• Biotechnology and Bioprocess Engineering:BBE
• /
• v.10 no.5
• /
• pp.432-443
• /
• 2005

Microarray technology has contributed Significantly to the understanding of bacterial genetics and transcriptional regulation. One neglected aspect of this technology has been optimization of microarray-generated signals and quality of generated information. Full genome microarrays were developed for Clostridium acetobutylicum through spotting of PCR products that were designed with minimal homology with all other genes within the genome. Using statistical analyses it is demonstrated that Signal quality is significantly improved by increasing the hybridization volume. possibly increasing the effective number of transcripts available to bind to a given spot, while changes in labeled probe amounts were found to be less sensitive to improving signal quality. In addition to Q-RT-PCR, array validation was tested by examining the transcriptional program of a mutant (M5) strain lacking the pSOL1 178-gene megaplasmid relative to the wildtype (WT) strain. Under optimal conditions, it is demonstrated that the fraction of false positive genes is 1% when considering differentially expressed genes and 7% when considering all genes with signal above background. To enhance genomic-scale understanding of organismal physiology, using data from these microarrays we estimated that $40{\sim}55%$ of the C. acetobutylicum genome is expressed at any time during batch culture, similar to estimates made for Bacillus subtilis.

• Biotechnology and Bioprocess Engineering:BBE
• /
• v.10 no.5
• /
• pp.385-399
• /
• 2005

The phenotypic response of a cell results from a well orchestrated web of complex interactions which propagate from the genetic architecture through the metabolic flux network. To rationally design cell factories which carry out specific functional objectives by controlling this hierarchical system is a challenge. Transcriptome analysis, the most mature high-throughput measurement technology, has been readily applied In strain improvement programs in an attempt to Identify genes involved in expressing a given phenotype. Unfortunately, while differentially expressed genes may provide targets for metabolic engineering, phenotypic responses are often not directly linked to transcriptional patterns, This limits the application of genome-wide transcriptional analysis for the design of cell factories. However, improved tools for integrating transcriptional data with other high-throughput measurements and known biological interactions are emerging. These tools hold significant promise for providing the framework to comprehensively dissect the regulatory mechanisms that identify the cellular control mechanisms and lead to more effective strategies to rewire the cellular control elements for metabolic engineering.

• Biotechnology and Bioprocess Engineering:BBE
• /
• v.9 no.4
• /
• pp.285-291
• /
• 2004

A simulated moving bed (SMB) chromatography system is a powerful tool for preparative scale separation, which can be applied to the separation of chiral compound. We have de-signed our own lab-scale SMB chromatography using 5 HPLC pumps, 6 stainless steel columns and 4 multi-position valves, to separate a racemic mixture of ketoprofen in to its enantiomers. Our design has the characteristics of the low cost for assembly for the SMB chromatography and easy repair of the unit, which differs from the designs suggested by other investigators. It is possible for the flow path through each column to be independently changed by computer control, using 4 multi-position rotary valves and 5 HPLC solvent delivery pumps. In order to prove the operability of our SMB system, attempts were made to separate the (S)-ketoprofen enantiomer from a ketoprofen racemic mixture. The operating parameters of the SMB chromatography were calculated for ketoprofen separation from a batch chromatography experiment as well as by the triangle theory. With a feed concentration of 1 mg/mL, (S)-ketoprofen was obtained with a purity of 96% under the calculated operating conditions.

• Journal of Microbiology and Biotechnology
• /
• v.23 no.9
• /
• pp.1229-1243
• /
• 2013

In this paper, an air isolate (NITT6L) has been screened based on hemolytic activity, emulsification activity, drop collapsing test, and oil displacement test, as well as lipase activity. It was found that strain NITT6L was able to reduce the surface tension of the medium from 61.5 to 39.83 mN/m and could form stable emulsions with tested vegetable oils. Morphological, biochemical, 16S rRNA sequencing analyses, and fatty acid methyl ester analysis using gas chromatography confirmed that the air isolate under study was Pseudomonas aeruginosa. Characterization of the biosurfactant using agar double diffusion assay revealed that the biosurfactant was anionic in nature, and CTAB-methylene blue assay and Molisch test revealed its glycolipid nature. The FT-IR spectrum confirmed that the crude biosurfactant was a rhamnolipid. Using unoptimized medium containing sucrose as the carbon source, the isolate was found to produce 0.3 mg/ml of rhamnolipid in batch cultivation (shake flask) at $37^{\circ}C$ and pH 7. Optimization of the medium components was carried out using design of experiments and the yield of rhamnolipid has been enhanced to 4.6 mg/ml in 72 h of fermentation.

• Biotechnology and Bioprocess Engineering:BBE
• /
• v.8 no.4
• /
• pp.233-239
• /
• 2003

For the quantitative analysis of an unknown sample a calibration curve should be obtained, as analytical instruments give relative, rather than absolute measurements. Therefore, researchers should make standard samples with various known concentrations, measure each standard and the unknown sample, and then determine the concentration of the unknown by comparing the measured value to those of the standards. These procedures are tedious and time-consuming. Therefore, we developed a polymer based microfluidic device from polydimethylsiloxane, which integrates serial dilution and capillary electrophoresis functions in a single device. The integrated microchip can provide a one-step analytical tool, and thus replace the complex experimental procedures. Two plastic syringes, one containing a buffer solution and the other a standard solution, were connected to two inlet holes on a microchip, and pushed by a hydrodynamic force. The standard sample is serially diluted to various concentrations through the microfluidic networks. The diluted samples are sequentially introduced through microchannels by electro-osmotic force, and their laser-induced fluorescence signals measured by capillary electrophoresis. We demonstrate the integrated microchip performance by measuring the fluorescence signals of fluorescein at various concentrations. The calibration curve obtained from the electropherograms showed the expected linearity.

• Biotechnology and Bioprocess Engineering:BBE
• /
• v.7 no.5
• /
• pp.237-251
• /
• 2002

The recent progress on metabolic systems engineering was reviewed based on our recent research results in terms of (1) metabolic signal flow diagram approach, (2) metabolic flux analysis (MFA) in particular with intracellular isotopomer distribution using NMR and/or GC-MS, (3) synthesis and optimization of metabolic flux distribution (MFD), (4) modification of MFD by gene manipulation and by controlling culture environment, (5) metabolic control analysis (MCA), (6) design of metabolic regulation structure, and (7) identification of unknown pathways with isotope tracing by NMR. The main characteristics of metabolic engineering is to treat metabolism as a network or entirety instead of individual reactions. The applications were made for poly-3-hydroxybutyrate (PHB) production using Ralstonia eutropha and recombinant Escherichia coli, lactate production by recombinant Saccharomyces cerevisiae, pyruvate production by vitamin auxotrophic yeast Toluropsis glabrata, lysine production using Corynebacterium glutamicum, and energetic analysis of photosynthesic microorganisms such as Cyanobateria. The characteristics of each approach were reviewed with their applications. The approach based on isotope labeling experiments gives reliable and quantitative results for metabolic flux analysis. It should be recognized that the next stage should be toward the investigation of metabolic flux analysis with gene and protein expressions to uncover the metabolic regulation in relation to genetic modification and/ or the change in the culture condition.

• Biotechnology and Bioprocess Engineering:BBE
• /
• v.1 no.1
• /
• pp.46-50
• /
• 1996

In order to design industrial scale reactors and proceises for multi-phase biocatalytic reactions, it is essential to understand the mechanisms by which such systems operate. To il-lustrate how such mechanisms can be modeled, the hydrolysis of the primary ester groups of triglycerides to produce fatty acids and monoglycerides by lipased (glycerol-ester hydrolase) catalysis has been selected as an example of multiphase biocatalysis. Lipase is specific in its behavior such that it can act only on the hydrolyzed (or emulsified) part of the substrate. This follows because the active center of the enzyme is catalytically active only when the substrate contacts it in its hydrolyzed form. In other words, lipase acts only when it can shuttleback and forth between the emulsion phase and the water phase, presumably within an interphase or boundary layer between these two phases. In industrial applications lipase is employed as a fat splitting enzyme to remove fat stains from fabrics, in making cheese, to flavor milk products, and to degrade fats in waste products. Effective use of lipase in these processes requires a fundamental understanding of its kinetic behavior and interactions with substrates under various environmental conditions. Therefore, this study focuses on modeling and simulating the enzymatic activity of the lipase as a step towards the basic understanding of multi-phase biocatalysis processes.

• Biotechnology and Bioprocess Engineering:BBE
• /
• v.10 no.1
• /
• pp.9-15
• /
• 2005

A bioartificial liver (BAL) is a medical device entrapping living hepatocytes or immortalized cells derived from hepatocytes. Many efforts have already been made to maintain the functions of the hepatocytes in a BAL device over a long term. However, there is still some uncertainty as to their efficacy. and their limitations are unclear. Therefore, it is important to quantitatively evaluate the metabolic functions of a BAL. In previous studies on in vitro BAL devices, two test methods, an initial bolus loading and constant-rate infusion plus initial bolus loading, were theoretically carried out to obtain physiologic data on drugs. However, in the current study, the same two methods were used as a perfusion model and derived the same clearance characterized by an interrelationship between the perfusate flow rate and intrinsic clearance. The interrelationship indicated that the CL increased with an increasing perfusate flow rate and approached its maximum value, i.e. intrinsic clearance. In addition, to set up an in vivo BAL system, the toxic plateau levels in the BAL system were calculated for both series and parallel circuit models. The series model had a lower plateau level than the parellel model. The difference in the toxic plateau levels between the parallel and series models increased with an increasing number of BAL cartridges.

• Biotechnology and Bioprocess Engineering:BBE
• /
• v.2 no.2
• /
• pp.77-81
• /
• 1997

Removal of nitrogen compound from waste water is essential and often accomplished by biological process. To prevent washout and to develop an efficient bioreactor, immobilization of sutibal microorganisms could be sensible approach. Strains and permeabilized cell encapsulated in cellulose nitrate microcapsules and immobilized on polystyrene films were prepared by the method described in the previous study. In the wastewater treatment system, nitrification of ammonia component is generally known as rate controlling step. To enhance the rate of nitrification, firstly nitrifying strains Nitrosomonas europaea(IFO14298), are permeabilized chemically, and immobilized on polystyrene films and secondly oxidation rates of strain system and permeabilized strain system are compared in the same condition. with 30 minute permeabilized cells, it took about 25 hours to oxidize 70% of ammonia in the solution, while it took about 40 hours to treat same amount of ammonia with untreated cells. All the immobilization procedures did not harm to the enzyme activity and no mass transfer resistance through the capsule well was shown. In the durability test of immobilized system, the system showed considerable activity for the repeated operation for 90 days. With these results, the system developed in this study showed the possibility to be used in the actual waste water treatment system.

• Biotechnology and Bioprocess Engineering:BBE
• /
• v.9 no.3
• /
• pp.191-195
• /
• 2004

Drug delivery systems that are based on pectin have been studied for colon specific delivery using the specific activity of colon microflora. The aim of this study was to design a novel method of manufacturing pectin microspheres without oils and surfactants and to investigate the potential use of the pectin microspheres as an oral colon-specific drug carrier. The pectin microspheres were successfully formed using the spray drying method and crosslinking with calcium chloride. From the crosslinked pectin microspheres, indomethacin (IND) release was more suppressed than its release from non-crosslinked microspheres. In a low pH (pH 1.4) environment, the pectin microspheres released IND at an amount of about 18${\pm}$2% of the total loaded weight for 24 h while the release rate of IND was stimulated at neutral pH (pH 7.4). IND release from the pectin microspheres was increased by the addition of pectinase. The results clearly demonstrate that the pectin microspheres that were prepared by the spray drying and crosslinking methods are potential carriers for colon-specific drug deliveries.