Recent trends in metabolic engineering of microorganisms for the production of advanced biofuels.

As climate change has become one of the major global risks, our heavy dependence on petroleum-derived fuels has received much public attention. To solve such problems, production of sustainable fuels has been intensively studied over the past years. Thanks to recent advances in synthetic biology and metabolic engineering technologies, bio-based platforms for advanced biofuels production have been developed using various microorganisms.

Universality classes of the generalized epidemic process on random networks.

We present a self-contained discussion of the universality classes of the generalized epidemic process (GEP) on Poisson random networks, which is a simple model of social contagions with cooperative effects. These effects lead to rich phase transitional behaviors that include continuous and discontinuous transitions with tricriticality in between. With the help of a comprehensive finite-size scaling theory, we numerically confirm static and dynamic scaling behaviors of the GEP near continuous phase transitions and at tricriticality, which verifies the field-theoretical results of previous studies.

One-step fermentative production of poly(lactate-co-glycolate) from carbohydrates in Escherichia coli.

Poly(lactate-co-glycolate) (PLGA) is a widely used biodegradable and biocompatible synthetic polymer. Here we report one-step fermentative production of PLGA in engineered Escherichia coli harboring an evolved polyhydroxyalkanoate (PHA) synthase that polymerizes D-lactyl-CoA and glycolyl-CoA into PLGA. Introduction of the Dahms pathway enables production of glycolate from xylose.

Advances in microbial biosynthesis of metal nanoparticles.

Metal nanoparticles are garnering considerable attention owing to their high potential for use in various applications in the material, electronics, and energy industries. Recent research efforts have focused on the biosynthesis of metal nanomaterials using microorganisms rather than traditional chemical synthesis methods. Microorganisms have evolved to possess molecular machineries for detoxifying heavy metals, mainly by employing metal-binding proteins and peptides.

Development of rice bran treatment process and its use for the synthesis of polyhydroxyalkanoates from rice bran hydrolysate solution.

Rice bran treatment process for the production of 43.7 kg of hydrolysate solution containing 24.41 g/L of glucose and small amount of fructose from 5 kg of rice bran was developed and employed to produce polyhydroxyalkanoates in recombinant Escherichia coli and Ralstonia eutropha strains.

Effects of junctional correlations in the totally asymmetric simple exclusion process on random regular networks.

We investigate the totally asymmetric simple exclusion process on closed and directed random regular networks, which is a simple model of active transport in the one-dimensional segments coupled by junctions. By a pair mean-field theory and detailed numerical analyses, it is found that the correlations at junctions induce two notable deviations from the simple mean-field theory, which neglects these correlations: (1) the narrower range of particle density for phase coexistence and (2) the algebraic decay of density profile with exponent 1/2 even outside the maximal-current phase. We show that these anomalies are attributable to the effective slow bonds formed by the network junctions.

A large-area hemispherical perforated bead microarray for monitoring bead based aptamer and target protein interaction.

Herein, we present a large-area 3D hemispherical perforated microwell structure for a bead based bioassay. Such a unique microstructure enables us to perform the rapid and stable localization of the beads at the single bead level and the facile manipulation of the bead capture and retrieval with high speed and efficiency. The fabrication process mainly consisted of three steps: the convex micropatterned nickel (Ni) mold production from the concave micropatterned silicon (Si) wafer, hot embossing on the polymer matrix to generate the concave micropattened acrylate sheet, and reactive ion etching to make the bottom holes.

Large-scale quantitative analysis of painting arts.

Scientists have made efforts to understand the beauty of painting art in their own languages. As digital image acquisition of painting arts has made rapid progress, researchers have come to a point where it is possible to perform statistical analysis of a large-scale database of artistic paints to make a bridge between art and science. Using digital image processing techniques, we investigate three quantitative measures of images - the usage of individual colors, the variety of colors, and the roughness of the brightness.

Combination of multiplex reverse-transcription loop-mediated isothermal amplification with an immunochromatographic strip for subtyping influenza A virus.

Considering the fatal human victims and economic loss by the annual epidemic influenza virus, the development of a rapid and convenient genetic analysis methodology is demanding for timely on-site pathogen detection. In this study, we utilized reverse-transcription loop-mediated isothermal amplification (RT-LAMP) for multiplex target gene amplification, and the resultant amplicons were analyzed on the immunochromatographic strip (ICS) for subtyping influenza A virus. Through the optimized primer design, reaction temperature and time, and concentration of enzymes (Bst DNA polymerase and AMV reverse transcriptase) and dNTP, the HA (H1, H3, and H5 gene) and conserved M gene were amplified.

Generalized epidemic process on modular networks.

Social reinforcement and modular structure are two salient features observed in the spreading of behavior through social contacts. In order to investigate the interplay between these two features, we study the generalized epidemic process on modular networks with equal-sized finite communities and adjustable modularity. Using the analytical approach originally applied to clique-based random networks, we show that the system exhibits a bond-percolation type continuous phase transition for weak social reinforcement, whereas a discontinuous phase transition occurs for sufficiently strong social reinforcement.

Dual role of blue luminescent MoS2 quantum dots in fluorescence resonance energy transfer phenomenon.

Homogeneous blue luminescent MoS2 quantum dots are fabricated by using a lithium intercalation method from MoS2 nanoparticles, and the unique blue photoluminescence property is utilized in the Alexa Fluor 430-dsDNA-MoS2 FRET system, demonstrating the dual function of MoS2 quantum dots as a donor and an acceptor.

Multiplex electrical detection of avian influenza and human immunodeficiency virus with an underlap-embedded silicon nanowire field-effect transistor.

The label-free electrical detection of the binding of antibodies and antigens of avian influenza (AI) and human immunodeficiency (HIV) viruses is demonstrated through an underlap-embedded silicon (Si) nanowire field-effect transistor. The proposed sensor was fabricated on a silicon bulk wafer by a top-down process. Specifically, a Si nanowire was fabricated by a combined isotropic and anisotropic patterning technique, which is one route plasma etching process.

Effect of chemical and structural feature of graphene on surface enhanced Raman scattering.

Graphene nanomaterial has been reported as a chemical mechanism based surface-enhanced Raman scattering (SERS) substrate which has advantages of accuracy in the peak assignment with less peak shift and broader choice in the laser sources. Here we present a systematic study to investigate the effect of graphene oxide (GO), reduced graphene oxide (RGO), two- and three-dimensional (2D and 3D) graphene structure as well as their nanocomposites with gold nanoparticle (Au NP) as a SERS substrate to detect Rhodamine 6G (R6G) molecules. Compared with a glass substrate, the Raman signals were enhanced by 1.

Circumferential alignment of vascular smooth muscle cells in a circular microfluidic channel.

The circumferential alignment of human aortic smooth muscle cells (HASMCs) in an orthogonally micropatterned circular microfluidic channel is reported to form an in vivo-like smooth muscle cell layer. To construct a biomimetic smooth muscle cell layer which is aligned perpendicular to the axis of blood vessel, a half-circular polydimethylsiloxane (PDMS) microchannel is first fabricated by soft lithography using a convex PDMS mold. Then, the orthogonally microwrinkle patterns are generated inside the half-circular microchannel by a strain responsive wrinkling method.

Metabolic engineering of Escherichia coli for biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) from glucose.

The Escherichia coli XL1-blue strain was metabolically engineered to synthesize poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] through 2-ketobutyrate, which is generated via citramalate pathway, as a precursor for propionyl-CoA. Two different metabolic pathways were examined for the synthesis of propionyl-CoA from 2-ketobutyrate. The first pathway is composed of the Dickeya dadantii 3937 2-ketobutyrate oxidase or the E.

Synthesis of a 3D graphite microball using a microfluidic droplet generator and its polymer composite with core-shell structure.

Spherical 3D graphite microballs (3D GMs) and their nanohybrids (3D GM-Fe3O4 nanoparticles) were synthesized by using a microfluidic droplet generator and a thermal evaporation-induced capillary compression method. Using the 3D GM-Fe3O4 nanoparticle as a support for polymerization, 3D GM-polypyrrole composites were produced with a unique core-shell structure.

A microbead-incorporated centrifugal sample pretreatment microdevice.

In this study, we present a novel bead-incorporated centrifugal sample pretreatment microdevice to purify influenza A H3N2 viral RNA. Simple revolution per minute (RPM) control can lead to RNA capture on a bead-bed, and the sequential loading of a washing solution and an elution solution. Tetraethoxy orthosilicate (TEOS)-treated glass microbeads were utilized as a capture matrix.

Facile synthetic method for pristine graphene quantum dots and graphene oxide quantum dots: origin of blue and green luminescence.

Pristine graphene quantum dots and graphene oxide quantum dots are synthesized by chemical exfoliation from the graphite nanoparticles with high uniformity in terms of shape (circle), size (less than 4 nm), and thickness (monolayer). The origin of the blue and green photoluminescence of GQDs and GOQDs is attributed to intrinsic and extrinsic energy states, respectively.

Fabrication of a circular PDMS microchannel for constructing a three-dimensional endothelial cell layer.

We describe a simple and efficient fabrication method for generating microfluidic channels with a circular cross-sectional geometry by exploiting the reflow phenomenon of a thick positive photoresist. Initial rectangular shaped positive photoresist micropatterns on a silicon wafer, which were fabricated by a conventional photolithography process, were converted into a half-circular shape by tuning the temperature to around 105 °C. Through optimization of the reflow conditions, we could obtain a perfect circular micropattern of the positive photoresist, and control the diameter in a range from 100 to 400 μm.

Photoluminescent graphene oxide microarray for multiplex heavy metal ion analysis.

An aptamer-linked graphene oxide (GO) microarray is synthesized for multiplex heavy metal ion detection. Fluorescent nanosized GO sheets are micropatterned, and specific aptamers targeting Ag(+) and Hg(2+) are immobilized on the GO array. Upon capture of the target heavy metal ions, electron transfer occurs between the GO (donors) and the heavy metal ions (acceptors), leading to fluorescence quenching of the GO.

Ultrafast rotary PCR system for multiple influenza viral RNA detection.

We presented a novel platform for an ultrafast PCR system, called the Rotary PCR Genetic Analyzer, which incorporates a thermal block and resistive temperature detector (RTD) for thermal cycling control, a disposable PCR microchip, and a stepper motor. The influenza viral RNAs from H3N2, H5N1, and H1N1 were simultaneously identified with high sensitivity and speed.

Three-dimensional graphene oxide nanostructure for fast and efficient water-soluble dye removal.

In this study, we demonstrated the potential of graphene nanomaterials as environmental pollutant adsorbents by utilizing the characteristics of ultralarge surface area and strong π-π interaction on the surface. We generated a three-dimensional (3D) graphene oxide sponge (GO sponge) from a GO suspension through a simple centrifugal vacuum evaporation method, and used them to remove both the methylene blue (MB) and methyl violet (MV) dyes which are main contaminants from the dye manufacturing and textile finishing. The efficiency and speed of dye adsorption on a GO sponge was investigated under various parameters such as contact time, stirring speed, temperature, and pH.

PCR-free digital minisatellite tandem repeat genotyping.

We demonstrated a proof-of-concept for novel minisatellite tandem repeat typing, called PCR-free digital VNTR (variable number tandem repeat) typing, which is composed of three steps: a ligation reaction instead of PCR thermal cycling, magnetic bead-based solid-phase capture for purification, and an elongated sample stacking microcapillary electrophoresis (μCE) for sensitive digital coding of repeat number. We designed a 16-bp fluorescently labeled ligation probe which is complementary to a repeat unit of a biotinylated synthetic template mimicking the human D1S80 VNTR locus and is randomly hybridized with the minisatellite tandem repeats. A quick isothermal ligation reaction was followed to link the adjacent ligation probes on the DNA templates, and then the ligated products were purified by streptavidin-coated magnetic beads.

Genome-wide identification of the subcellular localization of the Escherichia coli B proteome using experimental and computational methods.

Escherichia coli K-12 and B strains have most widely been employed for scientific studies as well as industrial applications. Recently, the complete genome sequences of two representative descendants of E. coli B strains, REL606 and BL21(DE3), have been determined.