Effect of pH on metabolic pathway shift in fermentation and electro-fermentation of xylose by Clostridium autoethanogenum.

Clostridium autoethanogenum can to convert waste gases (CO, CO, H) and xylose from hydrolyzed biomass into acetate, lactate, formate, ethanol and 2,3-butanediol, being a candidate for the transformation of waste streams of lignocellulosic biorefineries. Electro-fermentation (EF) modify the pattern of traditional fermentations resulting in improved product yields as has been shown when using Clostridium strains. The aim of this work was to evaluate the influence of pH on microbial growth and product distribution during fermentation and EF of xylose by C.

Phenotype-specific estimation of metabolic fluxes using gene expression data.

A cell's genome influences its metabolism via the expression of enzyme-related genes, but transcriptome and fluxome are not perfectly correlated as post-transcriptional mechanisms also regulate reaction's kinetics. Here, we addressed the question: given a transcriptome, how unobserved mechanisms of reaction kinetics should be systematically accounted for when inferring the fluxome? To infer the most likely and least biased fluxome, we present Pheflux, a constraint-based model maximizing Shannon's entropy of fluxes per mRNA. Benchmarked against C fluxes of yeast and bacteria, Pheflux accurately estimates the carbon core metabolism.

Kinetic model of Clostridium beijerinckii's Acetone-Butanol-Ethanol fermentation considering metabolically diverse cell types.

Clostridium beijerinckii population branches into metabolically diverse cell types in batch cultures. Here, we present a new kinetic model of C. beijerinckii's Acetone-Butanol-Ethanol fermentation that considers three cell types: producers of acids (acidogenic), consumer of acids and producers of solvents (solventogenic), and spores cells.

Metabolic flux configuration determination using information entropy.

Constraint-based models use steady-state mass balances to define a solution space of flux configurations, which can be narrowed down by measuring as many fluxes as possible. Due to loops and redundant pathways, this process typically yields multiple alternative solutions. To address this ambiguity, flux sampling can estimate the probability distribution of each flux, or a flux configuration can be singled out by further minimizing the sum of fluxes according to the assumption that cellular metabolism favors states where enzyme-related costs are economized.

Beyond Intracellular Accumulation of Polyhydroxyalkanoates: Chiral Hydroxyalkanoic Acids and Polymer Secretion.

Polyhydroxyalkanoates (PHAs) are ubiquitous prokaryotic storage compounds of carbon and energy, acting as sinks for reducing power during periods of surplus of carbon source relative to other nutrients. With close to 150 different hydroxyalkanoate monomers identified, the structure and properties of these polyesters can be adjusted to serve applications ranging from food packaging to biomedical uses. Despite its versatility and the intensive research in the area over the last three decades, the market share of PHAs is still low.

Ethanol production improvement driven by genome-scale metabolic modeling and sensitivity analysis in Scheffersomyces stipitis.

The yeast Scheffersomyces stipitis naturally produces ethanol from xylose, however reaching high ethanol yields is strongly dependent on aeration conditions. It has been reported that changes in the availability of NAD(H/+) cofactors can improve fermentation in some microorganisms. In this work genome-scale metabolic modeling and phenotypic phase plane analysis were used to characterize metabolic response on a range of uptake rates.

A generalized disjunctive programming framework for the optimal synthesis and analysis of processes for ethanol production from corn stover.

The aim of this study is to analyze the techno-economic performance of process configurations for ethanol production involving solid-liquid separators and reactors in the saccharification and fermentation stage, a family of process configurations where few alternatives have been proposed. Since including these process alternatives creates a large number of possible process configurations, a framework for process synthesis and optimization is proposed. This approach is supported on kinetic models fed with experimental data and a plant-wide techno-economic model.

In silico analysis of Clostridium acetobutylicum ATCC 824 metabolic response to an external electron supply.

The biological production of butanol has become an important research field and thanks to genome sequencing and annotation; genome-scale metabolic reconstructions have been developed for several Clostridium species. This work makes use of the iCAC490 model of Clostridium acetobutylicum ATCC 824 to analyze its metabolic capabilities and response to an external electron supply through a constraint-based approach using the Constraint-Based Reconstruction Analysis Toolbox. Several analyses were conducted, which included sensitivity, production envelope, and phenotypic phase planes.

Repeated-batch operation for the synthesis of lactulose with β-galactosidase immobilized by aggregation and crosslinking.

Synthesis of lactulose under repeated-batch operation was done with cross-linked aggregates of Aspergillus oryzae β-galactosidase (CLAGs). The effect of the crosslinking agent to enzyme mass ratio and cross-linking time were first evaluated. Best results were obtained at 5.

Transgalactosylation and hydrolytic activities of commercial preparations of β-galactosidase for the synthesis of prebiotic carbohydrates.

β-Galactosidases exhibit both hydrolytic and transgalactosylation activities; the former has been used traditionally for the production of delactosed milk and dairies, while the latter is being increasingly used for the synthesis of lactose-derived oligosaccharides: balance between both activities was highly dependent on the enzyme origin: β-galactosidases from Aspegillus oryzae and Bacillus circulans exhibited high transgalactosylation activity, while those from one from Kluyveromyces exhibited high hydrolytic activity but quite low transgalactosylation activity. Also the affinity for the donors (lactose or lactulose) and the acceptors (lactose, lactulose or fructose) of transgalactosylated galactose was dependent on the enzyme origin, as reflected by the Michaelis constants obtained in the synthesis of galacto-oligosaccharides, fructosyl-galacto-oligosaccharides and lactulose. Finally, the balance between transgalactosylation and hydrolytic activities of β-galactosidases could be tuned by changing the concentration of galactose donor.

Corn stover semi-mechanistic enzymatic hydrolysis model with tight parameter confidence intervals for model-based process design and optimization.

Uncertainty associated to the estimated values of the parameters in a model is a key piece of information for decision makers and model users. However, this information is typically not reported or the confidence intervals are too large to be useful. A semi-mechanistic model for the enzymatic saccharification of dilute acid pretreated corn stover is proposed in this work, the model is a modification of an existing one providing a statistically significant improved fit towards a set of experimental data that includes varying initial solid loadings (10-25% w/w) and the use of the pretreatment liquor and washed solids with or without supplementation of key inhibitors.

Genome-scale NAD(H/(+)) availability patterns as a differentiating feature between Saccharomyces cerevisiae and Scheffersomyces stipitis in relation to fermentative metabolism.

Scheffersomyces stipitis is a yeast able to ferment pentoses to ethanol, unlike Saccharomyces cerevisiae, it does not present the so-called overflow phenomenon. Metabolic features characterizing the presence or not of this phenomenon have not been fully elucidated. This work proposes that genome-scale metabolic response to variations in NAD(H/(+)) availability characterizes fermentative behavior in both yeasts.

Attainable region analysis for continuous production of second generation bioethanol.

Background: Despite its semi-commercial status, ethanol production from lignocellulosics presents many complexities not yet fully solved. Since the pretreatment stage has been recognized as a complex and yield-determining step, it has been extensively studied. However, economic success of the production process also requires optimization of the biochemical conversion stage.

Fed-batch synthesis of galacto-oligosaccharides with Aspergillus oryzae β-galactosidase using optimal control strategy.

Fed-batch synthesis of galacto-oligosaccharides (GOS) from lactose with β-galactosidase from Aspergillus oryzae was evaluated experimentally and reaction yield was maximized via optimal control technique. The optimal lactose and enzyme feed flow rate profiles were determined using a model for GOS synthesis previously reported by the authors. Experimentally it was found that fed-batch synthesis allowed an increase on the maximum total GOS concentration from 115 (batch synthesis) to 218 g L(-1) as consequence of the increase in total sugars concentration from 40 to 58% w/w.

Selection of process alternatives for lignocellulosic bioethanol production using a MILP approach.

This work proposes a decision-making framework for the selection of processes and unit operations for lignocellulosic bioethanol production. Process alternatives are described by its capital and operating expenditures, its contribution to process yield and technological availability information. A case study in second generation ethanol production using Eucalyptus globulus as raw material is presented to test the developed process synthesis tool.

Synthesis of galacto-oligosaccharides by β-galactosidase from Aspergillus oryzae using partially dissolved and supersaturated solution of lactose.

The effect of enzyme to substrate ratio, initial lactose concentration and temperature has been studied for the kinetically controlled reaction of lactose transgalactosylation with Aspergillus oryzae β-galactosidase, to produce prebiotic galacto-oligosaccharides (GOS). Enzyme to substrate ratio had no significant effect on maximum yield and specific productivity. Galacto-oligosaccharide syntheses at very high lactose concentrations (40, 50 and 60%, w/w, lactose monohydrate) were evaluated at different temperatures (40, 47.

A pseudo steady-state model for galacto-oligosaccharides synthesis with β-galactosidase from Aspergillus oryzae.

A pseudo steady-state model for the kinetically controlled synthesis of galacto-oligosaccharides (GOS) with Aspergillus oryzae β-galactosidase is presented. The model accounts for the dynamics of lactose consumption and production of galactose, glucose, di, tri, tetra, and penta-oligosaccharides during the synthesis, being able to describe the total GOS content in the reaction medium at the experimental conditions evaluated. Experimental results show that the formation of GOS containing only galactose residues is significant at high conversions of substrate, which was taken into account in the model.

Towards a long-term model construction for the dynamic simulation of HIV infection.

This study involves the mathematical modelling of long-term HIV dynamics. The proposed model is able to predict the entire trajectory of the disease: initial viremia in the early weeks of the infection, latency, and progression to AIDS; a range spanning approximately ten years. The model outcomes were compared to clinical data and significant agreement was achieved.