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Xun Chen

Publications and source records attributed to Xun Chen.

At least 19 recordsLinked to original sources
PubMed2007

Enhancement of riboflavin production by overexpression of acetolactate synthase in a pta mutant of Bacillus subtilis.

Genetic alterations of carbon flux into the acetoin biosynthesis pathway as a possible means to reduce acid accumulation were investigated in the riboflavin-producing Bacillus subtilis during growth on glucose. The lower rates of cell growth and riboflavin production were found in the pta-disrupted mutant while the rate of acetate formation was reduced. In contrast, acid accumulation was significantly reduced, to one-fifth that of the parental strain RH33::[pRB63](n), and a 50% increase in the riboflavin yield was obtained when the expression of the gene encoding acetolactate synthase was increased in the pta-disrupted mutant. Metabolic analysis, together with enzyme activity assays, indicated that the tricarboxylic acid cycle fluxes are significantly increased in response to acetolactate synthase overexpression in pta-disrupted mutant. Moreover, the intracellular ATP-to-ADP ratio also increased 5.8-fold. The high concentration of ATP could explain the increased riboflavin production.

Acetolactate Synthase↗
PubMed2006

Improved production of ethanol by deleting FPS1 and over-expressing GLT1 in Saccharomyces cerevisiae.

To improve ethanol production in Saccharomyces cerevisiae, two yeast strains were constructed. In the mutant KAM-3, the FPS1 gene, which encodes a channel protein responsible for glycerol export, was deleted. The mutant KAM-11 had the GLT1 gene (encoding glutamate synthase) placed under the PGK1 promoter while having the FPS1 deletion. Growth rate and biomass concentration remained virtually unchanged with the mutant KAM-11, compared to that of the parent. Over-expression of GLT1 by the PGK1 promoter along with FPS1 deletion resulted in a 14% higher ethanol production and a 30% lower glycerol formation compared to the parental strain under anaerobic fermentation conditions. Furthermore, acetate and pyruvic acid formation was also reduced in order for cells to maintain redox balance.

Efficiency↗
PubMed2006

Overexpressing GLT1 in gpd1Delta mutant to improve the production of ethanol of Saccharomyces cerevisiae.

To improve ethanol production in Saccharomyces cerevisiae, two yeast strains were constructed. In the mutant, KAM-4, the GPD1 gene, which encodes a glycerol 3-phosphate dehydrogenase of S. cerevisiae to synthesize glycerol, was deleted. The mutant KAM-12 had the GLT1 gene (encodes glutamate synthase) placed under the PGK1 promoter while harboring the GPD1 deletion. Notably, overexpression of GLT1 by the PGK1 promoter along with GPD1 deletion resulted in a 10.8% higher ethanol production and a 25.0% lower glycerol formation compared to the wild type in anaerobic fermentations. The growth rate of KAM-4 was slightly lower than that of the wild type under the exponential phase whereas KAM-12 and the wild type were indistinguishable in the biomass concentration at the end of growth period. Meanwhile, dramatic reduction of formation of acetate and pyruvic acid was observed in all the mutants compared to the wild type.

Biomass↗
PubMed2006

Genome-scale in silico aided metabolic analysis and flux comparisons of Escherichia coli to improve succinate production.

In the post-genome era, it is one challenge to understand the cellular metabolism at the systematic levels. Mathematical modeling of microorganisms and subsequent computer simulation are effective tools for systems biology. In this paper, based on the genome-scale Escherichia coli stoichiometric model iJR904, through the GAMS linear programming package, the in silico maximal succinate yield was estimated to be 1.714 mol/mol glucose. When another two constraints were added, the maximal succinate yield dropped to 1.60 mol/mol glucose. Further analysis substantiated the uniqueness of the flux distribution under such constraints. After comparisons with the metabolic flux analysis (MFA) results computed from the wet experimental data of the three kinds of E. coli, three potential improvement target sites, the glucose phosphotransferase transport system, the pyruvate carboxylase, and the glyoxylate shunt, were identified and selected for the genetic modifications. All the three genetic modified strains showed increased succinate yield. The final strain TUQ19/pQZ6 had a high yield of 1.29 mol succinate/mol glucose and high productivity. The success of the above experiments proved that this in silico optimal succinate production pathway is reasonable and practical. This method may also be used as a general strategy to help enhance the yields of other favorable metabolites in E. coli.

Anaerobiosis↗
PubMed2006

Over-expression of glucose dehydrogenase improves cell growth and riboflavin production in Bacillus subtilis.

Ribulose 5-phosphate is a precursor for riboflavin biosynthesis. Alteration of carbon flow into the pentose phosphate pathway will affect the availability of ribulose 5-phosphate and the riboflavin yield. We have modulated carbon flow in Bacillus subtilis through the gluconate bypass by over-expression of glucose dehydrogenase under the control of the constitutively expressed P43 promoter. Over-expression of glucose dehydrogenase resulted in low acid production (acetate and pyruvate). The substantial reduction in acid production is accompanied by increased riboflavin production and an increased rate of growth while glucose consumption remained unchanged. Metabolic analysis indicated that over-expression of glucose dehydrogenase increased intracellular pool of ribulose 5-phosphate. The high concentrations of ribulose 5-phosphate could explain the increased riboflavin production.

Acetic Acid↗
PubMed2006

Redirection electron flow to high coupling efficiency of terminal oxidase to enhance riboflavin biosynthesis.

The metabolic impact of redirection electron flow to high coupling efficiency of terminal oxidases on riboflavin biosynthetic ability was quantitatively assessed during batch culture in this paper. While disruption of the low coupling bd oxidase of the riboflavin overproducing B. subtilis PK, the apparent phenotype with more rapid specific growth rate and higher biomass yield was achieved. Compared to by-products formation, a discernible shift to less acetate and more acetoin in cyd mutant was observed. As the overflow metabolism was decreased in B. subtilis PK cyd, more carbon source was directed to biomass and riboflavin biosynthetic pathway, which resulted in higher biomass and about 30% improvement of riboflavin biosynthetic ability. The higher product-corrected biomass yield in mutant showed that the efficient energy generation is an important factor for exponential growth of riboflavin overproducing B. subtilis strain in batch culture.

Bacillus subtilis↗
PubMed2006

Choosing the analysis population in non-inferiority studies: per protocol or intent-to-treat.

For superiority trials, the intent-to-treat population (ITT) is considered the primary analysis population because it tends to avoid the over-optimistic estimates of efficacy that results from a per-protocol (PP) population. However, the roles of the ITT population and PP population in non-inferiority studies are not clearly defined as in superiority trials. In this paper, a simulation study is conducted to systematically investigate the impact of different types of missingness and protocol violations on the conservatism or anticonservatism of analyses based on the ITT and the PP population in non-inferiority trials. We find that conservatism or anticonservatism of the PP or ITT analysis depends on many factors, including the type of protocol deviation and missingness, the treatment trajectory (for longitudinal study) and the method of handling missing data in ITT population. The requirement that non-inferiority be shown for both PP and ITT populations does not necessarily guarantee the validity of a non-inferiority conclusion and a sufficiently powered PP analysis is not necessarily powered for ITT analysis. It is important to assess the potential types and rates of protocol deviation and missingness that might occur in a non-inferiority trial and to obtain some prior knowledge regarding the treatment trajectory of the test treatment versus the active control at the design stage so that a proper analysis plan and appropriate power estimation can be carried out. In general, for the types of protocol violations and missingness considered, we find that hybrid ITT/PP analysis, which excludes non-compliant patients as in the PP analysis and properly addresses the impact of non-trivial missing data as in the MLE-based ITT analysis, is more promising by way of providing reliable non-inferiority tests.

Analysis of Variance↗
PubMed2006

Integrating metabolomics into a systems biology framework to exploit metabolic complexity: strategies and applications in microorganisms.

As an important functional genomic tool, metabolomics has been illustrated in detail in recent years, especially in plant science. However, the microbial category also has the potential to benefit from integration of metabolomics into system frameworks. In this article, we first examine the concepts and brief history of metabolomics. Next, we summarize metabolomic research processes and analytical platforms in strain improvements. The application cases of metabolomics in microorganisms answer what the metabolomics can do in strain improvements. The position of metabolomics in this systems biology framework and the real cases of integrating metabolomics into a system framework to explore the microbial metabolic complexity are also illustrated in this paper.

Bacteria↗
PubMed2006

Expression of galactose permease and pyruvate carboxylase in Escherichia coli ptsG mutant increases the growth rate and succinate yield under anaerobic conditions.

In Escherichia coli, disruption of ptsG, which encodes the glucose-specific permease of the phosphotransferase transport system (PTS) protein EIICB(Glc), is crucial for high succinate production. This mutation can, however, cause very slow growth and low glucose consumption rates. The ptsG mutant (TUQ2), from wild type E. coli W1485, and E. coli galP (encoding galactose permease) and glk (encoding glucose kinase) gene expression plasmids were constructed. TUQ2 increased the generation time to approximately 4 h and gave a higher final cell density of 0.5 g/l by expression of galP. However, glk expression had no effect on the mutant. After expression of pyruvate carboxylase (PYC) and galactose permease, the ptsG mutant showed higher succinate yield (1.2 mol/mol glucose) and the specific rate of glucose consumption from 0.33 to 0.6 g/1 h.

Escherichia coli↗
PubMed2005

The application of enhanced parallel gatekeeping strategies.

The parallel gatekeeping strategy proposed by Dmitrienko et al. (Statist. Med. 2003; 22:2387-2400) provides a flexible framework for the pursuit of strong control on study wise type I error rate. This paper further explores the application of the weighted Simes parallel gatekeeping procedure recommended by Dmitrienko et al. and proposes some modifications to it to better incorporate the interrelationships of different hypotheses in actual clinical trials and to achieve better power performance. We first propose a simple method to quantitatively control the impact of secondary tests on the testing of primary hypotheses. We then introduce a matched gatekeeping procedure to exemplify how to address special relationships between individual primary and secondary tests following the parallel gatekeeping framework. Our simulation study demonstrates that the enhanced gatekeeping procedures generally result in more powerful tests than the parallel gatekeeping procedure in Dmitrienko et al. whenever applicable.

Analgesics↗
PubMed2005

Decision rule based multiplicity adjustment strategy.

To minimize potential controversies in determining the need for multiplicity adjustment for multiple hypotheses, we propose a decision rule based multiplicity adjustment strategy in this paper. Resorting to a predefined decision rule of a clinical trial, one may link the different hypotheses by their logical relationships and divide them into different families. A proper multiplicity adjustment procedure can then be developed by maintaining strong control of Type I error rate within each family. The paper applies the proposed multiplicity adjustment strategy to a published raloxifene clinical trial.

Bone Density Conservation Agents↗
PubMed2005

Study on model of indoor air pollution forecast for decoration under natural ventilation condition.

OBJECTIVE: To establish the model of indoor air pollution forecast for decoration. METHODS: The model was based on the balance model for diffusing mass. RESULTS: The data between testing concentration and estimating concentration were compared. The maximal error was less than 30% and average error was 14.6%. CONCLUSION: The model can easily predict whether the pollution for decoration exceeds the standard and how long the room is decorated.

Air Pollution, Indoor↗
PubMed2004

Interaction of catechins with aluminum in vitro.

Tea is one of the most popular beverages, consumed by over two thirds of the world's population; but the aluminum accumulation property of tea plant is becoming the focus of many researches because of aluminum's known adverse effect on human health. Investigation of the interactions of catechins with Al(3+) showed that during the interaction of catechins with Al(3+), the UV-vis spectrum of catechins was changed. Absorption of EGCG at 274 nm decreased and increased at 322 nm; EC and C's at 278 nm changed little. The ratio of Al(3+) to EGCG was 1:1 in pH 5.0 buffer solution; in pH 6.2 buffer solution, the ratio in the Al-EGCG complex was 1:1. Interestingly, while the ratio reached to over 2, after the complex of Al-EGCG started polymerization, the ratio in the polymer was 2:1. In pH 6.2 buffer solution, the complex behavior of C with Al(3+) was the same as that of EGCG, with a little difference for EC. When the ratio of Al(3+) to EC was <1, the complex in ratio was 1:2, but, the complex polymerized when the ratio of Al(3+) to EC was >1. It was found that the ratio of Al(3+) to EC in the polymer was 1:1. Polymerization of Al-catechin complexes might reduce aluminum absorption in the intestine. Kow value was also employed to study the properties of aluminum species in tea infusion (at gastric and intestine pH condition) and the effect of catechins and tea polyphenols on Kow in buffer solution. Results showed that Kow value rose much higher at the intestine pH than at the gastric pH. Tea polyphenols and catechins could greatly reduce aluminum Kow value in acetic buffer, indicating that these compounds may reduce aluminum absorption during tea intake.

Acetic Acid↗
PubMed2004

The effects of modifying in vivo cytochrome P450 3A (CYP3A) activity on etoricoxib pharmacokinetics and of etoricoxib administration on CYP3A activity.

To investigate the influence of modifying in vivo cytochrome P450 3A (CYP3A) activity on the pharmacokinetics of etoricoxib, a selective inhibitor of cyclooxygenase-2, and of etoricoxib administration on CYP3A activity, a 3-part, randomized, crossover study was conducted in 3 panels of healthy volunteers. In part I, 8 subjects were administered a single dose of 60 mg etoricoxib alone and following daily doses of 400 mg ketoconazole, a known strong inhibitor of CYP3A. In part II, 8 different subjects were administered a single dose of 60 mg etoricoxib alone and following daily doses of 600 mg rifampin, a known strong inducer of CYP3A. In parts I and II, plasma samples were collected following each etoricoxib dose and analyzed for etoricoxib. In part III, 8 different subjects were administered 120 mg etoricoxib or placebo once daily for 11 days, and the erythromycin breath test was administered on day 11 of each period. Coadministration of etoricoxib with daily doses of ketoconazole resulted in an average 43% increase in etoricoxib AUC; based on previous studies, this increase would not be expected to have any clinically meaningful effect. In contrast, coadministration of etoricoxib with daily doses of rifampin had a potentially clinically important effect on etoricoxib pharmacokinetics (average 65% decrease in etoricoxib AUC). Etoricoxib had no effect on hepatic CYP3A activity, as assessed by the erythromycin breath test.

Adult↗
PubMed2003

A comparison of recent methods for the analysis of small-sample cross-over studies.

The standard analysis of variance (ANOVA) method is usually applied to analyse continuous data from cross-over studies. The method, however, has been known to be not robust for general variance-covariance structure. The simple empirical generalized least squares (EGLS) method, proposed in an attempt to improve the precision of the standard ANOVA method for general variance-covariance structure, is usually insufficient for small-sample cross-over trials. In this paper we compare the following commonly used or recent approaches: standard ANOVA; simple EGLS; modified ANOVA method derived from a modified approximate F-distribution; and a modified EGLS method adjusted by the Kenward and Roger procedure in terms of robustness and power while applying to small-sample cross-over studies (say, the sample size is less than 40) over a variety of variance-covariance structures by simulation. We find that the unconditional modified ANOVA method has robust performance for all of the simulated small-sample cross-over studies over the various variance-covariance structures, and has comparable power with the standard ANOVA method whenever they are comparable in type I error rate. The EGLS method (simple or modified) is not reliable when the sample size of a cross-over study is too small, say, less than 24 in the simulation, unless a simple covariance structure is correctly assumed. Given a relatively larger sample size, the modified EGLS method, assuming an unstructured covariance matrix, demonstrates robust performance over the various variance-covariance structures in the simulation and provides more powerful tests than those of the modified (or standard) ANOVA method.

Analysis of Variance↗
PubMed2002

A note on ANOVA assumptions and robust analysis for a cross-over study.

Analysis of variance (ANOVA) methods are usually applied to analyse continuous data from cross-over studies. The analysis, however, may not have appropriate type I error when certain assumptions are violated. In this paper, we first clarify a conventionally minimum set of assumptions that validate the F-tests of ANOVA models for cross-over studies. We then provide a practical verification/remedy procedure based upon the theoretical developments. By applying the verification/remedy procedure, more robust analysis results can be expected from the ANOVA models.

Analysis of Variance↗