Analysis of Data on Xanthan Fermentation in Stationary Phase Using Black Box and Metabolic Network Models

The xanthan fermentation data in the stationary phase was analyzed using the black box and the metabolic network models. The data consistency is checked through the elemental balance in the black box model. In the metabolic network model, the metabolic flux distribution in the cell is calculated using the metabolic flux analysis method, then the maintenance coefficients is calculated.

Investigation of the Metabolic Flux Analysis Method for Overdetermined System

With the xanthan synthesis in Xanthomoaas campestris as an example, two methods for metabolic flux analysis of overdetermined system, the experimental data error minimization method and the equation error minimization method, are compared from their mathematical basis, rationality of the results and the easiness of computation. The results show that the experimental data error minimization method is appropriate in metabolic flux analysis of overdetermined system.

Development of cell metabolite analysis on microfluidic platform

Cell metabolite analysis is of great interest to analytical chemists and physiologists, with some metabolites having been identified as important indicators of major diseases such as cancer. A highthroughput and sensitive method for drug metabolite analysis will largely promote the drug discovery industry. The basic barrier of metabolite analysis comes from the interference of complex components in cell biological system and low abundance of target substances. As a powerful tool in biosample analysis, microfluidic chip enhances the sensitivity and throughput by integrating multiple functional units into one chip. In this review, we discussed three critical steps of establishing functional microfluidic platform for cellular metabolism study. Cell in vitro culture model, on chip sample pretreatment, and microchip combined detectors were described in details and demonstrated by works in five years. And a brief summary was given to discuss the advantages as well as challenges of applying microchip method in cell metabolite and biosample analysis.

Clinical metabolic analysis combined with traceability of biosynthetic pathway:a new approach to quality marker of Chinese materia medica

Quality marker(Q-marker)of Chinese materia medica(CMM)plays an important role in quality control of CMM products.However,its research strategy and technique remain unclear.Based on the fact that quality standard of CMM should be associated with clinical efficacy,taking Jinqi Jiangtang tablet treating type 2 diabetes as an example,the Q-marker related to activity via the reverse analysis of drug metabolism in clinic and traceability of botanic biosynthetic pathways is discovered and validated.Therefore,we proposed a new research strategy of Q-marker of CMM with"Discovery of clinical active constituents as guidance,Reverse analysis of metabolic transformations as link,and Traceability of biosynthesis pathways as key",to improve quality control of CMM products.

Ambient Light Alters Gene Expression Pattern of Enzymes and Transcription Factors Involved in Phenylpropanoid Metabolic Pathway in Potato under Chilling Stress

[Objective] Expressions of key enzymatic genes involved in phenyl-propanoid metabolic pathway in potato and StR2R3-MYB and StTGA transcripters were investigated in the present study. [Method] The primitive cultivar Yan was the materials for replicated trials and total RNA extracted from tissues of seedlings. Re-al-time florescent quantification PCR, multiple intervals of air temperature, light-il umi-nation and time-duration were factors of treatments in the experiment. Data on gene expressions were obtained and proceed to asses and compare effects based on statistical analysis. [Result] The results showed negative correlations between tem-perature degrees and expressions of StPAL, StDFR and StR2R3-MYB genes but not StTGA. Positive correlations, however, were derived between those of StCHS, StDFR and StR2R3-MYB and light-intensity. Significant interactive effects between expressions of StPAL and StDFR and treatments, light intensity and temperature degree, along the phenylpropanoid pathway were observed. Transcription regulator of StR2R3-MYB showed significant positive effect on the expression of StCHS of potato. StTGA transcription factor, on the other hand, gave significant negative ef-fects on the expression of StDFR. [Conclusion] Results from present study reveal the role of environmental factors and complicate interactions between such condi-tions as temperature-light il umination and mRNA function of target genes.

Process Control and Optimization for Heterologous Protein Production by Methylotrophic Pichia pastoris

The methylotrophic yeast Pichia pastoris is a highly successful system for production of a variety of heterologous proteins due to its unique features/abilities for effective protein expression, and tremendous efforts have been made to increase heterologous protein productivity by P. pastoris in recent years. When new engineered yeast strains are constructed and are ready to use tot industrial protein production, process control and optimization techniques should be applied to improve the fermentation performance in the following aspects： （1） increase recombinant cell concentrations in fermentor to high density during growth phase; （2） effectively induce heterologous proteins by enhancing/stabilizing titers or concentrations of the proteins during induction phase; （3） decrease operation costs by relieving the working loads of heat-exchange and oxygen supply. This article reviews and discusses the key and commonly used techniques in heterologous protein production by P. pastoris, with the focus on optimizations of fermentation media and basic operation conditions, development of optimal glycerol feeding strategies for achieving high density cultivation of P. pastoris and effective heterologous protein induction methods by regulating specific growth rate, methanol concentration, temperatures, mixture ratio of multi-carbon substrates, etc. Metabolic analysis for recombinant protein production by P. pastoris is also introduced to interpret the mechanism of sub-optimal heterologous protein production and to explore further optimal expression methods.

Exogenous strigolactones promote lateral root growth by reducing the endogenous auxin level in rapeseed

Strigolactones(SLs)are newly discovered plant hormones which regulate the normal development of different plant organs,especially root architecture.Lateral root formation of rapeseed seedlings before winter has great effects on the plant growth and seed yield.Here,we treated the seedlings of Zhongshuang 11(ZS11),an elite conventional rapeseed cultivar,with different concentrations of GR24(a synthetic analogue of strigolactones),and found that a low concentration(0.18μmol L–1)of GR24 could significantly increase the lateral root growth,shoot growth,and root/shoot ratio of seedlings.RNA-Seq analysis of lateral roots at 12 h,1 d,4 d,and 7 d after GR24 treatment showed that 2301,4626,1595,and 783 genes were significantly differentially expressed,respectively.Function enrichment analysis revealed that the plant hormone transduction pathway,tryptophan metabolism,and the phenylpropanoid biosynthesis pathway were over-represented.Moreover,transcription factors,including AP2/ERF,AUX/IAA,NAC,MYB,and WRKY,were up-regulated at 1 d after GR24 treatment.Metabolomics profiling further demonstrated that the amounts of various metabolites,such as indole-3-acetic acid(IAA)and cis-zeatin were drastically altered.In particular,the concentrations of endogenous IAA significantly decreased by 52.4 and 75.8%at 12 h and 1 d after GR24 treatment,respectively.Our study indicated that low concentrations of exogenous SLs could promote the lateral root growth of rapeseed through interaction with other phytohormones,which provides useful clues for the effects of SLs on root architecture and crop productivity.

1~H NMR-based serum metabolic profiling in compensatedand decompensated cirrhosis

AIM: To study the metabolic profiling of serum samples from compensated and decompensated cirrhosis patients. METHODS: A pilot metabolic profiling study was conducted using three groups: compensated cirrhosis patients (n = 30), decompensated cirrhosis patients (n = 30) and healthy controls (n = 30). A 1H nuclear magnetic resonance (NMR)-based metabonomics approach was used to obtain the serum metabolic profiles of the samples. The acquired data were processed by multivariate principal component analysis and orthogonal partial least-squares discriminant analysis (OPLS-DA). RESULTS: The OPLS-DA model was capable of distinguishing between decompensated and compensated cirrhosis patients, with an R2Y of 0.784 and a Q2Y of 0.598. Twelve metabolites, such as pyruvate, phenylala-nine and succinate, were identified as the most influential factors for the difference between the two groups. The validation of the diagnosis prediction showed that the accuracy of the OPLS-DA model was 85% (17/20). CONCLUSION: 1H NMR spectra combined with pattern recognition analysis techniques offer a new way to diagnose compensated and decompensated cirrhosis in the future.

Optimization of the bioconversion of glycerol to ethanol using Escherichia coli by implementing a bi-level programming framework for proposing gene transcription control strategies based on genetic algorithms

In silico approaches for metabolites optimization have been derived from the flood of sequenced and annotated genomes. However, there exist still numerous degrees of freedom in terms of optimization algorithm approaches that can be exploited in order to enhance yield of processes which are based on biological reactions. Here, we propose an evolutionary approach aiming to suggest different mutant for augmenting ethanol yield using glycerol as substrate in Escherichia coli. We found that this algorithm, even though is far from providing the global optimum, is able to uncover genes that a global optimizer would be incapable of. By over-expressing accB, eno, dapE, and accA mutants in ethanol production was augmented up to 2 fold compared to its counterpart E. coli BW25113.

Nephrocyte-neurocyte interaction and cellular metabolic analysis on membrane-integrated microfluidic device

Cell-cell interaction and cell metabolic analysis provide new opportunities for better understanding of critical biochemical processes. Advanced microfluidic technologies enable to create more realistic in vitro microenvironment by spatial and temporal control of cell growth and co-culture. In this work, we design a microfluidic device to achieve the co-culture of PC12 cells and 293 cells, and study in vitro cell-cell interaction via cell metabolic analysis by mass spectrometry. The membraneintegrated microfluidic device was firstly used for cell co-culture, and the cellular metabolite was further investigated by mass spectrometer(MS). Our results showed that the differentiation of PC12 cells could be successfully induced by m NGF and also greatly influenced by the microchannel treatment of fetal bovine serum(FBS) solution. The identification of cell morphology, microtubule-associated protein 2(MAP-2) expression and viability of differentiated PC12 cells were conducted before 293 cells being introduced into the top microfluidic channels and stimulated to secrete cell metabolism products. The developed microfluidic device is a potentially useful tool for high throughput of cell-cell interaction study.

Metabolic flux analysis on arachidonic acid fermentation

The analysis of flux distributions in metabolic networks has become an important approach for understand-ing the fermentation characteristics of the process.A model of metabolic flux analysis of arachidonic acid(AA)synthesis in Mortierella alpina ME-1 was established and carbon flux distributions were estimated in different fermentation phases with different concentrations of N-source.During the expo-nential,decelerating and stationary phase,carbon fluxes to AA were 3.28%,8.80%and 6.97%,respectively,with sufficient N-source broth based on the flux of glucose uptake,and those were increased to 3.95%,19.21%and 39.29%,respectively,by regulating the shifts of carbon fluxes via fermentation with limited N-source broth and adding 0.05% NaNO_(3) at 96 h.Eventually AA yield was increased from 1.3 to 3.5 g·L^(−1).These results suggest a way to improve AA fermentation,that is,fermentation with limited N-source broth and adding low concentration N-source during the stationary phase.