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Song Y.,CAS Tianjin Institute of Industrial Biotechnology | Song Y.,Chinese Academy of Sciences | Nikoloff J.M.,CAS Tianjin Institute of Industrial Biotechnology | Fu G.,CAS Tianjin Institute of Industrial Biotechnology | And 13 more authors.
PLoS ONE | Year: 2016

The use of Bacillus subtilis in synthetic biology and metabolic engineering is highly desirable to take advantage of the unique metabolic pathways present in this organism. To do this, an evaluation of B. subtilis' intrinsic biological parts is required to determine the best strategies to accurately regulate metabolic circuits and expression of target proteins. The strengths of promoter candidates were evaluated by measuring relative fluorescence units of a green fluorescent protein reporter, integrated into B. subtilis' chromosome. A total of 84 predicted promoter sequences located upstream of different classes of proteins including heat shock proteins, cell-envelope proteins, and proteins resistant against toxic metals (based on similarity) and other kinds of genes were tested. The expression levels measured ranged from 0.0023 to 4.53-fold of the activity of the well-characterized strong promoter P43. No significant shifts were observed when strains, carrying different promoter candidates, were cultured at high temperature or in media with ethanol, but some strains showed increased activity when cultured under high osmotic pressure. Randomly selected promoter candidates were tested and found to activate transcription of thermostable β-galactosidase (bgaB) at a similar level, implying the ability of these sequences to function as promoter elements in multiple genetic contexts. In addition, selected promoters elevated the final production of both cytoplasmic bgaB and secreted protein α-amylase to about fourfold and twofold, respectively. The generated data allows a deeper understanding of B. subtilis' metabolism and will facilitate future work to develop this organism for synthetic biology. © 2016 Song et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Lin H.-J.,Guangxi University | Lin H.-J.,National Engineering Research Center for Non food Biorefinery | Xian L.,Guangxi University | Xian L.,National Engineering Research Center for Non food Biorefinery | And 15 more authors.
Journal of Industrial Microbiology and Biotechnology | Year: 2011

A newly isolated strain Penicillium sp. GXU20 produced a raw starch-degrading enzyme which showed optimum activity towards raw cassava starch at pH 4.5 and 50°C. Maximum raw cassava starch-degrading enzyme (RCSDE) activity of 20 U/ml was achieved when GXU20 was cultivated under optimized conditions using wheat bran (3.0% w/v) and soybean meal (2.5% w/v) as carbon and nitrogen sources at pH 5.0 and 28°C. This represented about a sixfold increment as compared with the activity obtained under basal conditions. Starch hydrolysis degree of 95% of raw cassava flour (150 g/l) was achieved after 72 h of digestion by crude RCSDE (30 U/g flour). Ethanol yield reached 53.3 g/l with fermentation efficiency of 92% after 48 h of simultaneous saccharification and fermentation of raw cassava flour at 150 g/l using the RCSDE (30 U/g flour), carried out at pH 4.0 and 40°C. This strain and its RCSDE have potential applications in processing of raw cassava starch to ethanol. © Society for Industrial Microbiology 2010.


Yan S.-M.,National Engineering Research Center for Non food Biorefinery | Wu G.,National Engineering Research Center for Non food Biorefinery
Protein and Peptide Letters | Year: 2012

Cellulase is an important enzyme widely used in various industries, and now in fermentation of biomass into biofuels. Enzymatic function of cellulase is closely related to pH, temperature, substrate concentration, etc. For newly found cellulase, it would be more cost-effective to predict its optimal pH and temperature before conducting the costly experiments. In this study, we used a 20-2 feedforward backpropagation neural network to build the relationship between information obtained from primary structure of cellulase with optimal pH and temperature to predict the optimal pH and temperature in cellulases. The results show that the amino-acid distribution probability representing the primary structure of cellulase can predict both optimal pH and temperature, whereas various properties of amino acids related to the primary structure cannot do so. © 2012 Bentham Science Publishers.


Yan S.,National Engineering Research Center for Non food Biorefinery | Wu G.,National Engineering Research Center for Non food Biorefinery
Biotechnology for Biofuels | Year: 2013

Cellulase plays an important role in modern industry and holds great potential in biofuel production. Many different types of organisms produce cellulase, which go through secretory pathways to reach the extracellular space, where enzymatic reactions take place. Secretory pathways in various cells have been the focus of many research fields; however, there are few studies on secretory pathways of cellulases in the literature. It is therefore necessary and important to review the current knowledge on the secretory pathways of cellulases. In this mini-review, we address the subcellular locations of cellulases in different organisms, discuss the secretory pathways of cellulases in different organisms, and examine the secretory mechanisms of cellulases. These sections start with a description of general secreted proteins, advance to the situation of cellulases, and end with the knowledge of cellulases, as documented in UniProt Knowledgebase (UniProtKB). Finally, gaps in existing knowledge are highlighted, which may shed light on future studies for biofuel engineering. © 2013 Yan and Wu; licensee BioMed Central Ltd.


Xie Q.-R.,Guangxi University | Xie Q.-R.,Guangxi University of Technology | Xie Q.-R.,National Engineering Research Center for Non Food Biorefinery | Tong Z.-F.,Guangxi University | And 6 more authors.
Gao Xiao Hua Xue Gong Cheng Xue Bao/Journal of Chemical Engineering of Chinese Universities | Year: 2012

In order to increase the yield of bio-oil from bamboo biomass by fast pyrolysis process in a fluidized bed, the response surface methodology (RSM) was applied to optimize the process conditions, and the pyrolysis temperatures (450~550°C), vapor retention times (1.5~2.5 s), and particle sizes of bamboo (0.18~0.22 mm) were selected as independent variables. The central composite design (CCD) was used to build the model and to analyze the effects of the above variables on the yield of the bio-oil, and the results show that the three variables have obvious effects on the bio-oil yield. However, the interactions between the three variables have no significant influence. According to the established model, the optimal conditions within the experimental ranges for bio-oil yield are: pyrolysis temperature is 519.0°C, vapor retention time is 2.1 s, and the particle size is 0.18 mm, and the theoretical yield is 58.17% at the above optimal conditions. With these optimal conditions, the average actual value of the bamboo bio-oil yield in three replicated experiments is 57.85%, which is not significantly different from the predicted value of 58.17% by the model. The RSM is simple and convenient, and the results would provide a scientific reference for the preparation of bio-oil from bamboo biomass by fast pyrolysis in fluidized beds.


Sun Y.,Guangxi University | Xie Q.,Guangxi University | Xie Q.,Guangxi University of Technology | Wei T.,Guangxi University | And 3 more authors.
Huagong Xuebao/CIESC Journal | Year: 2011

Phase equilibria for three binary systems, water-acetic acid, water-furfural, and acetic acid-furfural, at various pressures were simulated by NRTL-HOC (Hayden-O'Connell equations)and UNIQUAC-HOC models. The association of acetic acid in vapor phase was considered and the nonideality of vapor phase was corrected by Virial and Hayden-O'Connell equations. Considering the non-ideal behavior of the liquid phase, the NRTL and UNIQUAC models were employed to account for nonidealities in the liquid phase. The data regression option was used with a generalized least-squares method based on the maximum likelihood principle. The results show that the NRTL-HOC model that describes binary vapor-liquid equilibrium for the water-acetic acid system is better than the UNIQUAC-HOC model, whereas the UNIQUAC-HOC model is more effective to describe the water-furfural and acetic acid-furfural binary systems. In addition, the UNIQUAC-HOC model presents a very good prediction to the phase equilibrium of the water-acetic acid-furfural ternary system at 101.33 kPa using the pertinent parameters of the binary systems, and the rectification process of water-acetic acid-furfural ternary system was simulated with the residue curve maps of the ternary system. The results indicate that the binary interaction parameters obtained are accurate and reliable. The residue curve maps are important for the design and operation of heterogeneous azeotrope rectification process of water-acetic acid-furfural ternary system. © All Rights Reserved.


Yan S.,National Engineering Research Center for Non food Biorefinery | Wu G.,National Engineering Research Center for Non food Biorefinery
Applied Biochemistry and Biotechnology | Year: 2013

This is the continuation of our studies to use very basic information on enzyme to predict optimal reaction parameters in enzymatic reactions because the gap between available enzyme sequences and their available reaction parameters is widening. In this study, 23 features selected from 540 plus features of individual amino acid as well as a feature combined whole protein information were screened as independents in a 20-1 feedforward backpropagation neural network for predicting optimal pH in beta-glucosidase's hydrolytic reaction because this enzyme drew attention recently due to its role in biofuel industry. The results show that 11 features can be used as independents for the prediction, while the feature of amino acid distribution probability works better than the rest independents for the prediction. Our study paves a way to predict the optimal reaction parameters of enzymes based on the amino acid features of enzyme sequences. © Springer Science+Business Media New York 2013.

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