Hardware Accelerators for Regular Expression Matching and Approximate String Matching

This paper introduces hardware accelerators for regular expression matching and approximate string matching. The hardware for regular expression matching accepts a subclass of regular expressions, and achieves a high throughput string matching for a wide range of patterns. In addition, since the hardware is pattern-independent, we can update patterns immediately without reconfiguring the hardware. Therefore, it is useful for applications that require quick pattern updating, such as network intrusion detection. The hardware for approximate string matching calculates the edit distance as a degree of similarity between two strings at high speed. Therefore, it accelerates processing for text retrieval in database, analysis of DNA, protein sequences in bioinformatics, and so on.APSIPA ASC 2009: Asia-Pacific Signal and Information Processing Association, 2009 Annual Summit and Conference. 4-7 October 2009. Sapporo, Japan. Panel session: Panel Discussion 3. Hardware Software Co-research for Efficient Information Processing (7 October 2009)

Mechanical Distortion of Single Actin Filaments Induced by External Force: Detection by Fluorescence Imaging

Actin is a major component of the cytoskeleton that transmits mechanical stress in both muscle and nonmuscle cells. As the first step toward developing a “bio-nano strain gauge” that would be able to report the mechanical stress imposed on an actin filament, we quantitatively examined the fluorescence intensity of dyes attached to single actin filaments under various tensile forces (5–20 pN). Tensile force was applied via two optically trapped plastic beads covalently coated with chemically modified heavy meromyosin molecules that were attached to both end regions of an actin filament. As a result, we found that the fluorescence intensity of an actin filament, where 20% of monomers were labeled with tetramethylrhodamine (TMR)-5-maleimide at Cys374 and the filamentous structure was stabilized with nonfluorescent phalloidin, decreased by ∼6% per 10 pN of the applied force, whereas the fluorescence intensity of an actin filament labeled with either BODIPY TMR cadaverin-iodoacetamide at Cys374 or rhodamine-phalloidin showed only an ∼2% decrease per 10 pN of the applied force. On the other hand, spectroscopic measurements of actin solutions showed that the fluorescence intensity of TMR-actin increased 1.65-fold upon polymerization (G-F transformation), whereas that of BODIPY-actin increased only 1.06-fold. These results indicate that the external force distorts the filament structure, such that the microenvironment around Cys374 approaches that in G-actin. We thus conclude that the fluorescent dye incorporated into an appropriate site of actin can report the mechanical distortion of the binding site, which is a necessary condition for the bio-nano strain gauge

学位論文審査報告

Lower Trophic Level Ecosystem in Banten and Jakarta Bays, Indonesia[Nurdjaman]酸化物薄膜のCVD合成に関する研究[申]Effects of Electromagnetic Waves on Low-Pressure PIG Discharge[Abolmasov]Recovery of Radioactive Gases in Nuclear Fuel Reprocessing Cycle[Ianovski]Experimental Study on the Void Fraction of Phase Change Process in Microfin Tubes[李]有機電界効果トランジスタのデバイス構造及び新規作製法に関する研究[安田]赤色蛍光・旧制材料の開発に関する研究[岩崎]リソグラフィー用レーザのスペクトル評価に関する研究[若林]発電用高温設備材料の組織変化の理論的解明と余寿命評価への適用[早川]新規なエチレン重合用4族遷移金属錯体の開発研究[羽村]自動車用エンジンおよび変速機の潤滑油による耐久性向上の研究[白濱]HYDROTREATING FOR DIESEL AND RESIDUAL OILS[井上]非共沸混合冷媒R123/R134aの千鳥配列フィン付き管群内凝縮に及ぼすフィン形状の影響[高田

Temperature change does not affect force between regulated actin filaments and heavy meromyosin in single-molecule experiments

The temperature dependence of sliding velocity, force and the number of cross-bridges was studied on regulated actin filaments (reconstituted thin filaments) when they were placed on heavy meromyosin (HMM) attached to a glass surface. The regulated actin filaments were used because our previous study on muscle fibres demonstrated that the temperature effect was much reduced in the absence of regulatory proteins. A fluorescently labelled thin filament was attached to the gelsolin-coated surface of a polystyrene bead. The bead was trapped by optical tweezers, and HMM–thin filament interaction was performed at 20–35°C to study the temperature dependence of force at the single-molecule level. Our experiments showed that there was a small increase in force with temperature (Q(10) = 1.43) and sliding velocity (Q(10) = 1.46). The small increase in force was correlated with the small increase in the number of cross-bridges (Q(10) = 1.49), and when force was divided by the number of cross-bridges, the result did not depend on the temperature (Q(10) = 1.03). These results demonstrate that the force each cross-bridge generates is fixed and independent of temperature. Our additional experiments demonstrate that tropomyosin (Tm) in the presence of troponin (Tn) and Ca(2+) enhances both force and velocity, and a truncated mutant, Δ23Tm, diminishes force and velocity. These results are consistent with the hypothesis that Tm in the presence of Tn and Ca(2+) exerts a positive allosteric effect on actin to make actomyosin linkage more secure so that larger forces can be generated