Knowledge-based potential defined for a rotamer library to design protein sequences

A knowledge-based potential for a rotamer library was developedto design protein sequences. Protein side-chain conformationsare represented by 56 templates. Each of their fitness to agiven structural site-environment is evaluated by a combinedfunction of the three knowledge-based terms, i.e. two-body side-chainpacking, one-body hydration and local conformation. The numberof matches between the native sequence and the structural site-environmentin the database and that of the virtually settled mismatches,counted in advance, were transformed into the energy scores.In the best-14 test (assessment for the reproduction abilityof the native rotamer on its structural site within a quarterof 56 fitness rank positions), the structural stability analysison mutants of human and T4 lysozymes and the inverse-foldingsearch by a structure profile against the sequence database,this function performs better than the function deduced withthe conventional normalization and our previously developedfunction. Targeting various structural motifs, de novo sequencedesign was conducted with the function. The sequences thus obtainedexhibit reasonable molecular masses and hydrophobic/hydrophilicpatterns similar to the native sequences of the target and actas if they were the homologs to the target proteins in BLASTPsearch. This significant improvement is discussed in terms ofthe reference state for normalization and the crucial role ofshort-range repulsion to prohibit residue bumps.     

Optical Properties of Au-Pt and Au-Pt-In Alloys

The effects of platinum addition to gold and indium addition to a gold-platinum alloy on their optical properties were investigated using a computer-controlled spectrophotometer. Spectral reflectance data from a polished sample for the incident CIE standard illuminant D65 was collected as a function of the wavelength at 10 nm intervals from 360 to 740 nm. Three coordinates,L* (lightness),a* (red-green),b* (yellow-blue), in the CIE 1976L*a*b* colour space, were determined to quantify the colour of experimental binary Au-Pt and ternary Au-Pt-In alloys. p ]The pronounced step near 520 nm (approximately 2.4 eV) in the spectral reflectance-wavelength curve for pure gold, which is responsible for the rich yellow colour of gold, became less pronounced with the addition of platinum. The decoloring effect of platinum was found to be due to this phenomenon. The addition of indium of up to ca 4 at% to a Au-10 at% Pt alloy increased both chromaticity indices, ie,a* andb* values, giving a gold tinge to the alloy: this effect was brought about by both the slight increase in reflectance in the long-wavelength range and the slight decrease in reflectance in the short-wavelength range of the visible spectrum.     

Prevalence of mutations in core promoter/precore region in Japanese patients with chronic hepatitis B virus infection

We examined the frequency and significance of mutations in the core promoter and precore region in 103 Japanese patients with chronic hepatitis B virus (HBV) infection. HBV DNAs from the patients' sera were amplified by polymerase chain reaction and were directly sequenced. A double mutation (T1762 A1764) in the core promoter was frequently observed in the patients regardless of HBeAg status except for asymptomatic carriers with HBeAg. Furthermore, a mutation at nucleotide 1753 from T to C or G was frequently found in anti-HBe positive patients and was often accompanied by the double mutation. The A1896 mutation was found in only about one fourth of the patients with anti-HBe. These data suggest that the patients with chronic liver diseases frequently had a double mutation regardless of HBeAg status and a mutation at nucleotide 1753 might be associated with HBeAg-negative chronic hepatitis B virus infection.     

Improvement of the physical properties of poly(methyl methacrylate) by copolymerization with pentafluorophenyl methacrylate

Copolymers of methyl methacrylate (MMA) and pentafluorophenyl methacrylate (PFPMA) of various compositions were prepared with a free‐radical initiator. When PFPMA was included in the copolymers, the glass‐transition temperatures increased and showed a positive deviation from the Gordon–Taylor equation. A copolymer containing 20 wt % PFPMA exhibited almost zero orientational birefringence, and the photoelastic birefringence became zero when the copolymer contained 13 wt % PFPMA. When 20 wt % PFPMA was incorporated into the MMA copolymer, its water absorption decreased to 0.4 wt % versus 1.8 wt % for poly(methyl methacrylate) (PMMA) under the same condition. The flammability of the PFPMA/MMA copolymer was reduced in comparison with that of the MMA homopolymer. The refractive indices of the PFPMA/MMA copolymers were very close to that of PMMA, and the transmittances of the copolymers were slightly better than that of PMMA. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci, 2007     

A case of multiple muscular abscesses of the lower limbs by Staphylococcus aureus after chemotherapy for lung cancer

A 67-year-old male was admitted to our hospital because of lung cancer and interstitial pneumonia. Cisplatin, vindesie and mitomycin C were administered for treatment of lung cancer. The leucocyte-counts declined to 1700/microliter on the eighth day after the chemotherapy. Though granulocyte colony-stimulating factor was administered, pain in the right thigh and high grade fever developed. Because Staphylococcus aureus was isolated from the blood specimen, piperacillin was administered. But the high grade fever continued and the pain was expanded to the right hip, left hip, thigh and leg. Because a computed tomograph of the lower limbs showed low density areas in bilateral gluteus maximus muscle right adductor magnus muscle, left biceps femoris muscle and left soleus muscle and the culture of an aspirate from abscess of right leg detected S. aureus, multiple muscular abscesses of the lower limbs was confirmed. We changed the antibiotics from PIPC to imipenem/cilastatin and minocycline on nineteenth day after the chemotherapy. His symptoms improved after the change of antibacterial agents. But he died of acute exacerbation of interstitial pneumonia, after about two months of the chemotherapy. Muscular abscesses of the limbs are very rare in Japan. Only four cases with muscular abscess of the limbs were reported in Japan, since 1988. This case suggests that a muscular abscess must be considered in the differential diagnosis of fever in patients with neutropenia.     

Symbolic chemical system based on abstract rewriting system and its behavior pattern

We develop an abstract computational model, the abstract rewriting system on multisets, called ARMS, to deal with systems with a large number of degree of freedom, like liquids, and to confirm that they can simulate the emergence of the complex behavior of cycles, such as autocatalytic cycles, with their period-doubling and fusion of cycles, which are often found in the emergence of life. Furthermore, we clarify the conditions in which ARMS generates cycles through the theoretical investigation of ARMS.     

Three distinct mechanisms for translocation and activation of the delta subspecies of protein kinase C

We expressed delta subspecies of protein kinase C (delta-PKC) fused with green fluorescent protein (GFP) in CHO-K1 cells and observed the movement of this fusion protein in living cells after three different stimulations. The delta-PKC-GFP fusion protein had enzymological characteristics very similar to those of the native delta-PKC and was present throughout the cytoplasm in CHO-K1 cells. ATP at 1 mM caused a transient translocation of delta-PKC-GFP to the plasma membrane approximately 30 s after the stimulation and a sequent retranslocation to the cytoplasm within 3 min. A tumor-promoting phorbol ester, 12-O-tetradecanoylphorbol 13-acetate (TPA; 1 microM), induced a slower translocation of delta-PKC-GFP, and the translocation was unidirectional. Concomitantly, the kinase activity of delta-PKC-GFP was increased by these two stimulations, when the kinase activity of the immunoprecipitated delta-PKC-GFP was measured in vitro in the absence of PKC activators such as phosphatidylserine and diacylglycerol. Hydrogen peroxide (H2O2; 5 mM) failed to translocate delta-PKC-GFP but increased its kinase activity more than threefold. delta-PKC-GFP was strongly tyrosine phosphorylated when treated with H2O2 but was tyrosine phosphorylated not at all by ATP stimulation and only slightly by TPA treatment. Both TPA and ATP induced the translocation of delta-PKC-GFP even after treatment with H2O2. Simultaneous treatment with TPA and H2O2 further activated delta-PKC-GFP up to more than fivefold. TPA treatment of cells overexpressing delta-PKC-GFP led to an increase in the number of cells in G2/M phase and of dikaryons, while stimulation with H2O2 increased the number of cells in S phase and induced no significant change in cell morphology. These results indicate that at least three different mechanisms are involved in the translocation and activation of delta-PKC.     

Vibration analysis and cutting simulation of structural nonlinearity for machine tool

The dynamic behavior of a machine tool is affected by the forces applied to the structure. However, cutting processes have been analyzed considering the linear systems in most of the studies so far. In this study, a machine tool structure was excited by using an electromagnetic shaker and the force-dependant frequency response characteristics were measured. Based on the measured result, the nonlinear characteristics of the machine tool structure was identified, and a machine tool with the nonlinear characteristics was mathematically reproduced, which enabled to analyse the nonlinear frequency response characteristics and simulate cutting processes.     

Study of Gas Core Behavior of Passive Cyclonic Two-Phase Separator for Microgravity Applications

Separating gas-liquid two-phase flow is of practical importance for many space engineering systems. While droplet and bubble removal is a naturally occurring phenomenon in most terrestrial situations, the absence of buoyancy in a microgravity environment often results in situations where two disparate phases have no distinct inclination to separate from one another. Passive cyclonic separators can perform this task without moving parts and the reliability concerns of active separators. In such separation devices, separation efficiency is strongly influenced by the gas core behavior. Based on experimental and numerical investigations, the behavior of the gas core with two-phase injection is studied. A control-volume model is developed to capture the relevant physics of the flow in the separator. It is shown that the injection nozzle design, swirl number, and volumetric gas quality all have a major influence on the core size. The present investigation covers a range of volumetric quality from 0 to 0.75, and a range of swirl number from 17 to 28. Both homogeneous and non-homogeneous nozzles are used. The implications of the results are discussed in detail.     

Chemiluminescent determination of cholesterol hydroperoxides in human erythrocyte membrane

A method for separating, detecting, and quantifying cholesterol hydroperoxide (Ch-OOH) based on extraction, purification by solid-phase extraction cartridge, high-performance liquid chromatography with chemiluminescent detection (HPIC-CI), and liquid chromatography mass spectrometry has been developed for human erythrocyte membrane. We prepared standard compounds of the cholesterol 5α-, 7α-, and 7β-hydroperoxides (Ch 5α-OOH, Ch 7α-OOH, and Ch 7β-OOH). An octyl silica column with methanol/water/acetonitrile 89∶9∶2 (by vol) as eluent was used to determine Ch-OOH. HPLC-CL that incorporated cytochrome c and luminol as the post-column luminescent reagent was used. We also investigated the optimal assay conditions and how to prevent formation of artifact Ch-OOH. Analysis of erythrocyte membranes from seven healthy volunteers identified Ch 7α-OOH and Ch 7β-OOH, but not Ch 5α-OOH, as commonly occurring components. The respective mean concentrations of Ch 7α-OOH and Ch 7β-OOH were 2,5±1.6 and 5A±3.5 pmol/mL blood.