Biomedical subjects

Naoto Yagi

Publications and source records attributed to Naoto Yagi.

At least 19 recordsLinked to original sources

PubMed2006

Small airway changes in healthy and ovalbumin-treated mice during quasi-static lung inflation.

Previously, we developed a synchrotron radiation CT system to evaluate the morphometric changes (length and diameter, D) and small airway compliance (sC(aw)) of euthanized mice under quasi-static inflation [Sera, T., Uesugi, K., Yagi, N., 2005. Localized morphometric deformations of small airways and alveoli in intact mouse lungs under quasi-static inflation. Respir. Physiol. Neurobiol. 147, 51-63). Using this system, this study compared normal and asthmatic small airways. Ovalbumin-treated mice were used as an asthma model. Compared with the values at functional residual capacity, D of normal and asthmatic small airways (D<200microm) increased by 48% and 36% at the end of tidal inspiration. For larger airways (D>500microm), the increases were 23% and 20%, respectively. The ratio of the sC(aw) of asthmatic small airways to that of healthy small airways was 0.57, and the ratio was 0.70 for larger airways. The morphometric changes and sC(aw) in asthma model mice were significantly lower than those of healthy mice. The differences in sC(aw) between healthy and asthma model mice were greater for smaller airways.

Animals↗

PubMed2006

A structural origin of latency relaxation in frog skeletal muscle.

A time-resolved x-ray diffraction study at a time resolution of 0.53 ms was made to investigate the structural origin of latency relaxation (LR) in frog skeletal muscle. Intensity and spacing measurements were made on meridional reflections from the Ca-binding protein troponin and the thick filament and on layer lines from the thin filament. At 16 degrees C, the intensity and spacing of all reflections started to change at 4 ms, simultaneously with the LR. At 0 degrees C, the intensity of the troponin reflection and the layer lines from the thin filament and the spacing of the 14.3-nm myosin meridional reflection, but not the spacing of other myosin meridional reflections, began to change at approximately 15 ms, when the LR also started. Intensity of myosin-based reflections started to change later. When the muscle was stretched to non-overlap length, the intensity and spacing changes of the myosin reflections disappeared. The simultaneous spacing change of the 14.3-nm myosin meridional reflection with the LR suggests that detachment of myosin heads that are bound to actin in the resting muscle is the cause of the LR.

Actin Cytoskeleton↗

PubMed2006

Structural changes of cross-bridges on transition from isometric to shortening state in frog skeletal muscle.

Structural changes in the myosin cross-bridges were studied by small-angle x-ray diffraction at a time resolution of 0.53 ms. A frog sartorius muscle, which was electrically stimulated to induce isometric contraction, was released by approximately 1% in 1 ms, and then its length was decreased to allow steady shortening with tension of approximately 30% of the isometric level. Intensity of all reflections reached a constant level in 5-8 ms. Intensity of the 7.2-nm meridional reflection and the (1,0) sampling spot of the 14.5-nm layer line increased after the initial release but returned to the isometric level during steady shortening. The 21.5-nm meridional reflection showed fast and slow components of intensity increase. The intensity of the 10.3-nm layer line, which arises from myosin heads attached to actin, decreased to a steady level in 2 ms, whereas other reflections took longer, 5-20 ms. The results show that myosin heads adapt quickly to an altered level of tension, and that there is a distinct structural state just after a quick release.

Actins↗

PubMed2006

Coexistence of two domains in intercellular lipid matrix of stratum corneum.

The outermost layer of the skin, the stratum corneum (SC), is composed of corneocytes and an intercellular lipid matrix. The matrix acts as both the main barrier and also as the pathway of water, drugs, etc. across the SC. In the mammalian SC, the longitudinal arrangement of the lipid molecules, consisting of long and short lamellar structures with repeat distances of about 13 nm and 6 nm, respectively, has been observed by small-angle X-ray diffraction. In the lateral arrangement of the lipid molecules, hexagonal and orthorhombic hydrocarbon-chain packing has been observed by wide-angle X-ray diffraction. From the systematic study of the temperature dependence of simultaneous small- and wide-angle X-ray diffraction patterns, we demonstrate that the intercellular lipid matrix forms two domains, which consist at room temperature of a long lamellar structure with hexagonal hydrocarbon-chain packing and a short lamellar structure with orthorhombic hydrocarbon-chain packing.

Animals↗

PubMed2006

Fast tomography using quasi-monochromatic undulator radiation.

A beamline with a helical undulator has been used without a monochromator for fast high-resolution tomographic imaging with an X-ray energy of 12.4-16.5 keV and an energy bandwidth of 2-3%. The X-ray beam was expanded with two mirrors to 12 mm x 4 mm. The X-ray field was made uniform by a diffuser. The detector pixel size was 9.9 microm x 9.9 microm. At the highest speed, a 180 degrees scan was completed in 6 s with 454 projections. Beam-hardening effects were not significant. This technique may be useful in studying time-dependent structural changes of soft materials such as polymers and biological samples.

Animals↗

PubMed2006

Combined effects of ethanol and L-menthol on hairless rat stratum corneum investigated by synchrotron X-ray diffraction.

Synchrotron X-ray diffraction was employed to evaluate the effect of ethanol and l-menthol on lipid arrangements in the stratum corneum of hairless rats. Two sharp diffractions (S=2.40 and S=2.67, corresponding to spacing of 0.417 nm and 0.374 nm respectively) were observed on the broad hump peak derived from soft keratin. To assist in understanding the effects of treatment with ethanol and l-menthol, an abundance ration of lipid hydrocarbon chain packing index (R(H/O)) was defined as R(H/O)=(Peak area at S=2.40 nm(-1))/(Peak area at S=2.67 nm(-1)). When ethanol was applied to the stratum corneum the intensities of diffraction peaks declined slightly. The R(H/O) values observed were not affected by variations in ethanol concentrations in the range 0-40% (w/w). The R(H/O) values did not change even when treatment with ethanol (40%, w/w) was extended to 8 h. These results suggested that lipid arrangements in the stratum corneum were not affected by ethanol. On the other hand, exposure of the stratum corneum to 2% (w/w) L-menthol caused a significant decrease in R(H/O) value. It was shown that L-menthol was dispersed through the stratum corneum, intruded mainly into hexagonal hydrocarbon chain packing, and disrupted the regular organization of these structures.

Animals↗

PubMed2006

Structural analysis of human hair single fibres by scanning microbeam SAXS.

The origin of the curliness of human hair was revealed by scanning microbeam small angle X-ray scattering (SAXS), based on the nanostructure of keratin fibre arrangement. Scanning microbeam SAXS patterns of single hair fibres have been measured across the fibres and the differences in the patterns between the inner and the outer sides of the curvature were successfully detected. The analysis of the equatorial and azimuthal scattering intensity profiles showed that the arrangement of the intermediate filaments was different between the inner and the outer sides of the curvature. From the analogy with Merino and Romny wool, it is suggested that different types of cortices exist in human hair. It is concluded that, regardless of the ethnic origins (African, Caucasian, and Asian), the macroscopic curl shape of the hair fibre originate from the inhomogeneity of the internal nanostructure, arising from inhomogeneous distribution of two types of cortices.

Black or African American↗

PubMed2006

High-resolution powder diffraction study of purple membrane with a large Guinier-type camera.

X-ray diffraction patterns from a film of oriented purple membranes, which comprise two-dimensional crystals of bacteriorhodopsin (BR) trimers, were recorded with a 1 m-pathlength Guinier-type camera at SPring-8 BL40B2. A well focused X-ray beam and a camera with a high angular resolution of 0.024 degrees enabled a powder diffraction profile with very sharp and well separated peaks to be obtained up to a resolution of 2.3 A. Using integrated diffraction intensities up to a Bragg spacing of 4.2 A, a cluster of bulky amino acid residues and the head group of the BR chromophore are apparent in the electron density map projected along the membrane normal. Thus, a combination of synchrotron X-rays and large Guinier camera can be used for analyzing the conformational changes of BR in the intact state. In addition, the method might be extended to the structural analysis of film materials composed of two-dimensional arrays of nanoparticles.

Equipment Design↗

PubMed2006

Evolution of long-range myofibrillar crystallinity in insect flight muscle as examined by X-ray cryomicrodiffraction.

Insect flight muscle is known for its crystal-quality regularity of contractile protein arrangement within a sarcomere. We have previously shown by X-ray microdiffraction that the crystal-quality regularity in bumble-bee flight muscle is not confined within a sarcomere, but extends over the entire length of a myofibril (>1000 sarcomeres connected in series). Because of this, the whole myofibril may be regarded as a millimetre-long, natural single protein crystal. Using bright X-ray beams from a synchrotron radiation source, we examined how this long-range crystallinity has evolved among winged insects. We analysed >4600 microdiffraction patterns of quick-frozen myofibrils from 50 insect species, covering all the major winged insect orders. The results show that the occurrence of such long-range crystallinity largely coincides with insect orders with asynchronous muscle operation. However, a few of the more skilled fliers among lower-order insects apparently have developed various degrees of structural regularity, suggesting that the demand for skillful flight has driven the lattice structure towards increased regularity.

Animals↗

PubMed2006

Naturally engineered glycolipid biosurfactants leading to distinctive self-assembled structures.

Self-assembling properties of "natural" glycolipid biosurfactants, mannosyl-erythritol lipids A and B (MEL-A, MEL-B), which are abundantly produced from yeast strains, were investigated by using the fluorescence-probe method, dynamic light-scattering (DLS) analysis, freeze-fracture transmission electron microscopy (FF-TEM), and synchrotron small/wide-angle X-ray scattering (SAXS/WAXS) analysis, among other methods. Both MEL-A and MEL-B exhibit excellent self-assembly properties at extremely low concentrations; they self-assemble into large unilamellar vesicles (LUV) just above their critical-aggregation concentration (CAC). The CAC(I) value was found to be 4.0x10(-6) M for MEL-A and 6.0x10(-6) M for MEL-B. Moreover, the self-assembled structure of MEL-A above a CAC(II) value of 2.0x10(-5) M was found to drastically change into sponge structures (L3) composed of a network of randomly connected bilayers that are usually obtained from a complicated multicomponent "synthetic" surfactant system. Interestingly, the average water-channel diameter of the sponge structure was 100 nm. This is relatively large compared with those obtained from "synthetic" surfactant systems. In addition, MEL-B, which has a hydroxyl group at the C-4' position on mannose instead of an acetyl group, gives only one CAC; the self-assembled structure of MEL-B seems to gradually move from LUV to multilamellar vesicles (MLV) with lattice constants of 4.4 nm, depending on the concentration. Furthermore, the lyotropic-liquid-crystal-phase observation at high concentrations demonstrates the formation of an inverted hexagonal phase (H2) for MEL-A, together with a lamella phase (L(alpha)) for MEL-B, indicating a difference between MEL-A and MEL-B molecules in the spontaneous curvature of the assemblies. These results clearly show that the difference in spontaneous curvature caused by the single acetyl group on the head group probably decides the direction of self-assembly of glycolipid biosurfactants. The unique and complex molecular structures with several chiral centers that are molecularly engineered by microorganisms must have led to the sophisticated self-assembling properties of the glycolipid biosurfactants.

Chemistry Techniques, Analytical↗

PubMed2005

An X-Ray diffraction study on mouse cardiac cross-bridge function in vivo: effects of adrenergic {beta}-stimulation.

To investigate how beta-stimulation affects the contractility of cardiac muscle, x-ray diffraction from cardiac muscle in the left ventricular free wall of a mouse heart was recorded in vivo. To our knowledge, this is the first x-ray diffraction study on a heart in a living body. After the R wave in electrocardiograms, the ratio of the intensities of the equatorial (1,0) and (1,1) reflections decreased for approximately 50 ms from a diastolic value of 2.1 to a minimum of 0.8, and then recovered. The spacing of the (1,0) lattice planes increased for approximately 90 ms from a diastolic value of 37.2 nm to a maximum of 39.1 nm, and then returned to the diastolic level, corresponding to approximately 10% stretch of sarcomere. Stimulation of beta-adrenergic receptor by dobutamine (20 microg/kg/min) accelerated both the decrease in the intensity ratio, which reached a smaller systolic value, and the increase in the lattice spacing. However, the intensity ratio and spacing at the end-diastole were unchanged. The recovery of the lattice spacing during relaxation was also accelerated. The mass transfer to the thin filaments at systole in a beta-stimulated heart was close to the peak value in twitch of frog skeletal muscle at 4 degrees C, showing that the majority of cross-bridges have been recruited with few in reserve.

Actins↗

PubMed2005

Crystal structure of M-Ras reveals a GTP-bound "off" state conformation of Ras family small GTPases.

Although some members of Ras family small GTPases, including M-Ras, share the primary structure of their effector regions with Ras, they exhibit vastly different binding properties to Ras effectors such as c-Raf-1. We have solved the crystal structure of M-Ras in the GDP-bound and guanosine 5'-(beta,gamma-imido)triphosphate (Gpp(NH)p)-bound forms. The overall structure of M-Ras resembles those of H-Ras and Rap2A, except that M-Ras-Gpp(NH)p exhibits a distinctive switch I conformation, which is caused by impaired intramolecular interactions between Thr-45 (corresponding to Thr-35 of H-Ras) of the effector region and the gamma-phosphate of Gpp(NH)p. Previous 31P NMR studies showed that H-Ras-Gpp(NH)p exists in two interconverting conformations, states 1 and 2. Whereas state 2 is a predominant form of H-Ras and corresponds to the "on" conformation found in the complex with effectors, state 1 is thought to represent the "off" conformation, whose tertiary structure remains unknown. 31P NMR analysis shows that free M-Ras-Gpp(NH)p predominantly assumes the state 1 conformation, which undergoes conformational transition to state 2 upon association with c-Raf-1. These results indicate that the solved structure of M-Ras-Gp-p(NH)p corresponds to the state 1 conformation. The predominance of state 1 in M-Ras is likely to account for its weak binding ability to the Ras effectors, suggesting the importance of the tertiary structure factor in small GTPase-effector interaction. Further, the first determination of the state 1 structure provides a molecular basis for developing novel anti-cancer drugs as compounds that hold Ras in the state 1 "off" conformation.

Amino Acid Sequence↗

PubMed2005

X-ray microdiffraction and conventional diffraction from frozen-hydrated biological specimens.

A system for recording microdiffraction patterns from micrometer-sized quick-frozen hydrated biological specimens at the high-flux beamline BL40XU of SPring-8 is described. The optics consists of a pair of pinholes drilled into tantalum substratum, with a defining aperture of diameter 2 microm. The frozen specimens are placed in an in-vacuum cryochamber mounted on a three-axis goniometer, where the specimens are stably held at a liquid-nitrogen temperature ( approximately 74 K). A beam size of 1.5 microm (full width at half-maximum) is attained at the sample position. By using this system, diffraction patterns have been recorded from an isolated single myofibril (diameter approximately 3 microm) of an insect flight muscle in an area equivalent to a single sarcomere (length approximately 3 microm). The technique is potentially applicable to other micrometer-sized hydrated biological specimens, which are more susceptible to radiation damage than dry synthetic polymers or biopolymers. The quick-freezing of biological specimens has also been proven useful in reducing the specimen volume in the beam in conventional diffraction recordings.

Animals↗

PubMed2005

Structural changes of actin-bound myosin heads after a quick length change in frog skeletal muscle.

Changes in the x-ray diffraction pattern from a frog skeletal muscle were recorded after a quick release or stretch, which was completed within one millisecond, at a time resolution of 0.53 ms using the high-flux beamline at the SPring-8 third-generation synchrotron radiation facility. Reversibility of the effects of the length changes was checked by quickly restoring the muscle length. Intensities of seven reflections were measured. A large, instantaneous intensity drop of a layer line at an axial spacing of 1/10.3 nm(-1) after a quick release and stretch, and its partial recovery by reversal of the length change, indicate a conformational change of myosin heads that are attached to actin. Intensity changes on the 14.5-nm myosin layer line suggest that the attached heads alter their radial mass distribution upon filament sliding. Intensity changes of the myosin reflections at 1/21.5 and 1/7.2 nm(-1) are not readily explained by a simple axial swing of cross-bridges. Intensity changes of the actin-based layer lines at 1/36 and 1/5.9 nm(-1) are not explained by it either, suggesting a structural change in actin molecules.

Actins↗

PubMed2005

Localized morphometric deformations of small airways and alveoli in intact mouse lungs under quasi-static inflation.

Localized morphometric deformations of small airways and alveoli during respiration have several biomechanical and physiological implications. We developed fast synchrotron radiation CT system to visualize the small airways and alveoli of an intact mouse lung without fixation and dehydration, and analyzed their localized morphometric deformations between functional residual capacity (FRC) and total lung capacity (TLC). The maximum resolution of 32.6lp/mm at the 5% modulation transfer function level can be achieved with 11.8-microm voxels and 7-min scanning. Compared with the values at FRC, the diameter and length for smaller airways (diameter at FRC <200 microm) increased by 68.8% and 29.5% (averaged value), and those for larger airways (diameter at FRC >400 microm) increased by 45.2 and 22.9% (averaged value), at TLC. Moreover we defined the volume behavior as the percentage of airway volume at FRC for TLC. The volume behavior for the small airways was not similar to that of the lung volume. These results indicated that all airways did not behave homogenously.

Animals↗

PubMed2005

Morphometric deformations of small airways and alveoli under quasi-static inflation process.

Localized morphometric deformations of small airways and alveoli during respiration have many biomedical and physiological implications. We developed fast synchrotron radiation CT system to visualize the small airways and alveoli of an intact mouse lung without fixation and dehydration, and analyzed their localized morphometric deformations between functional residual capacity (FRC) and total lung capacity (TLC). In the diameter behavior, the averaged and range values were significantly larger for smaller airways (68.8%, range: 0.36-0.89) than larger airways (45.2%, range: 0.40-0.57). These results indicated that the airway did not deformed in same manner and that these morphological differences characterized the heterogeneous lung function.

Air Pressure↗

PubMed2004

Structural transition of bacteriorhodopsin is preceded by deprotonation of Schiff base: microsecond time-resolved x-ray diffraction study of purple membrane.

The structural changes in the photoreaction cycle of bacteriorhodopsin, a light-driven proton pump, was investigated at a resolution of 7 angstroms by a time-resolved x-ray diffraction experiment utilizing synchrotron x rays from an undulator of SPring-8. The x-ray diffraction measurement system, used in coupling with a pulsed YAG laser, enabled us to record a diffraction pattern from purple membrane film at a time-resolution of 6 micros over the time domain of 5 micros to 500 ms. In the time domain, the functionally most important M-intermediate appears. A series of time-resolved x-ray diffraction data after photo-excitation showed clear intensity changes caused by the conformational changes of helix G in the M-intermediate. The population of the reaction intermediate was prominently observed at approximately 5 ms after a photo-stimulus. In contrast, absorption measurement indicated the deprotonation of the Schiff base predominantly occurred at approximately 300 micros after a photo-stimulus. These results showed that the conformational changes characterizing structurally the M-intermediate predominantly occur at a later stage of the deprotonation of the Schiff base. Thus, the M-intermediate can be divided into two metastable stages with different physical characteristics.

Bacteriorhodopsins↗

PubMed2004

CCD-based X-ray area detector for time-resolved diffraction experiments.

A fast X-ray area detector for diffraction, scattering and imaging experiments at microsecond to millisecond time resolution has been developed. The key element of the detector is a fast (291 frames s(-1)) framing camera with three CCDs. A prism forms identical images on the CCDs and the frame rate is increased three times by reading them alternately. In order to convert X-rays into visible light that is detectable with the CCDs, an X-ray image intensifier is used. The camera can also be used with a high-resolution X-ray detector. In both cases it was found to be important to use a phosphor with a short decay time to fully make use of the high-speed framing capability of the camera. Preliminary results of a fibre diffraction experiment on a skeletal muscle and coronary angiography are presented.

Animals↗