Serial intravascular ultrasound analysis of the main and side branches in bifurcation lesions treated with the T-stenting technique.

Objectives: This study sought to investigate the mechanism of restenosis and the predictive value of post-procedural minimum stent area (MSA) in the side branch (SB) after coronary bifurcation stenting.

Background: The mechanism of restenosis, especially at the SB ostium, has not been fully elucidated.

Methods: This study examined 73 bifurcation lesions with post-procedural and 9-month follow-up intravascular ultrasound images for both main vessel (MV) and SB.

Multiobjective flux balancing using the NISE method for metabolic network analysis.

Flux balance analysis (FBA) is well acknowledged as an analysis tool of metabolic networks in the framework of metabolic engineering. However, FBA has a limitation for solving a multiobjective optimization problem which considers multiple conflicting objectives. In this study, we propose a novel multiobjective flux balance analysis method, which adapts the noninferior set estimation (NISE) method (Solanki et al.

A self-assembled fusion protein-based surface plasmon resonance biosensor for rapid diagnosis of severe acute respiratory syndrome.

A surface plasmon resonance (SPR)-based biosensor was developed for simple diagnosis of severe acute respiratory syndrome (SARS) using a protein created by genetically fusing gold binding polypeptides (GBPs) to a SARS coronaviral surface antigen (SCVme). The GBP domain of the fusion protein serves as an anchoring component onto the gold surface, exploiting the gold binding affinity of the domain, whereas the SCVme domain is a recognition element for anti-SCVme antibody, the target analyte in this study. SPR analysis indicated the fusion protein simply and strongly self-immobilized onto the gold surface, through GBP, without surface chemical modification, offering a stable and specific sensing platform for anti-SCVme detection.

In silico analysis of the effects of H2 and CO2 on the metabolism of a capnophilic bacterium Mannheimia succiniciproducens.

This study presents an in-depth study on the physiological behavior of Mannheimia succiniciproducens, a capnophilic bacterium and an efficient succinic acid producer, under varying gas conditions as H(2) and CO(2) play important roles in the production of succinic acid. Constraints-based flux analysis of the genome-scale metabolic model of M. succiniciproducens was performed to estimate the production patterns of several organic acids in response to varying H(2), CO(2), and glucose uptake rates.

Proteome-based physiological analysis of the metabolically engineered succinic acid producer Mannheimia succiniciproducens LPK7.

Using two-dimensional gel electrophoresis (2-DE) and mass spectrometry, the proteome of a metabolically engineered succinic acid-overproducing bacterium, Mannheimia succiniciproducens LPK7, was examined and compared with that of its wild type strain, MBEL55E, to elucidate the physiological and metabolic changes responsible for succinic acid overproduction and cell growth. Comparative proteomic studies clearly showed that the expression levels of enzymes involved in the ATP formation and consumption (AtpD, Ppa, SerS, ProS, Pnp, PotD, MalK, RbsB, and TbpA), pyruvate metabolism (AceF and Lpd), glycolysis (GapA, Pgk, Fba, and TpiA), and amino acid biosynthesis (Asd, DapA, DapD, Gdh, ArgD, and ArgG) varied significantly in the LPK7 strain compared with those in the MBEL55E strain. Based on the comparative proteome profiling, the formation of pyruvic acid, a newly formed byproduct in the engineered LPK7 strain, could be reduced by adding into the culture medium pantothenate and L: -cysteine, which serve as precursors of CoA biosynthesis.

Spore display using Bacillus thuringiensis exosporium protein InhA.

A new spore display method is presented that enables recombinant proteins to be displayed on the surface of Bacillus spores via fusion with InhA, an exosporium component of Bacillus thuringiensis. The green fluorescent protein and beta-galactosidase as model proteins were fused to the C-terminal region of InhA, respectively. The surface expression of the proteins on the spores was confirmed by flow cytometry, confocal laser scanning microscopy, measurement of the enzyme activity, and an immunogold electron microscopy analysis.

Metabolite-centric approaches for the discovery of antibacterials using genome-scale metabolic networks.

Development of genome-scale metabolic models and various constraints-based flux analyses have enabled more sophisticated examination of metabolism. Recently reported metabolite essentiality studies are also based on the constraints-based modeling, but approaches metabolism from a metabolite-centric perspective, providing synthetic lethal combination of reactions and clues for the rational discovery of antibacterials. In this study, metabolite essentiality analysis was applied to the genome-scale metabolic models of four microorganisms: Escherichia coli, Helicobacter pylori, Mycobacterium tuberculosis and Staphylococcus aureus.

Constraints-based genome-scale metabolic simulation for systems metabolic engineering.

Random mutagenesis and selection approaches used traditionally for the development of industrial strains have largely been complemented by metabolic engineering, which allows purposeful modification of metabolic and cellular characteristics by using recombinant DNA and other molecular biological techniques. As systems biology advances as a new paradigm of research thanks to the development of genome-scale computational tools and high-throughput experimental technologies including omics, systems metabolic engineering allowing modification of metabolic, regulatory and signaling networks of the cell at the systems-level is becoming possible. In silico genome-scale metabolic model and its simulation play increasingly important role in providing systematic strategies for metabolic engineering.

A well-ordered flower-like gold nanostructure for integrated sensors via surface-enhanced Raman scattering.

A controllable flower-like Au nanostructure array for surface-enhanced Raman scattering (SERS) was fabricated using the combined technique of the top-down approach of conventional photolithography and the bottom-up approach of electrodeposition. Au nanostructures with a mean roughness ranging from 5.1 to 49.

High-throughput identification of clinically important bacterial pathogens using DNA microarray.

Rapid and accurate detection of pathogenic bacteria is important for the treatment of patients with suitable antibiotics. Here we report the development of a diagnostic DNA microarray for the high-throughput identification of 39 pathogenic bacteria selected based on their high prevalence rate and/or difficulty of cultivation. The 23S ribosomal DNA and 16S-23S rDNA intergenic spacer region were used as target DNAs for pathogen detection.

Optimization and scale-up of succinic acid production by Mannheimia succiniciproducens LPK7.

The effects of culture conditions on succinic acid production and its possible scale-up have been studied. Mannheimia succiniciproducens LPK7, engineered for enhanced production of succinic acid and reduced by-product secretion, was used for the experiments. Mannheimia succiniciproducens LPK7 is a knock-out strain of wild type deficient in the ldhA, pflB, and pta-ackA genes, and is derived from Mannheimia succiniciproducens MBEL55E.

Functional expression of SAV3818, a putative TetR-family transcriptional regulatory gene from Streptomyces avermitilis, stimulates antibiotic production in Streptomyces species.

Avermectin and its analogs are major commercial antiparasitic agents in the fields of animal health, agriculture, and human infections. Previously, comparative transcriptome analysis between the low-producer S. avermitilis ATCC31267 and the high-producer S.

Cytokine expression and cancer detection.

The purpose of the present article is to review the links between cancer and cytokine expression. Cytokines are proteins produced by cells that act as mediators of cell-to-cell communication. Many recent reports indicate that uncontrolled, constitutive cytokine expression in tumors contributes to tumor growth, tumor progression and immuno-suppression, activities that dexceed their usual functions in host anti-tumor response.

Development of a whole-cell biosensor by cell surface display of a gold-binding polypeptide on the gold surface.

Cell surface display was used as a strategy to display the gold-binding polypeptide (GBP) fusion protein on the surface of Escherichia coli, and consequently to immobilize the cells on the gold surface. The DNA encoding the GBP was fused to the truncated fadL gene and was expressed by the tac promoter. For the display of the core streptavidin (cSA) of Streptomyces avidinii, the cSA gene was fused to the truncated oprF gene.

Microarray of DNA-protein complexes on poly-3-hydroxybutyrate surface for pathogen detection.

A novel strategy was developed for the specific immobilization of DNA probes on poly-3-hydroxybutyrate (PHB) surface by using the substrate-binding domain (SBD) of PHB depolymerase as an active binding motif. To demonstrate whether this method can be used for the detection of clinical pathogens, the pathogen-specific biotin-labeled DNA probes were immobilized via core streptavidin (cSA) fused to the SBD. The pathogen-specific 15-mer oligonucleotide probes were designed for four model pathogens, while the target DNAs were prepared by PCR using universal primers.

Succinic acid production by Anaerobiospirillum succiniciproducens ATCC 29305 growing on galactose, galactose/glucose, and galactose/lactose.

Succinic acid-producing Anaerobiospirillum succiniciproducens was anaerobically grown on galactose, galactose/glucose, or galactose/lactose in order to study its galactose fermentation. Unlike a previous report, A. succiniciproducens was found to efficiently metabolize galactose as the sole carbon source at a rate of 2.

Characterizing Escherichia coli DH5alpha growth and metabolism in a complex medium using genome-scale flux analysis.

Genome-scale flux analysis of Escherichia coli DH5alpha growth in a complex medium was performed to investigate the relationship between the uptake of various nutrients and their metabolic outcomes. During the exponential growth phase, we observed a sequential consumption order of serine, aspartate and glutamate in the complex medium as well as the complete consumption of key carbohydrate nutrients, glucose and trehalose. Based on the consumption and production rates of the measured metabolites, constraints-based flux analysis of a genome-scale E.

Microbial small heat shock proteins and their use in biotechnology.

Small heat shock proteins (sHsps) exist in almost all organisms. Most organisms have more than one sHsp, but their number can be as high as 65, as found in the eukaryote, Vitis vinifera. The function of sHsps is well-known; they confer thermotolerance to cellular cultures and proteins in cellular extracts during prolonged incubations at elevated temperatures.

Metabolic engineering of microorganisms: general strategies and drug production.

Many drugs and drug precursors found in natural organisms are rather difficult to synthesize chemically and to extract in large amounts. Metabolic engineering is playing an increasingly important role in the production of these drugs and drug precursors. This is typically achieved by establishing new metabolic pathways leading to the product formation, and enforcing or removing the existing metabolic pathways toward enhanced product formation.

Towards systems metabolic engineering of microorganisms for amino acid production.

Microorganisms capable of efficient production of amino acids have traditionally been developed by random mutation and selection method, which might cause unwanted physiological changes in cellular metabolism. Rational genome-wide metabolic engineering based on systems and synthetic biology tools, which is termed 'systems metabolic engineering', is rising as an alternative to overcome these problems. Recently, several amino acid producers have been successfully developed by systems metabolic engineering, where the metabolic engineering procedures were performed within a systems biology framework, and entire metabolic networks, including complex regulatory circuits, were engineered in an integrated manner.

Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network.

To understand the metabolic characteristics of Clostridium acetobutylicum and to examine the potential for enhanced butanol production, we reconstructed the genome-scale metabolic network from its annotated genomic sequence and analyzed strategies to improve its butanol production. The generated reconstructed network consists of 502 reactions and 479 metabolites and was used as the basis for an in silico model that could compute metabolic and growth performance for comparison with fermentation data. The in silico model successfully predicted metabolic fluxes during the acidogenic phase using classical flux balance analysis.

Proteome-based identification of fusion partner for high-level extracellular production of recombinant proteins in Escherichia coli.

Extracellular production of recombinant proteins in Escherichia coli has several advantages over cytoplasmic or periplasmic production. However, nonpathogenic laboratory strains of E. coli generally excrete only trace amounts of proteins into the culture medium under normal growth conditions.