Complete Genome Sequences of Four Halophilic Thermus thermophilus Strains Isolated from Arima Hot Spring in Japan.

We isolated four Thermus thermophilus strains from Arima Hot Spring in Japan. Complete genome sequencing revealed that they showed average nucleotide identities of ≥99.21% to each other and to strains previously isolated from the same spot, but of ≤97.86% to strains from geographically different spots in Japan, reflecting habitat-specific genomic conservation.

Tough, permeable and biocompatible microfluidic devices formed through the buckling delamination of soft hydrogel films.

Microchannels in soft materials play an important role in developing movable, deformable, and biocompatible fluidic systems for applications in various fields. Intensively investigated approaches to create microscale channel architectures use mechanical instability in soft materials, which can provide intricate yet ordered architectures with low cost and high throughput. Here, for microchannel fabrication, we demonstrate the use of swelling-driven buckle delamination of hydrogels, which is a mechanical instability pattern found in compressed film/substrate layer composites. By spatially controlling interfacial bonding between a thin polyacrylamide (PAAm) gel film and glass substrate, swelling-driven compressive stress induces buckle delamination at programmed positions, resulting in the formation of continuous hollow paths as microchannels. Connecting flow tubes with a 3D-printed connecter provides a deformable microfluidic device, enabling pressure-driven flows without leakage from the connecter and rupture of the channels. Furthermore, by stacking less-swellable bulk gels on the device, we obtained a tough, permeable, and biocompatible microfluidic device. Finally, we performed a cell culture on the device and chemical stimulation to cells through the diffusion of molecules from the microchannels. The results of this work shed light on designing pressure sensitive/resistant microfluidic systems based on diverse hydrogels with intricate 3D morphologies and will be useful for applications in the fields of bioanalysis, biomimetics, tissue engineering, and cell biology.

Graphene-Based FRET Aptasensors.

Graphene-based FRET aptasensors can be realized only by unique combinations of aptamer that can be freely functionalized by chemical modification, and graphene/graphene oxide that works as an excellent fluorescence acceptor at the same time as aptamer adsorbates. This review describes the principles of the sensor, several applications to microchannel devices, improvement of the sensing performance by molecular design of the aptamer and remarks on future prospects based on an introduction of recent works and achievements, including the author's paper. The sensor employs DNA modified with graphene/graphene oxide at the terminal as the molecular probe. This system is supported by the excellent property of DNA that does not lose the molecular recognition ability even due to a chemical modification at the terminal. I hope that this review will be useful for developing research on higher performance of graphene aptasensors in the future.

Dopamine detection on activated reaction field consisting of graphene-integrated silicon photonic cavity.

Graphene is widely recognized as an outstanding and multi-functional material in various application fields such as electronics, photonics, mechanics, and life sciences. We propose a neurotransmitter sensor with ultra-small volume for detecting the photonic light-matter response. Such detection can be achieved using surface-activated monolayer graphene sheets and CMOS-compatible silicon-photonic circuits. Patterned pieces of CVD-grown graphene are integrated on the top of a silicon micro-ring resonator, which induce the adsorption of catecholamine molecules originated from the π-stacking effect. We used dopamine to demonstrate such detection and examine the sensitivity of graphene-dopamine coupling. To avoid high optical insertion loss and degradation of resonance characteristics caused by a graphene's extremely high optical absorption coefficient in the near infrared region, a ring resonator with adjusted coupling design is used to compensate for the drawbacks. Owing to the advanced nano-sensing platform and measurement system, an activated graphene-sensing surface of only ∼30 µm2/ch enables π coupling to dopamine with enough sensitivity to detect less than 10-µM solution concentration. The detection mechanism through the surface reaction is also verified by optical simulation and atomic force microscopy measurement, revealing that the flowing dopamine molecules can only occupy the outermost surface of graphene. We expect this sensor to contribute to the development of an innovative label-free and disposable bio-sensing platform with accurate, sensitive, and fast response.

Dynamic Creation of 3D Hydrogel Architectures via Selective Swelling Programmed by Interfacial Bonding.

The topological features of material surfaces are crucial to the emergence of functions based on characteristic architectures. Among them, the combination of surface architectures and soft materials, which are highly deformable and flexible, has great potential as regards developing functional materials toward providing/enhancing advanced functions such as switchability and variability. Therefore, a simple yet versatile method for creating three-dimensional (3D) architectures based on soft materials is strongly required. In this study, hydrogels are selected as the soft materials and hydrogel film/rigid substrate layer composites are fabricated to obtain a 3D hydrogel architecture based on swelling instability. When a hydrogel film weakly attached to a rigid substrate is exposed to water, swelling-driven compressive stress induces buckle-delamination of the film from the substrate. Utilizing the chemical modification of a rigid substrate and a conventional photolithography technique, the delamination location is successfully controlled, resulting in a high-aspect-ratio folding architecture at an arbitrary position. In addition, we systematically designed the delamination geometry and chemically tuned the swelling ratio of the hydrogel, leading to the discovery of several new morphology transitions and relationships between the morphologies and the controllable parameters. This work provides a new approach to fabricating highly programmable 3D architectures of soft materials.

Graphene-based neuron encapsulation with controlled axonal outgrowth.

Neuronal constructs with tuneable 3D geometry can contribute greatly to the construction of brain-like functional tissues for transplantable grafts and robust experimental models. In this study, we propose a self-folding graphene/polymer bilayer film that forms a micro-roll for neuron encapsulation, and highlight the importance of employing pores on the micro-roll to allow neurons to interact with their surroundings. The micro-patterns and varied thicknesses of the bilayer provide control over the 3D geometries of the micro-roll. The pores facilitate the diffusion of reagents, resulting in the adequate loading of probes for imaging and the successful stimulation of the encapsulated neurons. Moreover, the encapsulated neurons inside the micro-roll are functionally integrated into surrounding neuronal networks by extending their axons through the pores. Thus, our method for encapsulating neurons with a porous graphene-laden film allows the construction of precisely shaped neuronal tissues that interact with their surroundings. We believe that the method will open a new avenue for the reconstruction of functional neuronal tissues and is potentially applicable to other self-folding bilayers.

Self-Folded Three-Dimensional Graphene with a Tunable Shape and Conductivity.

Three-dimensional (3D) graphene architectures are of great interest as applications in flexible electronics and biointerfaces. In this study, we demonstrate the facile formation of predetermined 3D polymeric microstructures simply by transferring monolayer graphene. The graphene adheres to the surface of polymeric films via noncovalent π-π stacking bonding and induces a sloped internal strain, leading to the self-rolling of 3D microscale architectures. Micropatterns and varied thicknesses of the 2D films prior to the self-rolling allows for control over the resulting 3D geometries. The strain then present on the hexagonal unit cell of the graphene produces a nonlinear electrical conductivity across the device. The driving force behind the self-folding process arises from the reconfiguration of the molecules within the crystalline materials. We believe that this effective and versatile way of realizing a 3D graphene structure is potentially applicable to alternative 2D layered materials as well as other flexible polymeric templates.

Capturing the Freeze-Drying Dynamics of NaCl Nanoparticles Using THz Spectroscopy.

Sodium chloride (NaCl) aqueous solution becomes NaCl hydrate, NaCl·2H2O, at low temperature, which is different from potassium chloride and is a typical complex model for studying the freeze-drying process in foods and pharmaceuticals. Here, we detected unit-cell-sized NaCl particles in ice as precursor substances of NaCl·2H2O during freezing of NaCl solution by using terahertz (THz) spectroscopy. In the freezing process, Na+ and Cl- ions form two types of metastable unit-cell-sized NaCl particles on the pathway to the well-known NaCl·2H2O crystal production, which are not listed in the phase diagram of freezing of NaCl solution but have absorption peaks in THz spectra. This finding of single unit-cell-sized particles signifies the importance of studying the freeze-drying process in-depth and offers a new possibility for the development of freeze-drying technology for the manufacture of nanometer-sized particles such as ultrafine pharmaceutical powders, which more readily dissolve in water.

Cell Assembly in Self-foldable Multi-layered Soft Micro-rolls.

Multi-layered thin films with heterogeneous mechanical properties can be spontaneously transformed to realise various three-dimensional (3D) geometries. Here, we describe micro-patterned all-polymer films called micro-rolls that we use for encapsulating, manipulating, and observing adherent cells in vitro. The micro-rolls are formed of twin-layered films consisting of two polymers with different levels of mechanical stiffness; therefore they can be fabricated by using the strain engineering and a self-folding rolling process. By controlling the strain of the films geometrically, we can achieve 3D tubular architectures with controllable diameters. Integration with a batch release of sacrificial hydrogel layers provides a high yield and the biocompatibility of the micro-rolls with any length in the release process without cytotoxicity. Thus, the multiple cells can be wrapped in individual micro-rolls and artificially reconstructed into hollow or fibre-shaped cellular 3D constructs that possess the intrinsic morphologies and functions of living tissues. This system can potentially provide 3D bio-interfaces such as those needed for reconstruction and assembly of functional tissues and implantable tissue grafts.

Cu(In,Ga)Se2 Solar Cells with Amorphous In2O3-Based Front Contact Layers.

Amorphous (a-) In2O3-based front contact layers composed of transparent conducting oxide (TCO) and transparent oxide semiconductor (TOS) layers were proved to be effective in enhancing the short-circuit current density (Jsc) of Cu(In,Ga)Se2 (CIGS) solar cells with a glass/Mo/CIGS/CdS/TOS/TCO structure, while maintaining high fill factor (FF) and open-circuit voltage (Voc). An n-type a-In-Ga-Zn-O layer was introduced between the CdS and TCO layers. Unlike unintentionally doped ZnO broadly used as TOS layers in CIGS solar cells, the grain-boundary(GB)-free amorphous structure of the a-In-Ga-Zn-O layers allowed high electron mobility with superior control over the carrier density (N). High FF and Voc values were achieved in solar cells containing a-In-Ga-Zn-O layers with N values broadly ranging from 2 × 1015 to 3 × 1018 cm-3. The decrease in FF and Voc produced by the electronic inhomogeneity of solar cells was mitigated by controlling the series resistance within the TOS layer of CIGS solar cells. In addition, a-In2O3:H and a-In-Zn-O layers exhibited higher electron mobilities than the ZnO:Al layers conventionally used as TCO layers in CIGS solar cells. The In2O3-based layers exhibited lower free carrier absorption while maintaining similar sheet resistance than ZnO:Al. The TCO and TOS materials and their combinations did not significantly change the Voc of the CIGS solar cells and the mini-modules.

Self-propelled ion gel at air-water interface.

We report on a self-propelled gel using ionic liquid as a new type of self-propellant that generates a powerful and durable motion at an air-water interface. The gel is composed of 1-ethyl-3-methylimidazolium-bis(trifluoromethylsulfonyl)imide (EMIM-TFSI) and poly(vinylidene fluoride-co-hexafluoropropylene) (P(VDF-co-HFP)). A long rectangular ion gel piece placed on the interface shows rapid rotation motion with maximum frequency close to 10 Hz, corresponding to the velocity over 300 mms-1 at an outmost end of the piece. The rotation continues for ca. 102 s, followed by a reciprocating motion (<~103 s) and a nonlinear motion in long-time observations (>~103 s). The behaviours can be explained by the model considering elution of EMIM-TFSI to the air-water interface, rapid dissolution into water, and slow diffusion in an inhomogeneous polymer gel network. Because the self-propellants are promptly removed from the interface by dissolution, durable self-propelled motions are observed also at limited interface areas close in size to the gel pieces. A variety of motions are induced in such systems where the degree of freedom in motion is limited. As the ion gel possesses formability and processability, it is also advantageous for practical applications. We demonstrate that the gel does work as an engine.

Raman Spectroscopy of Pharmaceutical Cocrystals in Nanosized Pores of Mesoporous Silica.

The Raman spectroscopy of pharmaceutical cocrystals based on caffeine and oxalic acid in nanosized pores of mesoporous silica has been demonstrated at various molar amounts. The Raman peak shifts of caffeine molecules express the existence of pharmaceutical cocrystals in mesoporous silica. The molar amount dependence of the peak shifts describes that caffeine and oxalic acid cocrystallized on the surface of the nanosized pores and piled up layer by layer. This is the first report that shows the Raman spectroscopy is a powerful tool to observe the synthesis of pharmaceutical cocrystals incorporated in the nanosized pores of mesoporous silica. The results indicate a way to control the size of cocrystals on a nanometer scale, which will provide higher bioavailability of pharmaceuticals.

On-chip FRET Graphene Oxide Aptasensor: Quantitative Evaluation of Enhanced Sensitivity by Aptamer with a Double-stranded DNA Spacer.

We propose a molecular design for a biomolecular probe to realize an on-chip graphene oxide (GO) aptasensor with enhanced sensitivity. Here, GO works as an excellent acceptor for fluorescence resonance energy transfer. We inserted a rigid double-stranded DNA as a spacer between the GO surface and the aptamer sequence to extend the distance between a fluorescence dye and the GO surface during molecular recognition. We examined the dependence of the sensitivity on the length of the spacer quantitatively by using a 2×2 linear-array aptasensor. We used the modified aptamer with 10 and 30 base pair (bp) double-stranded DNA spacers. The signal with a 30bp-spacer was about twice as strong that with a 10bp-spacer as regards both thrombin and prostate specific antigen detections. The improvement in the sensitivity was supported by a model calculation that estimated the effect of spacer length on fluorescence recovery efficiency.

On-chip graphene oxide aptasensor for multiple protein detection.

The versatility of an on-chip graphene oxide (GO) aptasensor was successfully confirmed by the detection of three different proteins, namely, thrombin (TB), prostate specific antigen (PSA), and hemagglutinin (HA), simply by changing the aptamers but with the sensor composition remaining the same. The results indicate that both DNA and RNA aptamers immobilized on the GO surface are sufficiently active to realize an on-chip aptasensor. Molecular selectivity and concentration dependence were investigated in relation to TB and PSA detection by using a dual, triple, and quintuple microchannel configuration. The multiple target detection of TB and PSA on a single chip was also demonstrated by using a 2×3 linear-array GO aptasensor. This work enables us to apply this sensor to the development of a multicomponent analysis system for a wide variety of targets by choosing appropriate aptamers.

Molecular design for enhanced sensitivity of a FRET aptasensor built on the graphene oxide surface.

We designed a biomolecular probe for highly sensitive protein detection by modifying an aptamer with a DNA spacer. The spacer controls the distance between a fluorescence dye and a quencher, which is crucial for FRET-based sensors. We successfully demonstrated an improvement in the sensitivity of an on-chip graphene oxide aptasensor.

Increasing the electron-transfer ability of Cyanidioschyzon merolae ferredoxin by a one-point mutation--a high resolution and Fe-SAD phasing crystal structure analysis of the Asp58Asn mutant.

Cyanidioschyzon merolae (Cm) is a single cell red algae that grows in rather thermophilic (40-50°C) and acidic (pH 1-3) conditions. Ferredoxin (Fd) was purified from this algae and characterized as a plant-type [2Fe-2S] Fd by physicochemical techniques. A high resolution (0.97Å) three-dimensional structure of the CmFd D58N mutant molecule has been determined using the Fe-SAD phasing method to clarify the precise position of the Asn58 amide, as this substitution increases the electron-transfer ability relative to wild-type CmFd by a factor of 1.5. The crystal structure reveals an electro-positive surface surrounding Asn58 that may interact with ferredoxin NADP(+) reductase or cytochrome c.

Graphene-modified interdigitated array electrode: fabrication, characterization, and electrochemical immunoassay application.

We have developed a new procedure for fabricating interdigitated array gold electrodes (Au-IDA) modified with reduced graphene oxide (rGO). In this procedure, we coated the gold surface of the micrometer order electrodes with graphene oxide (GO) prior to the reduction and the lift-off processes to avoid short-circuiting the pair of electrodes by conductive rGO flakes after the reduction. We then studied the basic electrochemical activity of the prepared electrodes, rGO/Au-IDA, mainly on p-aminophenol (pAP), because pAP is a good probe for an electrochemical immunoassay. The voltammograms showed that denser rGO provides better electrode reactivity for pAP. We confirmed that redox cycling between the anode and cathode at the rGO/Au-IDA was established, which yields more sensitive detection than with a single electrode. As one application of the electrochemical immunoassay using the rGO/Au-IDA, we demonstrated the quantitative detection of cortisol, a stress marker, at levels found in human saliva.

Chemical mapping of pharmaceutical cocrystals using terahertz spectroscopic imaging.

Terahertz (THz) spectroscopic imaging is a promising technique for distinguishing pharmaceuticals of similar molecular composition but differing crystal structures. Physicochemical properties, for instance bioavailability, are manipulated by altering a drug's crystal structure through methods such as cocrystallization. Cocrystals are molecular complexes having crystal structures different from those of their pure components. A technique for identifying the two-dimensional distribution of these alternate forms is required. Here we present the first demonstration of THz spectroscopic imaging of cocrystals. THz spectra of caffeine-oxalic acid cocrystal measured at low temperature exhibit sharp peaks, enabling us to visualize the cocrystal distribution in nonuniform tablets. The cocrystal distribution was clearly identified using THz spectroscopic data, and the cocrystal concentration was calculated with 0.3-1.3% w/w error from the known total concentration. From this result, THz spectroscopy allows quantitative chemical mapping of cocrystals and offers researchers and drug developers a new analytical tool.

Protein recognition on a single graphene oxide surface fixed on a solid support.

We study protein recognition on a graphene oxide (GO) surface using a single GO piece fixed on a solid support. The GO surface is modified by newly designed processes using pyrene as a linker to an sp2 domain in the GO, an aptamer for thrombin recognition, and a probe dye for fluorescence detection. In this system, the dye probe fluorescence, which was initially quenched by GO, is recovered when the aptamer recognizes the corresponding protein. We demonstrate the label-free and selective protein recognition for thrombin. The elementary processes of protein recognition are observed directly with a confocal laser scanning microscope and an atomic force microscope using an identical piece of GO. They indicate that proteins are recognized homogeneously on the modified GO surface. We also show that the recognition system can be installed and operated in microchannel devices.