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Using reflective logic programming to describe domain knowledge as an aspect 1st

1st International Symposium on Generative and Component-Based Software Engineering (GCSE'99)

作者： D'Hondt, M De Meuter, W Wuyts, R Free Univ Brussels Syst & Software Engn Lab B-1050 Brussels Belgium Free Univ Brussels Programming Technol Lab B-1050 Brussels Belgium

ISBN: (纸本)3540411720

Software applications, mostly consisting of an algorithm applied to domain knowledge, are hard to maintain and to reuse as a result of their hard coded combination. We propose to follow the principles of aspect-oriented programming, separating the domain from the algorithm and describing then in a logic and conventional programming language respectively. In this paper, we report on an experiment that was conducted to validate this hypothesis, and to investigate the requirements of a programming environment for this configuration. An already existing environment that uses a logic meta-language to reason about object-oriented systems, SOUL, is used as a starting point for this experiment. The result is a working implementation in SOUL, which validates our ideas, reveals mechanisms that require more research, and points to other features that should be included.

关键词： Computer software reusability

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The role of the DELSEED motif of the β subunit in rotation of F₁-ATPase

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JOURNAL OF BIOLOGICAL CHEMISTRY 2000年第19期275卷 14260-14263页

作者： Hara, KY Noji, H Bald, D Yasuda, R Kinosita, K Yoshida, M Teikyo Univ Biotechnol Res Ctr 3F CREST Genet Programming Team 13Miyamae Ku Kawasaki Kanagawa 216000 Japan Tokyo Inst Technol Chem Resources Lab Yokohama Kanagawa 2268503 Japan Keio Univ Fac Sci & Technol Dept Phys Yokohama Kanagawa 2238522 Japan

F-1-ATPase is a rotary motor protein, and ATP hydrolysis generates torque at the interface between the gamma subunit, a rotor shaft, and the alpha(3)beta(3) substructure, a stator ring. The region of conserved acidic "DELSEED" motif of the beta subunit has a contact with gamma subunit and has been assumed to be involved in torque generation. Using the thermophilic alpha(3)beta(3)gamma complex in which the corresponding sequence is DELSDED, we replaced each residue and all five acidic residues in this sequence with alanine. In addition, each of two conserved residues at the counterpart contact position of gamma subunit was also replaced. Surprisingly, all of these mutants rotated with as much torque as the wild-type. We conclude that side chains of the DELSEED motif of the beta subunit do not have a direct role in torque generation.

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F₀F₁-ATP synthase:: general structural features of 'ATP-engine' and a problem on free energy transduction

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BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2000年第2-3期1458卷 467-481页

作者： Muneyuki, E Noji, H Amano, T Masaike, T Yoshida, M Tokyo Inst Technol Resources Utilizat Res Lab Midori Ku Yokohama Kanagawa 2268503 Japan Teikyo Univ Biotechnol Res Ctr 3F CREST Genet Programming Team 13 Miyamae Ku Kawasaki Kanagawa 2160001 Japan

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Observations of rotation within the F_OF_l-ATP synthase:: deciding between rotation of the F_Oc subunit ring and artifact

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FEBS LETTERS 2000年第3期470卷 244-248页

作者： Tsunoda, SP Aggeler, R Noji, H Kinosita, K Yoshida, M Capaldi, RA Tokyo Inst Technol Resources Utilizat Res Lab Yokohama Kanagawa 2268503 Japan Univ Oregon Inst Mol Biol Eugene OR 97403 USA Teikyo Univ Biotechnol Res Ctr 3F CREST Genet Programming Team 13 Kawasaki Kanagawa 2160001 Japan Keio Univ Fac Sci & Technol Dept Phys Yokohama Kanagawa 2238522 Japan

F0F1-ATP synthase mediates coupling of proton flow in F-0 and ATP synthesis/hydrolysis in F(0)c through rotation of central rotor subunits. A ring structure of F(0)c subunits is widely believed to be a part of the rotor. Using an attached actin filament as a probe, we have observed the rotation of the F(0)c subunit ring in detergent-solubilized F0F1-ATP synthase purified from Escherichia coli. Similar studies have been performed and reported recently [Sambongi ct al, (1999) Science 286, 1722-1724], However. in our hands this rotation has been observed only for the preparations which show poor sensitivity to dicyclohexylcarbodiimde, an F-0 inhibitor. We hare found that detergents which adequately disperse the enzyme for the rotation assay also tend to transform F0F1-ATP synthase into an F-0 inhibitor-insensitive state in which Fl can hydrolyze ATP regardless of the state of the F-0. Our results raise the important issue of whether rotation of the F(0)c ring in isolated F0F1-ATP synthase can be demonstrated unequivocally with the approach adopted here and also used by Sambongi et al. :(C) 2000 Federation of European Biochemical Societies.

关键词： FoFl-ATP synthase rotation c subunit ring detergent uncoupling

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Characterization of single actomyosin rigor bonds: Load dependence of lifetime and mechanical properties

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BIOPHYSICAL JOURNAL 2000年第2期79卷 962-974页

作者： Nishizaka, T Seo, R Tadakuma, H Kinosita, K Ishiwata, S Waseda Univ Sch Sci & Engn Dept Phys Shinjuku Ku Tokyo 1698555 Japan Genet Programming Team 13 Kanagawa 2160001 Japan Keio Univ Fac Sci & Technol Dept Phys Yokohama Kanagawa 2238522 Japan Waseda Univ Adv Res Inst Sci & Engn Tokyo Japan Waseda Univ Mat Res Lab Biosci & Photon Tokyo Japan

Load dependence of the lifetime of the rigor bonds formed between a single myosin molecule (either heavy meromyosin, HMM, or myosin subfragment-1, S1) and actin filament was examined in the absence of nucleotide by pulling the barbed end of the actin filament with optical tweezers. For S1, the relationship between the lifetime (tau) and the externally imposed load (F) at absolute temperature T could be expressed as tau(F) = tau(0).exp(-F.d/k(B)T) with tau(0) of 67 s and an apparent interaction distance d of 2.4 nm (k(B) is the Boltzmann constant). The relationship for HMM was expressed by the sum of two exponentials, with two sets of tau(0) and d being, respectively, 62 s and 2.7 nm, and 950 s and 1.4 nm. The fast component of HMM coincides with tau(F) for S1, suggesting that the fast component corresponds to single-headed binding and the slow component to double-headed binding. These large interaction distances, which may be a common characteristic of motor proteins, are attributed to the geometry for applying an external load. The pulling experiment has also allowed direct estimation of the number of myosin molecules interacting with an actin filament. Actin filaments tethered to a single HMM molecule underwent extensive rotational Brownian motion, indicating a low torsional stiffness for HMM. From these results, we discuss the characteristics of interaction between actin and myosin, with the focus on the manner of binding of myosin.

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Temperature dependence of force, velocity, and processivity of single kinesin molecules

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BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 2000年第3期272卷 895-899页

作者： Kawaguchi, K Ishiwata, S Waseda Univ Sch Sci & Engn Dept Phys Shinjuku Ku Tokyo 1698555 Japan Waseda Univ Adv Res Inst Sci & Engn Shinjuku Ku Tokyo 1698555 Japan Waseda Univ Mat Res Lab Biosci & Photon Shinjuku Ku Tokyo 1698555 Japan Core Res Evolut Sci & Technol Genet Programming Team 13 Kawasaki Kanagawa 2160001 Japan

Using the bead assay in optical microscopy equipped with optical tweezers, we have examined the effect of temperature on the gliding velocity, force, and processivity of single kinesin molecules interacting with a microtubule between 15 and 35 degrees C. The gliding velocity increased with the Arrhenius activation energy of 50 kJ/mol, consistent with the temperature dependence of the microtubule-dependent ATPase activity. Also, the average run length, i.e., a measure of processivity of kinesin, increased on increasing temperature. On the other hand, the generated force was independent of temperature, 7.34 +/- 0.33 pN (average +/- S.D., n = 70). The gliding velocities decreased almost linearly with an increase in force irrespective of temperature, implying that the efficiency of mechanochemical energy conversion is maintained constant in this temperature range. Th us, we suggest that the force generation is attributable to the temperature-insensitive nucleotide-binding state(s) and/or conformational change(s) of kinesin-microtubule complex, whereas the gliding velocity is determined by the ATPase rate. (C) 2000 Academic Press.

关键词： kinesin microtubule motor proteins processivity temperature effect single molecule analysis force generation gliding velocity Arrhenius activation energy

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Stepping rotation of F₁-ATPase visualized through angle-resolved single-fluorophore imaging

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2000年第13期97卷 7243-7247页

作者： Adachi, K Yasuda, R Noji, H Itoh, H Harada, Y Yoshida, M Kinosita, K Genet Programming Team 13 Core Res Evolut Sci & Technol Miyamae Ku Kawasaki Kanagawa 2160001 Japan Kanazawa Univ Fac Sci Dept Phys Kanazawa Ishikawa 9201192 Japan Hamamatsu Photon KK Tsukuba Res Lab Tsukuba Ibaraki 3002635 Japan Tokyo Inst Technol Resources Utilizat Res Lab Midori Ku Yokohama Kanagawa 2268503 Japan Keio Univ Fac Sci & Technol Dept Phys Kohoku Ku Yokohama Kanagawa 2238522 Japan

Orientation dependence of single-fluorophore intensity was exploited in order to videotape conformational changes in a protein machine in real time. The fluorophore Cy3 attached to the central subunit of F-1-ATPase revealed that the subunit rotates in the molecule in discrete 120 degrees steps and that each step is driven by the hydrolysis of one ATP molecule. These results, unlike those from the previous study under a frictional load, show that the 120 degrees stepping is a genuine property of this molecular motor. The data also show that the rate of ATP binding is insensitive to the load exerted on the rotor subunit.

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Supporting disciplined reuse and evolution of UML models 1st

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1st International Workshop UML 98: Beyond the Notation

作者： Mens, T Lucas, C Steyaert, P Free Univ Brussels Programming Technol Lab B-1050 Brussels Belgium

ISBN: (纸本)3540662529

UML provides very little support for modelling evolvable or reusable specifications and designs. To cope with this problem, the UML needs to be extended with support for reuse and evolution of model components. As a first step, this paper enhances the UML metamodel with the "reuse contract" formalism to deal with evolution of collaborating class interfaces. Such a formal semantics for reuse allows us to detect evolution and composition conflicts automatically.

关键词： Unified Modeling Language

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Optimizing object-oriented languages through architectural transformations 8th

Optimizing object-oriented languages through architectural t...

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Joint European Conference on Theory and Practice of Software (ETAPS 99)

作者： Tourwé, T De Meuter, W Free Univ Brussels Programming Technol Lab B-1050 Brussels Belgium

ISBN: (纸本)3540657177

Certain features of the object-oriented paradigm are a serious impediment for the runtime performance of object-oriented programs. Although compiler techniques to alleviate this problem were developed over the years, we will present some real-world examples which show that these solutions fall short in making any significant optimizations to systems that are required to be very flexible and highly reusable. As a solution, we propose a radically different approach: using an open compiler to "compile away" whole designs by performing architectural transformations based on programmer annotations. We win discuss this approach in detail and show why it is more suited to solve the efficiency problems inherently associated with object-oriented programming.

关键词： Object oriented programming

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ε Subunit, an endogenous inhibitor of bacterial F₁-ATPase, also inhibits F₀F₁-ATPase

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JOURNAL OF BIOLOGICAL CHEMISTRY 1999年第48期274卷 33991-33994页

作者： Kato-Yamada, Y Bald, D Koike, M Motohashi, K Hisabori, T Yoshida, M Tokyo Inst Technol Resources Utilizat Res Lab Yokohama Kanagawa 2268503 Japan Teikyo Univ Biotechnol Res Ctr 3F Core Res Evolut Sci & Technol Genet Programming Team 13 Kawasaki Kanagawa 2160001 Japan

Since the report by Sternweis and Smith (Sternweis, P. C., and Smith, J. B. (1980) Biochemistry 19, 526-531), the epsilon subunit, an endogenous inhibitor of bacterial F-1-ATPase, has long been thought not to inhibit activity of the holo enzyme, F0F1-ATPase. However, we report here that the epsilon subunit is exerting inhibition in F0F1-ATPase. We prepared a C-terminal half-truncated epsilon subunit (epsilon(Delta C)) of the thermophilic Bacillus PS3 F0F1-ATPase and reconstituted F-1- and F0F1-ATPase containing epsilon(Delta C). Compared with F-1- and F0F1-ATPase containing intact epsilon, those containing epsilon(Delta C) showed uninhibited activity;severalfold higher rate of ATP hydrolysis at low ATP concentration and the start of ATP hydrolysis without an initial lag at high ATP concentration. The F0F1-ATPase containing epsilon(Delta C) was capable of ATP-driven H+ pumping. The time-course of pumping at low ATP concentration was faster than that by the F0F1-ATPase containing intact epsilon. Thus, the comparison with noninhibitory epsilon(Delta C) mutant shed light on the inhibitory role of the intact epsilon subunit in F0F1-ATPase.

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