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[Display omitted] • Microbes periodically experience substrate gradients at large-scale fermentor. • Analysis of cell lifelines provides a basis for the rational scale-down design. • An application was developed for the rational design of scale-down simulator. • Three representative metabolic regimes at large-scale were successfully mimicked. The influence of extracellular variations on the cellular metabolism and thereby the process performance at large-scale can be evaluated using the so-called scale-down simulators. Nevertheless, the major challenge is to design an appropriate scale-down simulator, which can accurately mimic the cell lifelines that record the flow paths and experiences of cells circulating in large-scale bioreactors. To address this, a dedicated SDSA (scale-down simulator application) was purposedly developed on the basis of black box model and process reaction model established for Penicillium chrysogenum strain as well as cell lifelines or trajectories information in an industrial-scale fermentor. Guided by the SDSA, the industrial-relevant metabolic regimes for substrate availability, i.e., excess, limitation and starvation, were successfully reproduced at laboratory-scale three-compartment scale-down (SD) system. In addition, such SDSA can also display individual process dynamics in each compartment, and demonstrate how individual factors influence the entire bioprocess performance, thus serving both educational and research purposes. [ABSTRACT FROM AUTHOR]

Fuel ethanol has drawn extensive attention as renewable energy. However, modeling the fuel ethanol batch fermentation process is still a critical task. The unstructured kinetic model (UKM) is often utilized to model the process, but it encounters two problems due to the large differences in initial glucose concentrations. First, the UKM has poor predictions of the yeast growth, which is a crucial production index. Second, the kinetic parameters of the UKM are time-varying because of the changing environmental conditions. The constant manually set kinetic parameters affect the prediction accuracy. To tackle the problems, we propose a dynamic hybrid model of the fuel ethanol fermentation process. First, a biomass concentration prediction model based on extreme gradient boosting is developed. It predicts the values of biomass concentrations and mycelium growth rate as supplementary mechanism knowledge. Then, we present an artificial neural network-based model to determine the time-varying kinetic parameters. Our model can accurately predict the time series of biomass, ethanol, and glucose concentrations, with RMSEs reaching 0.3323, 1.9295, and 3.0540. Experimental results show that the dynamic hybrid model performs with satisfactory accuracy in modeling the fuel ethanol fermentation process. [ABSTRACT FROM AUTHOR]

• A data enhancement method based on generative adversarial network is proposed. • The method combines the advantages of data augmentation and feature selection. • Case studies on a simulated case and two real industrial processes are provided. • Comparisons to state-of-the-arts show effectiveness of the proposed method. Soft sensor plays an important role in improving product quality; however, practical applications may often face with the problem of small sample size, which is challenging for developing data-driven models in terms of feature selection and good generalization. This paper proposes a data enhancement approach for small sample size data-driven problems based on generative adversarial networks integrated with maximum relevance minimum redundancy (MRMR). First, sample expansion is performed on the initial data by using a generative adversarial network. Second, irrelevant variables are eliminated by the MRMR and optimal features are obtained. Finally, neural networks-based soft sensor modeling is performed using the augmented dataset and the selected features. The proposed method is tested on a simulated penicillin case, an actual penicillin production case and an actual erythromycin production case. Experimental results show that the proposed method outperforms state-of-the-art existing methods, which verify the effectiveness and superiority of the proposed method. [ABSTRACT FROM AUTHOR]

Highlights: [•] The penalized histogram difference criterion, PHDC, to determine the number of clusters of finite mixture models. [•] The PHDC guarantees a minimum at optimal number of clusters. [•] The utility of the PHDC is evaluated with respect to other criteria, such as HDC, AIC, MML, ICOMP, and EDC. [Copyright &y& Elsevier]

Abstract: The aromatic polyketide antibiotic, oxytetracycline (OTC), is produced by Streptomyces rimosus as an important secondary metabolite. High level production of antibiotics in Streptomycetes requires precursors and cofactors which are derived from primary metabolism; therefore it is exigent to engineer the primary metabolism. This has been demonstrated by targeting a key enzyme in the oxidative pentose phosphate pathway (PPP) and nicotinamide adenine dinucleotide phosphate (NADPH) generation, glucose-6-phosphate dehydrogenase (G6PDH), which is encoded by zwf1 and zwf2. Disruption of zwf1 or zwf2 resulted in a higher production of OTC. The disrupted strain had an increased carbon flux through glycolysis and a decreased carbon flux through PPP, as measured by the enzyme activities of G6PDH and phosphoglucose isomerase (PGI), and by the levels of ATP, which establishes G6PDH as a key player in determining carbon flux distribution. The increased production of OTC appeared to be largely due to the generation of more malonyl-CoA, one of the OTC precursors, as observed in the disrupted mutants. We have studied the effect of zwf modification on metabolite levels, gene expression, and secondary metabolite production to gain greater insight into flux distribution and the link between the fluxes in the primary and secondary metabolisms. [Copyright &y& Elsevier]

Abstract: The developments of the systems biotechnology and its application in the industrial process open up new horizons to industrial biotechnology. The unprecedented understanding of the relationships between cellular behaviors and the surrounding environments during the bioprocess has been achieved. In this paper, we review new advances in the strain improvement, bioprocess control and optimization. The holistic viewpoints and ideas applied in industrial bioprocesses and their future prospects are discussed by illustrating some successful cases. [Copyright &y& Elsevier]

The specific activities of key enzymes relating to the pathway of inosine synthesis of three different bacterial strains including high-yield, low-yield and wild strains were determined and compared systematically. A close relationship between inosine production and the specific activities of key enzymes was found. According to the enzyme characteristics of the high-yield strain, suggestions on further strain improvement by genetic engineering were proposed. An enzymology study is suggested as an effective way to facilitate the screening of high-yield strain. [Copyright &y& Elsevier]

When adenine (Ade) was added to basal culture medium at 12 h after inoculation, antivirus activity and specific activity of interferon-α2a (IFN-α2a) were increased. Expression of IFN-α2a was realized when a low residual glucose concentration was maintained during the mid- and late-phase of cultivation. In addition, biological activity and specific activity of IFN-α2a were increased by more than 100% if the ratio of glucose and sucrose in the basal medium was 1:0.1. The addition of glutamate also led to the intensive enhancement of the expression level of IFN-α2a. The initial pH of the basal medium proved to be crucial to the expression level. When the above optimal cultivation condition obtained in the shake flask was applied to the fed-batch culture using a 2.6 l jar fermenter, human IFN-α2a biological activity reached 1.3×107 IU/ml, which was four times that of the control. [Copyright &y& Elsevier]

The present study emphasizes improving the overall yield, productivity and quality of xanthan by Xanthomonas campestris using different carbon sources via optimizing the fermentation media and kinetic modelling work. After optimization, six carbon sources and one nitrogen source were selected for xanthan production in 5 L bioreactor. Kinetic modelling was applied to assess the experimental fermentation data and to check its influence on scale-up production. In this work, xanthan production reached 40.65 g/L with a growth-associated rate constant (α) of 2.831, and highest specific growth rate (μm) of 0.37/h while using maltose as the sole carbon source. Furthermore, rheological properties were determined, and Herschel-Bulkley model was employed to assess the experimental data. Interestingly, xanthan obtained from sucrose and glucose showed the highest yield stress (τ 0) of 12.50 ± 0.31 and 7.17 ± 0.21. Moreover, the highest xanthan molecular weight of 3.53 × 107 and 3.25 × 107 g/mol were also found with sucrose and glucose. At last, the proposed mechanism of sugar metabolism and xanthan biosynthesis pathway were described. Conclusively, maltose appeared as the best carbon source for maximum xanthan production: while sucrose and glucose gave qualitatively best results. In short, this systematically modelled approach maximizes the potential output and provides a solid base for continuous cultivation of xanthan at large-scale production. [Display omitted] • Kinetic modelling was proposed for xanthan production with six different carbon sources. • Highest xanthan production of 40.65 g/L (with μ m = 0.37/h) was achieved under maltose. • Herschel-Bulkley model was used to assess the experimental rheological data. • Acetate and pyruvate content influenced the viscosity and molecular weight of xanthan. • Highest xanthan molecular weight of 3.53 × 107 g/mol was found under sucrose. [ABSTRACT FROM AUTHOR]

The biosynthesis of gentamicin (GM) in shake flask cultivation and a resting cell system were studied. Suitable amounts of NaNO3, MgSO4, NaCl, penicillin, fosfomycin, cephradine, α-ketoglutarate, biotin and Tween 20 favoured the biosynthesis of GM. The ingredients of the optimum synthetic medium for the resting cell system are given. The amount of GM adsorbed on 1 g of wet mycelia and wet cell wall was 4775 and 20 000 U, respectively. Usually only 20–30% of the GM is excreted into the broth during fermentation, whereas about 75% of the bound GM can be released by ultrasonic treatment. The production of GM increased by 70% when 0.8 ml of mycelia (GM depleted) were added into 25 ml of fermentation broth at 90 h after inoculation. [Copyright &y& Elsevier]

In this study, we prepared a series of edible blend films of xanthan and curdlan by mixing different ratios of these two biopolymers. Characterization techniques like FTIR, XRD, TGA and SEM analysis were applied to investigate the newly formed films. Moreover, mechanical properties, moisture absorbance properties and water solubility of these films were also determined. The obtained results demonstrated that the strong intermolecular hydrogen bonding was observed between xanthan and curdlan at pH 5. At this pH, the xanthan-curdlan hydrogel retained the original structure of xanthan and sustained self-aggregation of xanthan chains via hydrogen bonding, which led to strong intermolecular bonding between xanthan and curdlan. Furthermore, the 5:5 and 4:6 ratios of xanthan and curdlan showed greater interaction in the blend films that resulted in their excellent miscibility. Moreover, highest tensile strength of 28.13 and 26.45 MPa were also found in the same rational of XG/CG blend films. In addition, it was observed that the curdlan incorporation improved the water solubility properties of XG/CG blend films. Conclusively, this xanthan/curdlan nexus with excellent mechanical and moisture barrier properties confirm its potential application and prospective use as food packaging material. Unlabelled Image • Xanthan-Curdlan nexus for preparing edible food packaging films • Exploration of optimum pH for the synthesis of XG/CG blend films • Curdlan incorporation improved water solubility properties of XG/CG blend films. • Enhancement in the Tensile strength of XG/CG blend films [ABSTRACT FROM AUTHOR]

Bioprocess scale-up is a critical step in process development. However, loss of production performance upon scaling-up, including reduced titer, yield, or productivity, has often been observed, hindering the commercialization of biotech innovations. Recent developments in scale-down studies assisted by computational fluid dynamics (CFD) and powerful stimulus–response metabolic models afford better process prediction and evaluation, enabling faster scale-up with minimal losses. In the future, an ideal bioprocess design would be guided by an in silico model that integrates cellular physiology (spatiotemporal multiscale cellular models) and fluid dynamics (CFD models). Nonetheless, there are challenges associated with both establishing predictive metabolic models and CFD coupling. By highlighting these and providing possible solutions here, we aim to advance the development of a computational framework to accelerate bioprocess scale-up. Metabolomics has been used alone or combined with other 'omics' tools to contribute to industrial systems biology and synthetic biology. Mechanisms governing population heterogeneity in industrial bioprocessing need rigorous investigation, and thereafter should be incorporated into more powerful cellular models. A predictive scale-down model should be rationally guided by model fluid studies in large-scale bioprocesses. Coupling cellular kinetics with fluid dynamics accelerates science-based design of both microbial cell factories and industrial-scale bioreactors. [ABSTRACT FROM AUTHOR]

• Flow field characteristics were evaluated by laser particle image velocimetry system in nemadectin fermentation. • Physiological parameters showed that shear stress seriously affect the mycelium growth and mycelial differentiation. • The higher batch yield of nemadectin reached 1543.27 μg/mL under the radial-axial flow group. • The radial-axial flow impeller combinations were conducive to nemadectin fermentation of Streptomyces cyaneogriseus. Mass transfer and shear force have significant effects on nemadectin production by Streptomyces cyaneogriseus ssp. noncyanogenus. They are always the conflict-ridden problems in nemadectin fermentation process. In this study, the flow field characteristics under different impeller combinations were quantitatively evaluated in 5 L stirred-tank bioreactor through the laser particle image velocimetry (PIV) system. Results demonstrated that the radial-axial impeller combinations with the time average velocity at 0.38-0.54 U tip , the turbulent kinetic energy dissipation rate at 6.4–10.6 ε/N3D2, and the shear stress rate was 40-150 s−1, were more conductive to cell growth, nemadectin biosynthesis, cell's activity, respiratory metabolism than other combinations. The highest nemadectin yield was evaluated up to 1543.3 ± 18.5 μg/mL, which was 31.68 % higher than that of the radial flow impeller combinations. This study provided the important guideline for the selection impeller combinations' on large-scale nemadectin production. [ABSTRACT FROM AUTHOR]

Highlights • P. chrysogenum mutant strains with altered trehalose metabolism were constructed. • Metabolic profiles were compared between the mutant and original strains. • Genome-scale model was used to locate central metabolic flux distributions. • The important role of trehalose metabolism in penicillin production was discussed. Abstract In Penicillium chrysogenum , it has been observed that turnover of storage carbohydrates (trehalose, mannitol, arabitol, erythritol and glycogen) resulting in an extra ATP expenditure might partly account for the reduced penicillin productivity under dynamic cultivation conditions. In this work, Penicillium chrysogenum mutants with altered trehalose metabolism were constructed using the Agrobacterium -mediated transformation method. It was observed that impaired trehalose biosynthesis did not result in growth arrest and change of glucose sensitivity to high glucose levels, but negatively influenced the sporulation. Compared with the original strain, in glucose-limited chemostat cultures, the biomass yield on glucose and energy efficiency were slightly enhanced; however, the penicillin productivity was significantly lowered in the trehalose mutant strains. Comparison with a high-yielding P. chrysogenum strain revealed that the original and mutant strains had a lower glucose uptake capacity but higher intracellular levels of free amino acids. Flux estimates through the central carbon metabolism showed distinctive difference in the upper part of the glycolysis and in the pentose phosphate pathway but comparable flux through the TCA cycle. Combining, the striking phenotypic effects observed in the trehalose mutants of P. chrysogenum indicated that trehalose metabolism plays an important role in metabolic regulation and is central to maintaining higher penicillin productivity under glucose-limited chemostat cultures. [ABSTRACT FROM AUTHOR]

Highlights • A novel algorithm, IDU, that is capable to model large scale isotopomer labeling system is proposed. • Comparing to EMU and cumomer, the IDU results in another set of balance equations with different coefficients. • One variant of IDU algorithms, IDU-B, has fewer number of balance equations than that of EMU balance equations. • The efficiency of the IDU approach is demonstrated with two simulated examples. Abstract In the past three decades, various computational frameworks for the modelling of the intracellular isotopic distribution have been proposed by different research groups. Among them the cascaded linear systems are the most popular approaches since they can transfer the nonlinear isotopomer labeling system into cascaded linear sub-systems. In this work, a novel two-step decomposition algorithm to model isotopomer labeling system is proposed. It can be utilized to decompose large metabolic networks. For convenience purpose, a new concept of isotopomer decomposition units (IDUs) is defined to distinguish the approach from others. Comparing to other cascaded linear systems, the IDU method follows a different decomposition procedure and results in another set of cascaded linear systems with different coefficients. Two variants of IDU algorithms are proposed, while one variant of them (IDU-B) has fewer number of balance equations than that of EMU balance equations. The efficiency of the IDU approach is demonstrated through two simulated examples. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Drying kinetics of orange peel for effective waste biomass utilization. • Saccharification and detoxification of orange peel substrate for curdlan biosynthesis. • Highest curdlan production (P m = 23.24 g/L) with maximum specific growth rate (μ m = 0.23/h). • Qualitative characterization of curdlan with average M w of 5.2 × 105 Da. Abstract This study presents an engineered approach for sustainable biosynthesis of curdlan by Alcaligenes faecalis using orange peels. To confirm the substrate suitability a four step study was organized. Firstly, drying of substrate was carried within temperature range of 60–120 °C, along with the application of moisture diffusion control model. Secondly, fermentation medium was obtained via saccharification and detoxification, releasing highest sugar at 72.34 g/L with phenolics removal of 95–98%. Thirdly, curdlan fermentation was conducted in detoxified orange peel hydrolysate followed by optimization of batch culture fermentation via kinetic modeling using Logistic and Luedeking-Piret equations. In 5 L bioreactor, highest specific growth rate (μ m = 0.233/h), highest curdlan production (P m = 23.24 g/L) and growth associated rate constant (α = 3.403) were achieved. Moreover, the total sugar consumption and conversion rates were 83.27% and 53.20%. Lastly, characterization techniques such as FTIR, NMR, XRD, TGA, HPGPC and EDS were applied to biosynthesized curdlan for qualitative validation. [ABSTRACT FROM AUTHOR]

Variable selection plays an important role in soft sensor development. Either including redundant variables or missing important variables can degrade the modeling performance, affecting practical industrial applications. This paper proposes a novel neural networks-based hybrid beneficial variable selection (HBVS) and modeling method for effective soft sensing. First, irrelevant variables are removed through evaluating mutual information (MI) between all candidate variables and the quality variable. Second, proxy variables are introduced and a hidden gain-based evaluation method is employed to temporarily sort variables according to their significance, which facilitates to make use of process knowledge. Then, false discovery rate is employed to identify the model consistency, through which beneficial variables are determined. The proposed soft sensor development method is tested on a penicillin simulation process, and two actual industrial processes, including an oil refining process and an actual penicillin production process. Comparisons to state-of-the-art existing methods verify the effectiveness and superiority of the proposed method. • A neural networks-based variable selection and modeling method is proposed. • It is an end-to-end feature selection method for nonlinear soft sensor. • Three application examples are provided. • Comparisons to state-of-the-arts show effectiveness of the proposed method. [ABSTRACT FROM AUTHOR]

Curdlan has wide-ranging benefits in food and pharmaceutical industries for its unique rheological and thermal gelling properties. To analyze the cell growth and curdlan biosynthesis kinetics of Alcaligenes faecalis , the kinetic properties of the curdlan fermentation under different carbon sources conditions (maltose, sucrose, glucose and fructose) were investigated using Logistic and Luedeking-Piret equations. The results demonstrated that curdlan fermentation is partial growth-associated process. With maltose as the sole carbon source, the highest curdlan production ( P m  = 39.3 g/L), the maximum specific growth rate ( μ m  = 0.44/h) and the growth-associated rate constant (α = 2.05 g curdlan/g cell) were achieved. In contrast, the fructose was the less desired carbon source in both the cell growth and curdlan production. Further, the results demonstrated that slow-releasing glucose from maltose boosted cell growth and curdlan production. [ABSTRACT FROM AUTHOR]

In this study, the impacts of oxygen metabolism characterized by oxygen uptake rate (OUR) on lactic acid production in Lactobacillus paracasei were investigated through metabolite profiling and metabolic flux analysis. At growth phase, with the cost of declining lactic acid yield, the cells shifted pyruvate metabolism from lactic acid production to ATP high-yielding acetate synthesis to guarantee sufficient energy supply for cell growth under high OUR condition. When the cells reached to stationary phase, significant glucose metabolism inhibition happened with high OUR level due to much more reactive oxygen species (ROS) accumulation in the cells, which subsequently would attack glycolytic key enzyme, glycerate-3-phosphate dehydrogenase (GAPDH), leading to the substantial limitation of glucose consumption. Moreover, other than glucose metabolism restriction, the decline on metabolic level regulation of lactic acid yield further decreased lactic acid productivity. On the other hand, it was interestingly found that intracellular redox balance was greatly dependent on acetyl-CoA node (acetate/ethanol) in growth phase, and acetoin node (acetoin/2,3-butanediol) in stationary phase respectively. The application of integrated metabolite profiling and metabolic flux analysis highlighted the regulation of energy and redox metabolism in lactic acid production by L. paracasei . [ABSTRACT FROM AUTHOR]

Herein, an enhanced green production of xanthan gum has been achieved by utilizing orange peels. Response surface methodology and kinetic modeling were adapted for the process optimization and its influence on scale up production respectively. Optimal conditions for the maximum xanthan production were 1.62% acid hydrolysis, 85% carbon source of orange peel hydrolysate and 30.4 °C temperature. Furthermore, the optimized treatment was conducted in the batch culture fermentor to observe the associated variations during scale up process. In bio-fermentor, to the first time ever, xanthan production along with reducing sugar conversion and utilization rates reached 30.19 g/L, 69.29% and 99.99%, respectively. Employed characterization techniques of FTIR, XRD and HPLC confirmed the fermented product as xanthan gum and obtained an average molecular weight of 1.01 × 10 6 g/mol. This work on account of optimized process parameters presented maximum xanthan production from a waste material. [ABSTRACT FROM AUTHOR]

In this study, the influences of major nutrients on cell growth and lipid production were investigated in heterotrophic culture of Chlorella protothecoides . The results demonstrated that phosphorus depletion had no effect on lipid accumulation but restricted cell growth; however, nitrogen depletion could enhance lipid accumulation thus benefiting lipid production. Furthermore, the effects of glucose inhibition were comparatively investigated with osmotic stress, showing that the effects of glucose inhibition were similar to the effect of osmotic stress at equivalent osmotic pressures only if the glucose concentration was less than 100 g/L, otherwise the effects of glucose inhibition became much stronger than osmotic stress. Interestingly, it was found that a specific hyperosmotic stress could significantly enhance lipid accumulation, thus providing a new stress strategy for efficient lipid production. Finally, a novel two-stage fed-batch culture consisting of a growth phase and a lipid accumulation phase with nitrogen depletion and hyperosmotic stress was proposed, yielding a final lipid productivity of 177.3 mg/L/h with a very high lipid yield of 207.0 mg/g glucose and lipid content of 39.2% after 180 h culture, which were 1.60, 1.79 and 1.92-fold of those obtained in one-stage fed-batch culture without stress phase, respectively. [ABSTRACT FROM AUTHOR]

Bioconversion of C1 gases to produce chemicals has good application prospects. Here, the combination of trace metals optimization using a statistical method with variable-temperature cultivation was used to enhance alcohol synthesis during CO-rich off-gas fermentation by Clostridium carboxidivorans P7. Based on ATCC medium 1754, the optimum concentration of the trace metals was found to be 5-fold Ni 2+ , Co 2+ , SeO 4 2+ , and WO 4 2+ ; 3.48-fold Cu 2+ ; 0.55-fold MoO 4 2+ ; 0.5-fold Zn 2+ and (NH 4 ) 2 SO 4 ·FeSO 4 ·6H 2 O; and additional 44.32 μM FeCl 3 ·6H 2 O. The production of alcohol and organic acid changed to 4.40 g/L and 0.50 g/L from 2.16 g/L and 2.37 g/L, respectively, yielding an increase of alcohol-to-product ratio from 47.7% to 89.8%. By fermenting with the optimized medium and timed control of the incubation temperature (37 °C [0–24 h]–25 °C [24–144 h]), the alcohol titre further increased to 6.97 g/L with 1.67 g/L butanol and 1.33 g/L hexanol, exceeding those previously reported for strain P7. [ABSTRACT FROM AUTHOR]

In this study, the influences of oxygen supply and nitrogen starvation on cell growth and lipid production by heterotrophic culture of Chlorella protothecoides were investigated in a 5-L stirred-tank bioreactor. The results demonstrated that both a low oxygen supply and nitrogen starvation are favorable for lipid accumulation, but limit cell growth and may therefore reduce the overall lipid production. Hence, a novel two-stage strategy for oxygen supply and nitrogen starvation was proposed in a batch culture, increasing the lipid content and yield on glucose by a factor 2.14 and 2.03 compared to the one-stage batch culture with high oxygen supply and sufficient nitrogen availability, respectively. Applying the two-stage process in a fed-batch culture further increased the lipid productivity to 175.2 mg/(L·h), giving a lipid yield of 195.6 mg/g. Furthermore, a dual-mode culture, coupling a heterotrophic process with autotrophic process, was implemented to allow for CO 2 recycling. This improved the lipid productivity and carbon utilization efficiency, further contributing towards cost-effective and environment-friendly algal lipid production. [ABSTRACT FROM AUTHOR]