–1173, 2016     

Advances in flux balance analysis

Biology is going through a paradigm shift from reductionist to holistic, systems-based approaches. The complete genome sequence for a number of organisms is available and the analysis of genome sequence data is proving very useful. Thus, genome sequencing projects and bioinformatic analyses are leading to a complete 'parts catalog' of the molecular components in many organisms. The next challenge will be to reconstruct and simulate overall cellular functions based on the extensive reductionist information. Recent advances have been made in the area of flux balance analysis, a mathematical modeling approach often utilized by metabolic engineers to quantitatively simulate microbial metabolism.     

The effects of amino acid supplementation on muscular performance during resistance training overreaching

The purpose of this study was to examine the effects of amino acid supplementation on muscular strength, power, and high-intensity endurance during short-term resistance training overreaching. Seventeen resistance-trained men were randomly assigned to either an amino acid (AA) or placebo (P) group and underwent 4 weeks of total-body resistance training consisting of two 2-week phases of overreaching (phase 1: 3 x 8-12 repetitions maximum [RM], 8 exercises; phase 2: 5 x 3-5 RM, 5 exercises). Muscle strength, power, and high-intensity endurance were determined before (T1) and at the end of each training week (T2-T5). One repetition maximum squat and bench press decreased at T2 in P (5.2 and 3.4 kg, respectively) but not in AA, and significant increases in 1 RM squat and bench press were observed at T3-T5 in both groups. A decrease in the ballistic bench press peak power was observed at T3 in P but not AA. The fatigue index during the 20-repetition jump squat assessment did not change in the P group at T3 and T5 (fatigue index = 18.6 and 18.3%, respectively) whereas a trend for reduction was observed in the AA group (p = 0.06) at T3 (12.8%) but not T5 (15.2%; p = 0.12). These results indicate that the initial impact of high-volume resistance training overreaching reduces muscle strength and power, and it appears that these reductions are attenuated with amino acid supplementation. In addition, an initial high-volume, moderate-intensity phase of overreaching followed by a higher intensity, moderate-volume phase appears to be very effective for enhancing muscle strength in resistance-trained men.     

Single-step enantioselective amino acid flux analysis by capillary electrophoresis using on-line sample preconcentration with chemical derivatization

Capillary electrophoresis (CE) represents a versatile platform for integrating sample pretreatment with chemical analysis because of its ability to tune analyte electromigration and band dispersion properties in discontinuous electrolyte systems. In this article, a single-step method that combines on-line sample preconcentration with in-capillary chemical derivatization is developed for rapid, sensitive, and enantioselective analysis of micromolar levels of amino acids that lack intrinsic chromophores by CE with UV detection. Time-resolved electrophoretic studies revealed two distinct stages of amino acid band narrowing within the original long sample injection plug occurring both prior to and after in-capillary labeling via zone passing by ortho-phthalaldehyde/N-acetyl l-cysteine (OPA/NAC). This technique enabled direct analysis of d-amino acids in a 95% enantiomeric excess mixture with sub-micromolar detection limits and minimal sample handling, where the capillary functions as a preconcentrator, microreactor, and chiral selector. On-line sample preconcentration with chemical derivatization CE (SPCD-CE) was applied to study the enantioselective amino acid flux in Escherichia coli bacteria cultures, which demonstrated a unique l-Ala efflux into the extracellular medium. New strategies for high-throughput analyses of low-abundance metabolites are important for understanding fundamental physiological processes in bacteria required for screening the efficacy of new classes of antibiotics as well as altered metabolism in genetically modified mutant strains.     

MDCK microcarrier cultures: Seeding density effects and amino acid utilization

Summary The growth of Madin Darby canine kidney cells on microcarriers was studied at different cell seeding densities. Maximum growth was attained when a cell-to-bead ratio of 7∶1 was used. Under these conditions an initial concentration of above 3×10⁵ cells/ml resulted in a yield of over 2×10⁶ cells/ml in 2 d. The amino acid utilization of cells from Dulbecco's modified Eagle medium was studied under the above conditions. Eight amino acids (arg, cys, gln, ile, leu, met, ser, and val) showed rapid and near complete depletion from the medium. Five amino acids (his, lys, phe, thr, and tyr) showed limited depletion. Two amino acids (ala and gly) were released into the medium by the cells.     

Colorimetic amino acid analysis using fluorescamine.

Fluorescamine reacts efficiently with primary and secondary amino acids to form fluorescent pyrrolinone and nonfluorescent aminoenone type chromophores, respectively. A procedure is described for quantitative colorimetric determination at one fixed wavelength of the full array of natural amino acids, including proline and its derivatives. Simultaneous colorimetric-fluorometric analysis enables distinction between primary and secondary amino acids and permits their quantitative analysis with fluorescamine over a broad concentration range. These methods can also be applied for peptide analyses.     

Biosynthesis of 6beta-hydroxymethyltestosterone using bovine hepatocyte cultures

Usually performed to investigate biotransformations of xenobiotics, in vitro liver models could become useful tools for the synthesis of not commercially available compounds. In this study, bovine hepatocyte cultures were used to biosynthesise, on the laboratory scale, one major metabolite of methyltestosterone: 6beta-hydroxymethyltestosterone. After incubation of bovine hepatocytes with methyltestosterone for 24 h, culture medium was removed and stored at -20 degrees C until analysis. The sample was extracted and purified on a reversed-phase HPLC system. The metabolite of interest was then analysed in LC-MS and GC-MS for structural identification. The purity and the isomery of the 6 and 17 positions were confirmed by NMR analyses. This first success in producing purified 6beta-hydroxymethyltestosterone from bovine hepatocyte cultures allowed us to consider that in vitro liver models could be reliable tools for standard biosynthesis.     

Prediction of effects of amino acid supplementation on growth of E. coli B/r

A mathematical model for the growth of a single cell of E. coli on medium containing amino acid is presented. A mixture of purified amino acids (glutamate, aspartate, serine, tyrosine, and leucine) combined in the ratios found in a natural digest (casein) were employed as the nitrogen source. Each of these amino acids is the representative of a different family of amino acids. The transport mechanisms and assimilation routes for each amino acid were inserted into the prototype model. The enzyme activities and saturation constants used in the model were based on literature data. The maximum velocities for uptake systems were calculated from experimental data. The formation and homeostasis of amino acid pools were regulated through cross-control of the activities of biosynthetic enzymes and of membrane transport of exogenous nutrients. The size of each amino acid pool was determined with mass balance equations that included terms for a transport system, a biosynthesis system, a transaminase enzyme system for interchange between the amino acid families, and a consumption system. The predictions of the extended model with regard to nutrient concentrations and growth rates compared well with the experimental data.     

Analysis of gamma-carboxyglutamic acid via amino acid analysis.

Modifications of the analysis of protein-bound residues of γ-carboxyglutamic acid (Gla) via alkaline hydrolysis are presented. The method described allows easier sample manipulation than that heretofore required and insures quantitative recovery of hydrolyzed amino acids. A possible explanation of the shoulder which sometimes appears near Gla on some amino acid analyzers is presented.     

Metabolomic analysis of amino acid and fat metabolism in rats with l-tryptophan supplementation

Tryptophan (TRP) is an important precursor for several neurotransmitters and metabolic regulators, which play a vital role in regulating nutrient metabolism. The purpose of this study was to investigate the effects of tryptophan supplementation on the biochemical profiles, intestinal structure, liver structure and serum metabolome in rats. Rats received daily intragastric administration of either tryptophan at doses of 200 mg/kg body weight per day or saline (control group) for 7 days. TRP supplementation had a tendency to decrease the body weight of rats (P > 0.05). The levels of urea and CHO in serum were decreased in the TRP-supplemented group rats compared with control group rats (P < 0.05). TRP supplementation increased the villus height and the ratio of villus height to crypt depth in the jejunum compared to control group rats (P < 0.05). Metabolic effects of tryptophan supplementation include: (1) increases in the serum concentrations of lysine, glycine, alanine, glutamate, glutamine, citrulline, methionine, tyrosine, 1-methylhistidine, and albumin, and decreases in the concentrations of serum branched-chain amino acid (isoleucine, valine and leucine); (2) decreases in the serum concentrations of formate and nitrogenous products (trimethylamine, TMAO, methylamine and dimethylamine), and in the contraction of trimethylamine in feces; (3) decreases in serum levels of lipids, low density lipoprotein, very low density lipoprotein, together with the elevated ratio of acetoacetate to β-hydroxybutyrate. The results indicate that tryptophan supplementation reduced the catabolism of dietary amino acids and promoted protein synthesis in rats, promoted the oxidation of fatty acid and reduced fat deposition in the body of rats.     

Protein and amino acid supplementation in older humans

The aging process is a continuum throughout life and often associated with deterioration of body function as well as accumulation of chronic disabilities and of disease. The impact of nutritional status on morbidity and mortality is unquestioned. Malnutrition increases the risk for frailty and nutritional deficits can influence immune status, response to medical treatments and recovery from acute illnesses, including surgery. Health-promoting interventions implemented individually, such as exercise programs, preventive home visits, comprehensive geriatric evaluation and management, and attention to adequate nutrition with or without nutritional supplements, have been shown in separate studies to be both feasible and effective in reducing age-related deterioration. Protein and its constituent amino acids (AA) are key components of any healthy diet. Sarcopenia, the slow but progressive loss of lean muscle mass associated with advancing age, has been the focus of many studies but there is no clear-cut answer to the question of how to restrain the process. The more general question of how the requirements for protein and specific AA change with age continues to be investigated. A shift towards studying the efficacy and safety of specific AA or combination of AA that may sustain and/or enhance physiologic processes, ranging from specific tissue metabolism to overall function (e.g. exercise performance, immune function, cognition, and chronic disease development) has occurred. This review focuses on recent studies examining the use of specific AA or mixtures as supplements in the elderly and whether/how AA may assist in the maintenance of health and independence.     

Soft constraints-based multiobjective framework for flux balance analysis

The current state of the art for linear optimization in Flux Balance Analysis has been limited to single objective functions. Since mammalian systems perform various functions, a multiobjective approach is needed when seeking optimal flux distributions in these systems. In most of the available multiobjective optimization methods, there is a lack of understanding of when to use a particular objective, and how to combine and/or prioritize mutually competing objectives to achieve a truly optimal solution. To address these limitations we developed a soft constraints based linear physical programming-based flux balance analysis (LPPFBA) framework to obtain a multiobjective optimal solutions. The developed framework was first applied to compute a set of multiobjective optimal solutions for various pairs of objectives relevant to hepatocyte function (urea secretion, albumin, NADPH, and glutathione syntheses) in bioartificial liver systems. Next, simultaneous analysis of the optimal solutions for three objectives was carried out. Further, this framework was utilized to obtain true optimal conditions to improve the hepatic functions in a simulated bioartificial liver system. The combined quantitative and visualization framework of LPPFBA is applicable to any large-scale metabolic network system, including those derived by genomic analyses.     

Effect of glucose analog supplementation on metabolic flux distribution in anaerobic chemostat cultures of Escherichia coli

Previous work in our laboratories investigated the use of methyl alpha-glucoside (alpha-MG), a glucose analog that shares a phosphotransferase system with glucose, to modulate glucose uptake and therefore reduce acetate accumulation. The results of that study showed a significant improvement in batch culture performance and a reduction in acetate excretion without any significant effect on the growth rate in complex medium. The current study investigates the effect of supplementing the culture medium with the glucose analog alpha-MG on the metabolic fluxes of Escherichia coli under anaerobic chemostat conditions at two different dilution rates. Anaerobic chemostat studies utilizing complex media supplemented with glucose or glucose and alpha-MG at dilution rates of 0.1 and 0.4 h(-1), were performed, and the metabolic fluxes were analyzed. It was found that the addition of the glucose analog alpha-MG has an effect on the specific production rate of various extracellular metabolites. This effect is slightly greater at the higher dilution rate of 0.4 h(-1). However, the glucose analog does not cause any major shift in the central metabolic patterns. It was further observed that alpha-MG supplementation does not result in the reduction in specific acetate synthesis rate in anaerobic chemostat cultures. These results emphasize the importance of testing different strategies for metabolic manipulation under the actual operating conditions.     

Identification of active constraints in dynamic flux balance analysis

This study deals with the calibration of dynamic metabolic flux models that are formulated as the maximization of an objective subject to constraints. Two approaches were applied for identifying the constraints from data. In the first approach a minimal active number of limiting constraints is found based on data that are assumed to be bounded within sets whereas, in the second approach, the limiting constraints are found based on parametric sensitivity analysis. The ability of these approaches to finding the active limiting constraints was verified through their application to two case studies: an in‐silico (simulated) data‐based study describing the growth of E. coli and an experimental data‐based study for Bordetella pertussis (B. pertussis). © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:26–36, 2017     

Family of hemorphins: co-relations between amino acid sequences and effects in cell cultures

Hemorphins, i.e. endogenous fragments of beta-globin chain segment (32-41) LVVYPWTQRY(F) suppress the growth of transformed murine fibroblasts L929 cell culture, the effect is due to cytotoxicity and inhibition of cell proliferation. The contribution of cytotoxicity depends on the presence of Leu(32): VV-hemorphins, except VV-hemorphin-4, exhibit cytotoxicity significantly higher than respective LVV-hemorphins. Decrease of cell number induced by hemorphins depend on the extent of N- and C-terminal degradation of hemorphins: VV-hemorphins in most cases are more active than LVV-, V-hemorphins, and hemorphins. In the group of VV-hemorphins the activity of VV-hemorphin-5 (valorphin) is significantly higher than of VV-hemorphin-7, VV-hemorphin-6, and VV-hemorphin-4, meaning that the presence of C-terminal Gln is important for suppressing of cell number. The amino acid sequence VVYPWTQ corresponding to valorphin was identified as important for manifestation of the both cytotoxic and antiproliferative effects.