Quantitative analysis of DNA with single-molecule sequencing

Cancer can be diagnosed by identifying DNA and microRNA base sequences that have the same base length yet differ in a few base sequences, if the abundance ratios of these slightly deviant base sequences can be determined. However, such quantitative analyses cannot be performed using the current DNA sequencers. Here we determine entire base sequences of four types of DNA corresponding to the let-7 microRNA, which is a 22-base cancer marker. We record the single-molecule conductances of the base molecules using current-tunneling measurements. In addition, we count the numbers of molecules in a solution to determine the abundance ratios of two DNA strands that differ by a single base sequence.

Measuring Single-Molecule Conductance at An Ultra-Low Molecular Concentration in Vacuum

We report on systematic investigation of single-molecule detection mechanisms in break junction experiments in vacuum. We found molecular feature in the conductance traces at an extremely low concentration of molecules of 10 nM. This was attributed to condensation of the molecular solution on the junction surface upon evaporation of the solvent during evacuation. Furthermore, statistical analyses of the temporal dependence of molecular junction formation probabilities suggested accumulation effects of the contact mechanics to concentrate molecules absorbed on a remote area to the tunneling current sensing zone, which also contributed to the capability of molecular detections at the low concentration condition. The present findings can be used as a useful guide to implement break junction measurements for studying electron and heat transport through single molecules in vacuum.

Identification of patterns of factors preceding severe or life-threatening asthma exacerbations in a nationwide study

BACKGROUND

Reducing near-fatal asthma exacerbations is a critical problem in asthma management.

OBJECTIVES

To determine patterns of factors preceding asthma exacerbations in a real-world setting.

METHODS

In a nationwide prospective study of 190 patients who had experienced near-fatal asthma exacerbation, cluster analysis was performed using asthma symptoms over the 2-week period before admission.

RESULTS

Three distinct clusters of symptoms were defined employing the self-reporting of a visual analogue scale. Cluster A (42.1%): rapid worsening within 7.4 hours from moderate attack to admission, young to middle-aged patients with low Body mass index and tendency to depression who had stopped anti-asthma medications, smoked, and hypersensitive to environmental triggers and furred pets. Cluster B (40.0%): fairly rapid worsening within 48 hours, mostly middle-aged and older, relatively good inhaled corticosteroid (ICS) or ICS/long-acting beta-agonist (LABA) compliance, and low perception of dyspnea. Cluster C (17.9%): slow worsening over 10 days before admission, high perception of dyspnea, smokers, and chronic daily mild-moderate symptoms. There were no differences in overuse of short-acting beta-agonists, baseline asthma severity, or outcomes after admission for patients in these 3 clusters.

CONCLUSION

To reduce severe or life-threatening asthma exacerbation, personalized asthma management plans should be considered for each cluster. Improvement of ICS and ICS/LABA compliance and cessation of smoking are important in cluster A. To compensate for low perception of dyspnea, asthma monitoring of peak expiratory flow rate and/or exhaled nitric oxide would be useful for patients in cluster B. Avoidance of environmental triggers, increase usual therapy, or new anti-type 2 response-targeted therapies should be considered for cluster C.

Anti-platelet effects of chalcones from Angelica keiskei Koidzumi (Ashitaba) in vivo

Angelica keiskei Koidzumi (Ashitaba) is a traditional folk medicine that is also regarded in Japan as a health food with potential antithrombotic properties. The ability of the major chalcones, xanthoangelol (XA) and 4-hydroxyderricin (4-HD) extracted from Ashitaba roots to inhibit platelet aggregation activity in vitro was recently determined. However, the anti-platelet activities of Ashitaba chalcones in vivo have remained unclear. The present study examines the anti-platelet effects of Ashitaba exudate and its constituent chalcones using mouse tail-bleeding models that reflect platelet aggregation in vivo. Ashitaba exudate and the major chalcone subtype XA, suppressed the lipopolysaccharide (LPS)-induced shortening of mouse tail bleeding. However, trace amounts of other Ashitaba chalcone subtypes including xanthoangelols B (XB), D (XD), E (XE) and F (XF) did not affect tail bleeding. These results suggest that the major chalcone subtype in Ashitaba, XA, has anti-platelet-activities in vivo.

Identification of Individual Bacterial Cells through the Intermolecular Interactions with Peptide-Functionalized Solid-State Pores

Bioinspired pore sensing for selective detection of flagellated bacteria was investigated. The Au micropore wall surface was modified with a synthetic peptide designed from toll-like receptor 5 (TLR5) to mimic the pathogen-recognition capability. We found that intermolecular interactions between the TLR5-derived recognition peptides and flagella induce ligand-specific perturbations in the translocation dynamics of Escherichia coli, which facilitated the discrimination between the wild-type and flagellin-deletion mutant (ΔfliC) by the resistive pulse patterns thereby demonstrating the sensing of bacteria at a single-cell level. These results provide a novel concept of utilizing weak intermolecular interactions as a recognition probes for single-cell microbial identification.

Electrokinetic Analysis of Energy Harvest from Natural Salt Gradients in Nanochannels

The Gibbs free energy released during the mixing of river and sea water has been illustrated as a promising source of clean and renewable energy. Reverse electrodialysis (RED) is one major strategy to gain electrical power from this natural salinity, and recently by utilizing nanochannels a novel mode of this approach has shown improved power density and energy converting efficiency. In this work, we carry out an electrokinetic analysis of the work extracted from RED in the nanochannels. First, we outline the exclusion potential effect induced by the inhomogeneous distribution of extra-counterions along the channel axis. This effect is unique in nanochannel RED and how to optimize it for energy harvesting is the central topic of this work. We then discuss two important indexes of performance, which are the output power density and the energy converting efficiency, and their dependence on the nanochannel parameters such as channel material and geometry. In order to yield maximized output electrical power, we propose a device design by stepwise usage of the saline bias, and the lengths of the nanochannels are optimized to achieve the best trade-off between the input thermal power and the energy converting efficiency.

Hard x-ray photoemission study of Yb1-x Zr x B12: the effects of electron doping on the Kondo insulator YbB12

We have carried out hard x-ray photoemission spectroscopy (HAXPES) of Yb_1-x Zr _x B₁₂ ([Formula: see text]) to study the effects of electron doping on the Kondo insulator YbB₁₂. The Yb valences of Yb_1-x Zr _x B₁₂ at 300 K estimated from the Yb 3d HAXPES spectra decreased after substituting Yb with Zr from 2.93 for YbB₁₂ to 2.83 for Yb_0.125Zr_0.875B₁₂. A temperature dependent valence decrease was found upon cooling for all doping concentrations. We found peak shifts of the B 1s and Zr 3d_5/2, and Yb³⁺ 4f spectra toward the deeper binding-energy with increasing Zr concentration, which indicates a shift of the Fermi level to the higher energy and that of the Yb 4f hole level close to the Fermi level, respectively, due to electron doping. These results qualitatively show the enhanced hybridization between the Yb 4f and conduction-band states with Zr substitution, consistent with magnetic susceptibility measurements.

Rotatable high-resolution ARPES system for tunable linear-polarization geometry

A rotatable high-resolution angle-resolved photoemission spectroscopy (ARPES) system has been developed to utilize tunable linear-polarization geometries on the linear undulator beamline (BL-1) at Hiroshima Synchrotron Radiation Center. By rotating the whole ARPES measurement system, the photoelectron detection plane can be continuously changed from parallel to normal against the electric field vector of linearly polarized undulator radiation. This polarization tunability enables us to identify the symmetry of the initial electronic states with respect to the mirror planes, and to selectively observe the electronic states based on the dipole selection rule in the photoemission process. Specifications of the rotatable high-resolution ARPES system are described, as well as its capabilities with some representative experimental results.

Chlorogenic acid supplementation during in vitro maturation improves maturation, fertilization and developmental competence of porcine oocytes

Chlorogenic acid (CGA) is a quinic acid conjugate of caffeic acid, and a phytochemical found in many fruits and beverages that acts as an antioxidant. The present study investigated the effects of CGA supplementation during in vitro maturation (IVM), on in vitro development of porcine oocytes, to improve the porcine in vitro production (IVP) system. Oocytes were matured either without (control) or with CGA (10, 50, 100 and 200 μM). Subsequently, the matured oocytes were fertilized and cultured in vitro for 7 day. The rates of maturation, fertilization and blastocyst formation of oocytes matured with 50 μM CGA were significantly (p < .05) higher than those of the control oocytes. Hydrogen peroxide (H₂ O₂ ) is one of the reactive oxygen species and induces DNA damage in porcine oocytes. When oocytes were matured with 1 mM H₂ O₂ to assess the protective effect of CGA, 50 μM CGA supplementation improved the maturation rate and the proportion of DNA-fragmented nuclei in oocytes compared with control oocytes matured without CGA. Moreover, when oocytes were matured with either 50 μM CGA (control) or caffeic acid (10, 50 and 100 μM), the rates of maturation, fertilization and the blastocyst formation of oocytes matured with 50 μM CGA were similar to those of oocytes matured with 10 and 50 μM caffeic acid. Our results suggest that CGA has comparable effects to caffeic acid, and IVM with 50 μM CGA is particularly beneficial to IVP of porcine embryos and protects oocytes from DNA damage induced by oxidative stress. Supplementation of CGA to the maturation medium has a potential to improve porcine IVP system.

Rapid structural analysis of nanomaterials in aqueous solutions

Rapid structural analysis of nanoscale matter in a liquid environment represents innovative technologies that reveal the identities and functions of biologically important molecules. However, there is currently no method with high spatio-temporal resolution that can scan individual particles in solutions to gain structural information. Here we report the development of a nanopore platform realizing quantitative structural analysis for suspended nanomaterials in solutions with a high z-axis and xy-plane spatial resolution of 35.8 ± 1.1 and 12 nm, respectively. We used a low thickness-to-diameter aspect ratio pore architecture for achieving cross sectional areas of analyte (i.e. tomograms). Combining this with multiphysics simulation methods to translate ionic current data into tomograms, we demonstrated rapid structural analysis of single polystyrene (Pst) beads and single dumbbell-like Pst beads in aqueous solutions.

Fast and low-noise tunnelling current measurements for single-molecule detection in an electrolyte solution using insulator-protected nanoelectrodes

Reliable ways of DNA sequencing by tunnelling current require low-noise and high-speed measurements of tunnelling current in aqueous environments. Here we report a use of insulator-protected nanoprobes for achieving 7.6 pA rms noise at 50 kHz sampling rates in an electrolyte solution. We utilized dielectric-covered mechanically-controllable break junctions to create a pair of nano-exposed insulator/Au coaxial electrodes closely separated by 1 nm. We observed insulator layer thickness dependent noise levels, which was attributed to decreased capacitance through replacing capacitive electric double layers by the low-k dielectrics. We also demonstrated the detection of sharpened features in tunnelling current signatures that reflect dynamic motions of single-nucleotides in the electrode gaps by virtue of suppressed smearing effects in the low-capacitance nanoelectrode system.

Roles of vacuum tunnelling and contact mechanics in single-molecule thermopower

Molecular junction is a chemically-defined nanostructure whose discrete electronic states are expected to render enhanced thermoelectric figure of merit suitable for energy-harvesting applications. Here, we report on geometrical dependence of thermoelectricity in metal-molecule-metal structures. We performed simultaneous measurements of the electrical conductance and thermovoltage of aromatic molecules having different anchoring groups at room temperature in vacuum. We elucidated the mutual contributions of vacuum tunnelling on thermoelectricity in the short molecular bridges. We also found stretching-induced thermoelectric voltage enhancement in thiol-linked single-molecule bridges along with absence of the pulling effects in diamine counterparts, thereby suggested that the electromechanical effect would be a rather universal phenomenon in Au-S anchored molecular junctions that undergo substantial metal-molecule contact elongation upon stretching. The present results provide a novel concept for molecular design to achieve high thermopower with single-molecule junctions.

Orbital-Dependent Band Narrowing Revealed in an Extremely Correlated Hund's Metal Emerging on the Topmost Layer of Sr_{2}RuO_{4}

We use a surface-selective angle-resolved photoemission spectroscopy and unveil the electronic nature on the topmost layer of Sr_{2}RuO_{4} crystal, consisting of slightly rotated RuO_{6} octahedrons. The γ band derived from the 4d_{xy} orbital is found to be about three times narrower than that for the bulk. This strongly contrasts with a subtle variation seen in the α and β bands derived from the one-dimensional 4d_{xz/yz}. This anomaly is reproduced by the dynamical mean-field theory calculations, introducing not only the on-site Hubbard interaction but also the significant Hund's coupling. We detect a coherence-to-incoherence crossover theoretically predicted for Hund's metals, which has been recognized only recently. The crossover temperature in the surface is about half that of the bulk, indicating that the naturally generated monolayer of reconstructed Sr_{2}RuO_{4} is extremely correlated and well isolated from the underlying crystal.

Proving Nontrivial Topology of Pure Bismuth by Quantum Confinement

The topology of pure Bi is controversial because of its very small (∼10  meV) band gap. Here we perform high-resolution angle-resolved photoelectron spectroscopy measurements systematically on 14-202 bilayer Bi films. Using high-quality films, we succeed in observing quantized bulk bands with energy separations down to ∼10  meV. Detailed analyses on the phase shift of the confined wave functions precisely determine the surface and bulk electronic structures, which unambiguously show nontrivial topology. The present results not only prove the fundamental property of Bi but also introduce a capability of the quantum-confinement approach.