Global Conformational Changes of Ribosome Observed by Normal Mode Fitting for 3D Cryo-EM Structures

SummaryMany three-dimensional density maps of 70S ribosome at various functional states are available now in the Electron Microscopy DataBank at EBI. We used our new flexible-fitting approach to systematically analyze these maps to reveal the global conformational differences between the EM structures. Large-scale ratchet-like deformations were observed in an EM structure of the initiation complex and in some EM structures bound with EFG, RF3, and RRF. In most of them, the L1 stalk, which interacts with the tRNA molecule at the E site of ribosome and is considered to be involved in the release of the tRNA, was in “the blocking state” for the E-tRNA. Furthermore, we found that the EM structures bound with EFG or RRF were aligned in the conformational space, suggesting that the large-scale conformational changes of the 70S ribosome bound with these factors occur along a specific pathway in a concerted manner

Near ML detection using Dijkstra's algorithm with bounded list size over MIMO channels

We propose Dijkstra's algorithm with bounded list size after QR decomposition for decreasing the computational complexity of near maximum-likelihood (ML) detection of signals over multiple-input-multiple-output (MIMO) channels. After that, we compare the performances of proposed algorithm, QR decomposition M-algorithm (QRD-MLD), and its improvement. When the list size is set to achieve the almost same symbol error rate (SER) as the QRD-MLD, the proposed algorithm has smaller average computational complexity.Comment: 8 pages, two column, 14 figures, LaTeX2

Spray characterization of flex-fuel gasoline di injectors and spray interaction with charge motion in a variable valve actuation engine

The objective of this study is to understand the characteristics of GDI sprays and behavior of in-cylinder charge motion in a GDI engine which is equipped with variable valve actuation. High speed spray visualization in a spray chamber was conducted for a study of spray development. By Schlieren visualization technique, the effect of different conditions including ambient conditions (temperature, pressure) and injection conditions (fuel type, fuel temperature, nozzle design) on spray formation was discussed in both qualitative and quantitative methods. High-speed visualization of the in-cylinder charge motion was carried out as well using an optical accessible engine. The testing was conducted for the conventional valve strategy with the production cam, and for the advanced valve strategies with the prototype cams. Multi-dimensional CFD was carried out to support the optical engine work. By the experiments, Schlieren visualization was found to be very effective method to observe the vapor phase of the fuel spray, and the 2-stage thresholding image processing method was developed to process Schlieren images. Evaluation of the spray images revealed that the effect of flash boiling could change the spray shape drastically by plume collapse. Significance of flash boiling depended not only on ambient condition, but on injection condition and a combination of other effects including fuel properties and nozzle design. The optical engine testing revealed that the interaction of spray and in-cylinder flow, especially contradiction of the direction of spray momentum and tumble rotation, was a key factor for mixture formation. Stronger inlet air flow by low-lift cam resulted in higher turbulent energy and enhanced vaporization rate which was proven in both experiment and simulation. Deactivation of one of the intake valves produced swirl charge motion in the cylinder which was mixed with tumble. Soot emission caused by piston impingement of the early injection could be reduced by valve deactivation. The use of high-lift long-duration cam promoted more vigorous charge motion, but dynamic ratios of low-lift short-duration cam developed faster

<ORIGINAL ARTICLE>Characterization of a new coagulant enzyme isolated from Trimeresurus okinavensis (Himehabu snake) venom

A potent, proteinaceous inducer of coagulation factors, has been purified to homogeneity from Trimeresurus okinavensis (Himehabu snake) by ion exchange chromatography and molecular sieving. It has an apparent molecular weight of 28,000 and it specifically converts fibrinogen to fibrin through an enzymatic reaction. This activity was confirmed by a method using synthetic substrate S-2238, though the fraction from a DEAE sephacel column chromatography shows amidolytic activity of S-2251 and S-2366, which are commonly used to measure plasmin and activated protein C activity, respectively, as well as S-2238. This thrombin-like activity of the final product was not affect by the addition of heparin and AT-III. This enzyme also aggregates normal platelets. It is considered that this purified enzyme would be useful as a hemostatic agent or research reagent

X-Ray Reflection Nebulae with Large Equivalent Widths of Neutral Iron Ka Line in the Sgr C Region

This paper reports on the first results of the Suzaku observation in the Sgr C region. We detected four diffuse clumps with strong line emission at 6.4keV, Ka from neutral or low-ionized Fe. One of them, M359.38-0.00, is newly discovered with Suzaku. The X-ray spectra of the two bright clumps, M359.43-0.07 and M359.47-0.15, after subtracting the Galactic center diffuse X-ray emission (GCDX), exhibit strong Ka line from FeI with large equivalent widths (EWs) of 2.0-2.2keV and clear Kb of FeI. The GCDX in the Sgr C region is composed of the 6.4keV- and 6.7keV-associated components. These are phenomenologically decomposed by taking relations between EWs of the 6.4keV and 6.7keV lines. Then the former EWs against the associated continuum in the bright clump regions are estimated to be 2.4(+2.3_-0.7)keV. Since the two different approaches give similar large EWs of 2keV, we strongly suggest that the 6.4keV clumps in the Sgr C region are due to X-ray reflection/fluorescence (the X-ray reflection nebulae).Comment: Accepted for publication in PAS

The C. elegans Thermosensory Neuron AFD Responds to Warming

AbstractThe mechanism of temperature sensation is far less understood than the sensory response to other environmental stimuli such as light, odor, and taste. Thermotaxis behavior in C. elegans requires the ability to discriminate temperature differences as small as ∼0.05°C and to memorize the previously cultivated temperature [1, 2]. The AFD neuron is the only major thermosensory neuron required for the thermotaxis behavior [3]. Genetic analyses have revealed several signal transduction molecules that are required for the sensation and/or memory of temperature information in the AFD neuron [4–7], but its physiological properties, such as its ability to sense absolute temperature or temperature change, have been unclear. We show here that the AFD neuron responds to warming. Calcium concentration in the cell body of AFD neuron is increased transiently in response to warming, but not to absolute temperature or to cooling. The transient response requires the activity of the TAX-4 cGMP-gated cation channel, which plays an essential role in the function of the AFD neuron [5]. Interestingly, the AFD neuron further responds to step-like warming above a threshold that is set by temperature memory. We suggest that C. elegans provides an ideal model to genetically and physiologically reveal the molecular mechanism for sensation and memory of temperature information

Drum Beating and a Martial Art Bojutsu Performed by a Humanoid Robot

Over the past few decades a considerable number of studies have been made on impact dynamics. Zheng and Hemami discussed a mathematical model of a robot that collides with an environment (Zheng &amp; Hemami, 1985). When a robot arm fixed on the ground collides with a hard environment, the transition from the free space to constrained space may bring instabilit

Electrochemical Capacitors Using Fluorohydrogenate Ionic Liquid Electrolytes

Electrochemical capacitors using fluorohydrogenate ionic liquids show a large voltage dependence of capacitance with a maximum at a charging voltage around 2.5 V, resulting in a larger capacitance than those using other typical ionic liquid electrolytes. The voltage dependence becomes less remarkable with decrease in the HF composition n in EMIm(FH)nF (EMIm: 1-ethyl-3-methylimidazolium). Cyclic voltammetry using an activated carbon working electrode revealed that two redox reactions occur at the higher and lower potentials against the rest potential in EMIm(FH)2.3F. These Faradaic processes contribute to the voltage dependence of capacitance