Development of a first-class undergraduate major in bioengineering facing the emerging engineering direction of biomedicine / 生物工程学报

In the "Tutorial for outline of the healthy China 2030 plan", biomedicine was listed as a key planning and development area. Shanghai government also lists biomedicine as an emerging pillar industry. The rapid development of biomedicine industry put higher requirement for talents. Taking the idea of cross integration, mutually beneficial development, inheritance and innovation, the School of Biotechnology of East China University of Science and Technology organically integrates bioengineering and pharmaceutical majors to develop a new undergraduate engineering program of biomedicine, which specially reforms the talent training practice from the aspects of developing a "trinity teaching" standard system, a "three integration, three convergence" curriculum system, and a "three comprehensive education" innovative talent training system. We put forward the trinity of "value guidance, knowledge system, technology and non-technical core competence literacy" to foster emerging biomedicine engineering talents, and developed a comprehensive innovative talents training mode featured by "covering class-in and class-out, covering every student, and covering ideology and curriculum". Moreover, we established effective connections between courses and training goals, between general education courses and professional courses, and between top-notch talent training systems and training programs. Based on the achievements of teaching reform of the emerging engineering program "intelligent bio-manufacturing", the experience we obtained may provide ideas for development of the first-class bioengineering major in China.

Advances in the development of constraint-based genome-scale metabolic network models / 生物工程学报

Genome-scale metabolic network model (GSMM) is becoming an important tool for studying cellular metabolic characteristics, and remarkable advances in relevant theories and methods have been made. Recently, various constraint-based GSMMs that integrated genomic, transcriptomic, proteomic, and thermodynamic data have been developed. These developments, together with the theoretical breakthroughs, have greatly contributed to identification of target genes, systems metabolic engineering, drug discovery, understanding disease mechanism, and many others. This review summarizes how to incorporate transcriptomic, proteomic, and thermodynamic-constraints into GSMM, and illustrates the shortcomings and challenges of applying each of these methods. Finally, we illustrate how to develop and refine a fully integrated GSMM by incorporating transcriptomic, proteomic, and thermodynamic constraints, and discuss future perspectives of constraint-based GSMM.

Exploration of an integrated competency development model for undergraduates training by participating the international Genetic Engineering Machine Competition / 生物工程学报

Starting from participating the high-level professional competition, our school has built a talent training system with the spirit of "biomaker" and an innovative practical ability training system. Such system takes the interest of student as the starting point, and relies on the strong scientific research and teaching infrastructure. The programme gives full play to students' initiatives and enhances the scientific research literacy and comprehensive ability of undergraduates majoring in biotechnology. It is an effective exploration of the traditional university education model and meets the urgent demand for innovative talents training in the era of rapid development of life sciences.

New opportunities and challenges for hybrid data and model driven bioprocess optimization and scale-up / 生物工程学报

Currently, biomanufacturing technology and industry are receiving worldwide attention. However, there are still great challenges on bioprocess optimization and scale-up, including: lacing the process detection methods, which makes it difficult to meet the requirement of monitoring of key indicators and parameters; poor understanding of cell metabolism, which arouses problems to rationally achieve process optimization and regulation; the reactor environment is very different across the scales, resulting in low efficiency of stepwise scale-up. Considering the above key issues that need to be resolved, here we summarize the key technological innovations of the whole chain of fermentation process, i.e., real-time detection-dynamic regulation-rational scale-up, through case analysis. In the future, bioprocess design will be guided by a full lifecycle in-silico model integrating cellular physiology (spatiotemporal multiscale metabolic models) and fluid dynamics (CFD models). This will promote computer-aided design and development, accelerate the realization of large-scale intelligent production and serve to open a new era of green biomanufacturing.

Numerical simulation and optimization of impeller combination used in stirred bioreactor / 生物工程学报

Bioreactors have been central in monoclonal antibodies and vaccines manufacturing by mammalian cells in suspension culture. Numerical simulation of five impeller combinations in a stirred bioreactor was conducted, and characteristics of velocity vectors, distributions of gas hold-up, distributions of shear rate in the bioreactor using 5 impeller combinations were numerically elucidated. In addition, genetically engineered CHO cells were cultivated in bioreactor installed with 5 different impeller combinations in fed-batch culture mode. The cell growth and antibody level were directly related to the maximum shear rate in the bioreactor, and the highest viable cell density and the peak antibody level were achieved in FBMI3 impeller combination, indicating that CHO cells are sensitive to shear force produced by impeller movement when cells were cultivated in bioreactor at large scale, and the maximum shear rate would play key roles in scaling-up of bioreactor at industrial scale.

Progress in intelligent control of industrial bioprocess / 生物工程学报

Industrial bioprocess is a complex systematic process and bio-manufacturing can be realized on the basis of understanding the metabolism process of living cells. In this article, the multi-scale optimization principle and practice of industrial fermentation process are reviewed, including multi-scale optimizing theory and equipment, on-line sensing technology for cellular macroscopic metabolism, and correlated analysis of physiological parameters. Furthermore, intelligent control of industrial bioprocess is further addressed, in terms of new sensing technology for intracellular physiological metabolism, big database establishment and data depth calculation, intelligent decision.

Accurate Detemination of Isotopic Abundance of Intracellular Metabolites of Saccharopolysporaerythraea Based on Ultra Performance Liquid Chromatography-Triple Quadrupole Mass Spectrometry / 分析化学

A method for measuring 13C isotopic abundance of intracellular metabolites of Saccharopolysporaerythraea by ultra-high performance liquid chromatography (UPLC)-triple quadrupole mass spectrometry was established.First, the chromatographic conditions of UPLC were optimized, and then the MS conditions such as unique tube lens voltage, collision energy, and ion pair were optimized.On the bases of length of the parent and daughter ions carbon chains and whether the daughter ions contain 13C atoms, the one-to-one method, one-to-many method and SIM method were established for measuring 13C isotopic abundance.Then these methods were used to measure naturally labeled intracellular metabolite standards and 13C labeled samples, and according to the gap between the experimental value and the theoretical value, the best method was established for each metabolite of different characteristics.The results showed that one-to-one method was most effective for measuring the metabolites of daughter ions not containing 13C atoms represented by sugar phosphates, one-to-many method was the best for measuring the metabolites of both parent and daughter ions containing 13C short carbon chains represented by carboxylic acids, SIM method could play a role in measuring the metabolites of both parent and daughter ions containing 13C long carbon chains represented by coenzyme A.This method had a good measurement precision and could be applied to the measurement of Saccharopolysporaerythraea intracellular metabolites, which contributed to the consequent study of metabolic mechanism and the efficient expression of erythromycin.

Preparation of isotope dilution mass spectrometry standards based on glucose pulse / 生物工程学报

Isotope Dilution Mass Spectrometry (IDMS) is the most accurate method for high-throughput detection of intracellular metabolite concentrations, and the key is getting the corresponding fully uniformly(U) ¹³C-labeled metabolites to be measured. The conventional procedure for getting fully U ¹³C-labeled metabolites is through batch cultivation, but intracellular metabolites concentrations by this method are generally low. By applying U ¹³C-labeled glucose pulse, combined with fast sampling and quenching, mixture of fully U ¹³C-labeled intracellular metabolites was successfully extracted with higher concentration from Pichia pastoris G/DSEL fed with fully U ¹³C-labeled glucose as only carbon source. Quantitative results from liquid chromatography tandem mass spectrometry (LC-MS) and gas chromatography tandem mass spectrometry (GC-MS) show that concentrations of organic acids, sugar phosphates, amino acids and nucleotides were 2-10 folds higher than those without glucose pulse. Therefore, the glucose pulse method can efficiently improve the usage of fully U ¹³C-labeled glucose converting to ¹³C-labeled metabolites, and achieve the detection of intracellular metabolites with lower concentrate than the instrument detection limit.

Rapid cryopreservation for Siraitia grosvenorii cells based on cells' capacitance detection / 生物工程学报

A rapid quantitative evaluation method for Siraitia grosvenorii cells was successfully developed based on plant cells' capacitance value detected by a viable cell mass monitor and the cryopreservation of S. grosvenorii suspension cells was optimized. The survival rate of S. grosvenorii cells was quantitatively measured by viable cell mass monitor and 2, 3, 5-triphenyltetrazolium chloride (TTC). An optimum cryoprotectant recipe is that the growth medium contained 10% sucrose and 10% DMSO. The experimental results also showed higher cell survival rates and cell viabilities were achieved when suspension cells were treated with pretreatment of 0.2 mol/L sucrose. With the increase of concentration of sucrose, however, the cell survival rate was decreased. And the cell survival rate represented a bell shape with the increase of pretreatment time. The highest cell survival rate and cell viability were obtained with the 9 h' s pretreatment. In addition, there was a good correlation between the cell survival rate measured by cell recovery test and that measured by viable cell mass monitor, while there were no significant differences in the cell morphology and the ability of mogrosides V production by S. grosvenorii cells cultured in suspension after cryopreservation. Therefore, the evaluation method developed based on the viable cell mass monitor has good feasibility and reliability.

Low field nuclear magnetic resonance for rapid quantitation of microalgae lipid and its application in high throughput screening / 生物工程学报

A rapid and accurate determination method of lipids in microalgae plays a significant role in an efficient breeding process for high-lipid production of microalgae. Using low field nuclear magnetic resonance (LF-NMR), we developed a direct quantitative method for cellular lipids in Chlorella protothecoides cells. The LF-NMR signal had a linear relationship with the lipid content in the microalgae cells for both dry cell samples and algal broth samples (R2 > 0.99). These results indicated that we could use this method for accurate determination of microalgal lipids. Although LF-NMR is a rapid and easy lipid determination method in comparison to conventional methods, low efficiency would limit its application in high throughput screening. Therefore, we developed a novel combined high throughput screening method for high-lipid content mutants of C. protothecoides. Namely, we initially applied Nile red staining method for semi-quantification of lipid in the pre-screening process, and following with LF-NMR method for accurate lipid determination in re-screening process. Finally, we adopted this novel screening method in the breeding process of high-lipid content heterotrophic cells of C. protothecoides. From 3 098 mutated strains 108 high-lipid content strains were selected through pre-screening process, and then 9 mutants with high-lipid production were obtained in the re-screening process. In a consequence, with heterotrophical cultivation of 168 h, the lipid concentration could reach 5 g/L, and the highest lipid content exceeded 20% (W/W), which was almost two-fold to that of the wild strain. All these results demonstrated that the novel breeding process was reliable and feasible for improving the screening efficiency.

Progress in omics research of Aspergillus niger / 生物工程学报

Aspergillus niger, as an important industrial fermentation strain, is widely applied in the production of organic acids and industrial enzymes. With the development of diverse omics technologies, the data of genome, transcriptome, proteome and metabolome of A. niger are increasing continuously, which declared the coming era of big data for the research in fermentation process of A. niger. The data analysis from single omics and the comparison of multi-omics, to the integrations of multi-omics based on the genome-scale metabolic network model largely extends the intensive and systematic understanding of the efficient production mechanism of A. niger. It also provides possibilities for the reasonable global optimization of strain performance by genetic modification and process regulation. We reviewed and summarized progress in omics research of A. niger, and proposed the development direction of omics research on this cell factory.

Development and application of morphological analysis method in Aspergillus niger fermentation / 生物工程学报

Filamentous fungi are widely used in industrial fermentation. Particular fungal morphology acts as a critical index for a successful fermentation. To break the bottleneck of morphological analysis, we have developed a reliable method for fungal morphological analysis. By this method, we can prepare hundreds of pellet samples simultaneously and obtain quantitative morphological information at large scale quickly. This method can largely increase the accuracy and reliability of morphological analysis result. Based on that, the studies of Aspergillus niger morphology under different oxygen supply conditions and shear rate conditions were carried out. As a result, the morphological responding patterns of A. niger morphology to these conditions were quantitatively demonstrated, which laid a solid foundation for the further scale-up.

Preface for special issue on industrial bioprocess technique front (2015) / 生物工程学报

Industrial bioprocess is one of the most important research fields supports the promoting of biological manufacturing industry in China, and guarantees the implementation of bioscience and biotechnology research results into the industrial applications. For improving the interconnection between academic researchers and industrial stuffs and pushing research achievement into industrial implementation, bioprocess modelling and control committee of Chinese Society for Microbiology organized two tandem conferences separately in 2012 and 2014 on the topic of "Industrial bioprocess technology", focusing mainly technique front of industrial bioprocess. A special session on industrial technique applications was hold to stimulate cooperation. The conference received many good submissions from academic and industrial sectors. This special issue is based on selected excellent papers from the submissions, together with free submissions. The special issue consists of reviews and original papers, mainly involving the aspects closely related to the bio-industrial sectors including, i) high yield strain constructing and high throughput screening; ii) optimization and modification of industrial enzymes, and iii) bioprocess modelling and high efficient scale-up method.

Construction and application of black-box model for glucoamylase production by Aspergillus niger / 生物工程学报

Carbon-limited continuous culture was used to study the relationship between the growth of Aspergillus niger and the production of glucoamylase. The result showed that when the specific growth rate was lower than 0.068 h(-1), the production of glucoamylase was growth-associated, when the specific growth rate was higher than 0.068 h(-1), the production of glucoamylase was not growth-associated. Based on the result of continuous culture, the Monod dynamics model of glucose consumption of A. niger was constructed, Combining Herbert-Pirt equation of glucose and oxygen consumption with Luedeking-Piret equation of enzyme production, the black-box model of Aspergillus niger for enzyme production was established. The exponential fed-batch culture was designed to control the specific growth rate at 0.05 h(-1) by using this model and the highest yield for glucoamylase production by A. niger reached 0.127 g glucoamylase/g glucose. The black-box model constructed in this study successfully described the glucoamylase production by A. niger and the result of the model fitted the measured value well. The black-box model could guide the design and optimization of glucoamylase production by A. niger.

Progress in industrial bioprocess engineering in China / 生物工程学报

The advances of industrial biotechnology highly depend on the development of industrial bioprocess researches. In China, we are facing several challenges because of a huge national industrial fermentation capacity. The industrial bioprocess development experienced several main stages. This work mainly reviews the development of the industrial bioprocess in China during the past 30 or 40 years: including the early stage kinetics model study derived from classical chemical engineering, researching method based on control theory, multiple-parameter analysis techniques of on-line measuring instruments and techniques, and multi-scale analysis theory, and also solid state fermentation techniques and fermenters. In addition, the cutting edge of bioprocess engineering was also addressed.

Accurate Determination of 13 C Isotopic Abundances of Free Intracellular Amino acids with Low Concentration by GC-MS-Selective Ion Monitoring Method / 分析化学

13 C isotopic abundance of intracellular free amino acid with a characteristic of fast- turnover can quickly reflect changes in intracellular metabolic state. But the concentration of intracellular free amino acid is low, the existed 13 C isotope detection method based on GC-MS can not satisfy the requirement with full scan mode. In this study, the selected ion monitoring method was used to detect accuracy higher likelihood of analysis of 13 C isotopic abundance of free intracellular amino acid. First, in the full scan mode we analyzed of the fracture law of different amino acids, found the feature corresponding to each amino acid fragments, and established 16 kinds of free intracellular amino acids characteristic fragment library. Then using this characteristic fragment library, only specific m/z signal was detected in sample analysis, which realized the selected ion monitoring and improved the quality of signal. The results of amino acid standards showed that the signal-to-noise ratio, measurement precision and accuracy were improved by 17, 2. 0 and 3. 8 times compared with the full scan mode. In the analysis of coenzyme Q10 producing strains of samples, this method was successfully used to detect isotopic abundance of 8 kinds of free intracellular amino acids. This method plays an important role in the detection of 13 C isotopic abundance of the intracellular free amino acid in cell metabolism research.

Influence of methanol concentration on purification recovery of consensus interferon-a produced by Pichia pastoris / 生物工程学报

We observed the influence of methanol concentration on purification recovery of recombinant human consensus interferon-a (cIFN) produced by Pichia pastoris. Fermentations controlled at 0.75% (W/V) methanol showed a 24% increase in clFN expression compared to using 0.25% methanol. However, the purification recovery rate of cIFN at 0.25% methanol was 3.75-fold higher than that at 0.75% methanol. To seek the reason, we analyzed the stability of clFN by SDS-PAGE and Native-PAGE as well as Western blotting. The electrophoresis results revealed that cIFN formed a lot of aggregates in media when the induction was controlled at 0.75% methanol, and two different aggregate forms were found: disulfide bond covalent aggregates and non-covalent aggregates. However, these aggregates almost disappeared when the methanol concentration was controlled at 0.25%, at the same time, cIFN bioactivity of supernatant increased almost 4.48-fold. Finally, 0.73g monomer cIFN was obtained after purification from 1 liter supernatant at 0.25% methanol induction, showed a 2.84-fold increase compare to the induction at 0.75% methanol.

SCALE UP OF GUANOSINE FERMENTATION BASED ON SCALE-DOWN TECHNOLOGY / 微生物学通报

Based on the optimized technology on 50L scale, B subtilis 754# was used to manufacture guanosine on pilot scale (12M 3) and plant scale (100M 3) to give the production of 29 4g/L and 21 4g/L successively Through scale down the process of plant scale to pilot scale, based on the theory of dynamic metabolic flux, DO was found to be another key factor that limited the scale up process After conquering the DO limitation, the optimized technology was successfully scaled up to plant scale and the production was further increased by 18% to 25 2 g/L

STUDIES ON CONDITIONS OF CELL HIGH DENSITY CULTIVATION FOR GENETICALLY ENGINEERED METHYLOTROPHIC PICHIA PASTORIS / 微生物学通报

Recently the methylotrophic Pichia pastoris,with many advantages such as high expression,stable genetics and protein secretion,has been used extensively as a host expressing heterologous proteins.The optimal seed medium among seven media MM,MD,MGY,BMGY,YMPD,YMPGy and MGyB is BMGY with addition of 4mL/L PTM1 The high density synthesized medium in shake flask culture is as follows: Glycerol 4%(NH 4) 2SO 4 10g/L,CaSO 4 0.93g/L,K 2SO 4 18 2g/L,MgSO 4?7H 2O 14 9g/L,add 0.1mol/L PBS(pH=6 0) to 1 0 liter.The harvested yeast cell optical density (OD 600 ) reached 65 or more after 26 hours cultivation.By analysis of SDS\|PAGE,the results of Pichia pastoris culture by methanol inducement for 72 hours showed that the expression of recombinant human serum albumin had been achieved by methanol inducement after 12 hours,and the mount of targeted protein reached the summit after 24 hours inducement by methanol.The high density synthesized medium in shake flask culture in this experiment,which is similar to the mediums of batch fermentation and batch\|fed fermentation,is benefit to direct the P.pastoris fermentation in the fermentor.