Stable Sugar‐Chain‐Immobilized Fluorescent Nanoparticles for Probing Lectin and Cells

Sugar chains are important molecules in cellular recognition and signaling, and quantum dots (QDs) are a very powerful tool for in vitro and in vivo imaging. Herein, we report the preparation of stable sugar‐chain‐immobilized fluorescent nanoparticles (SFNPs) and their application to the analysis of sugar‐chain–protein interactions and cellular imaging. SFNPs were easily prepared by mixing CdTe/CdS core/shell QDs with our previously developed sugar‐chain–ligand conjugates. The obtained SFNPs were very stable and could be stored for several months. In the binding analysis, β‐galactose‐ and α‐glucose‐immobilized SFNPs were specifically interacted with Ricinus communis agglutinin I and concanavalin A, respectively, and made into aggregates. The binding interaction was detected visually, fluorescently, or both. In the experiment for cellular imaging, it was found that SFNPs were predominantly taken up by human hepatocyto carcinoma cells (HepG2), suggesting the possible usage of our designed SFNPs for various biochemical analyses of sugar chains.     

Multi-angle observation scheme for bubbles and droplets

Abstract  

The split-screen imaging technique, in which the field of view of a single video/still camera is divided into two (or more) regions, is one of the techniques for observing, using a single camera, liquid droplets, bubbles or particles translating in another fluid from two (or more) different directions. A drawback of the split-screen imaging technique is that it generally requires a longer optical path than the ordinary multi-camera technique that allots each view axis to each of two (or more) synchronized cameras. This study presents an optical arrangement that minimizes the optical path for the two-directional split-screen imaging so as to allow the use of a camera lens with a short working distance. Its modification configured for the three-directional split-screen imaging of translating bubbles or drops is also presented.     

Dynamics and Control at Feedback Vertex Sets. I: Informative and Determining Nodes in Regulatory Networks

We consider systems of differential equations which model complex regulatory networks by a graph structure of dependencies. We show that the concepts of informative nodes (Mochizuki and Saito, J Theor Biol 266:323–335, 2010) and determining nodes (Foias and Temam, Math Comput 43:117–133, 1984) coincide with the notion of feedback vertex sets from graph theory. As a result we can determine the long-time dynamics of the entire network from observations on only a feedback vertex set. We also indicate how open loop control at a feedback vertex set, only, forces the remaining network to stably follow prescribed stable or unstable trajectories. We present three examples of biological networks which motivated this work: a specific gene regulatory network of ascidian cell differentiation (Imai et al., Science 312:1183–1187, 2006), a signal transduction network involving the epidermal growth factor in mammalian cells (Oda et al., Mol Syst Biol 1:1–17, 2005), and a mammalian gene regulatory network of circadian rhythms (Mirsky et al., Proc Natl Acad Sci USA 106:11107–11112, 2009). In each example the required observation set is much smaller than the entire network. For further details on biological aspects see the companion paper (Mochizuki et al., J Theor Biol, 2013, in press). The mathematical scope of our approach is not limited to biology. Therefore we also include many further examples to illustrate and discuss the broader mathematical aspects.     

Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvation

Fragment Molecular Orbital based-Molecular Dynamics (FMO-MD, Komeiji et al., Chem Phys Lett 2003, 372, 342) is an ab initio MD method suitable for large molecular systems. Here, FMO-MD was implemented to conduct full quantum simulations of chemical reactions in explicit solvation. Several FMO-MD simulations were performed for a sphere of water to find a suitable simulation protocol. It was found that annealing of the initial configuration by a classical MD brought the subsequent FMO-MD trajectory to faster stabilization, and also that use of bond constraint in the FMO-MD heating stage effectively reduced the computation time. Then, the blue moon ensemble method (Sprik and Ciccotti, J Chem Phys 1998, 109, 7737) was implemented and was tested by calculating free energy profiles of the Menschutkin reaction (H3N + CH3Cl --> +H3NCH3 + Cl-) in the presence and absence of the solvent water via FMO-MD. The obtained free energy profiles were consistent with the Hammond postulate in that stabilization of the product by the solvent, namely hydration of Cl-, shifted the transition state to the reactant-side. Based on these FMO-MD results, plans for further improvement of the method are discussed.     

Theoretically predicted picosecond optical switching of spin chirality in multiferroics

We show theoretically with an accurate spin Hamiltonian describing the multiferroic Mn perovskites that the application of the picosecond optical pulse with a terahertz frequency can switch the spin chirality through intensely exciting the electromagnons. There are four states with different spin chiralities, i.e., clockwise and counterclockwise ab/bc-plane spin spirals, and by tuning the strength, shape and length of the pulse, the switching among these states can be controlled at will. Dynamical pattern formation during the switching is also discussed.     

Observation of the quantum Hall effect in cleaved InAs surfaces

We have performed the in-plane magnetotransport measurements on the two-dimensional electron gas at the cleaved p-InAs (1 1 0) surface by deposition of Ag. The surface electron density N_s is determined from the Hall coefficient at . The coverage dependence of N_s is well explained by the assumption that each adsorbed Ag atom denotes one electron into InAs until the surface Fermi level reaches the adsorbate-induced donor level. The electron mobility μ is about and does not show a clear dependence on the coverage over . In the high-magnetic field regime of B>1/μ, Shubnikov–de Hass oscillations were observed. A beating pattern due to the strong spin–orbit interaction appears for high N_s. For lower N_s of , an apparent quantum Hall plateau for ν=4 and vanishing of the longitudinal resistivity were observed around .     

Asymmetric Michael addition of malonic diesters to acrylates by phase-transfer catalysis toward the construction of quaternary stereogenic α-carbons

A highly enantioselective construction of an all-carbon quaternary stereogenic center at the α-position of malonic diesters has been achieved by Michael addition using phase-transfer catalysis. The reaction of α-monosubstituted malonates with acrylates in the presence of N-(9-anthracenylmethyl)quininium chloride as a phase-transfer catalyst afforded the corresponding α,α-disubstituted malonic diesters in high chemical yields (up to >95% yield) with high enantioselectivities (up to 95% ee). Furthermore, the product was amenable to chemoselective transformation and could be successfully converted to the corresponding α,α-disubstituted amino acid derivatives through Curtius rearrangement.     

Splash formation by a spherical body plunging into water

Splashes caused by a spherical body plunging into water were investigated experimentally using a high speed CMOS camera. We categorized types of splash according to impact velocities of the sphere. Three types of splash were found: Type-I is a thin spire-type splash, Type-II is a mushroom-type splash with many droplets, and Type-III is a crown-type splash with many droplets. The reaction to the concave water surface attached to the sinking sphere is a cause of the Type-I splash. The film flow climbing up the sphere is a dominant cause of the Type-II splash. The velocity of the film flow, which is proportional to the impact velocity of the sphere, affects the fingers of the film flow, detaching of droplets, and maximum height of the Type-II splash. The Type-III crown-type splash is characterized by water jets with many droplets. A bulky air column in water is formed behind the sinking sphere, and longitudinal ridges and ripples on the surface of the air column were observed.     

QEX: target-specific druglikeness filter enhances ligand-based virtual screening

Molecular Diversity - Druglikeness is a useful concept for screening drug candidate compounds. We developed QEX, which is a new druglikeness index specific to individual targets. QEX is an...     

Evidence for an electric-dipole active continuum band of spin excitations in multiferroic TbMnO3

The wide range optical spectra on a multiferroic prototype TbMnO3 have been investigated to clarify the origin of spin excitations observed in the far-infrared region. We elucidate the full band structure, whose high energy edge (133 cm;{-1}) exactly corresponds to twice of the highest-lying magnon energy. Thus the origin of this absorption band is clearly assigned to two-magnon excitation driven by the electric field of light. There is an overlap between the two-magnon and phonon energy ranges, where the strong coupling between them is manifested by the frequency shift and transfer of oscillator strength of the phonon mode.