Biomedical subjects

Shigeru Sugiyama

Publications and source records attributed to Shigeru Sugiyama.

At least 19 recordsLinked to original sources

PubMed2005

Asymmetric swimming pattern of Vibrio alginolyticus cells with single polar flagella.

The swimming pattern of bacteria with single polar flagella has usually been described as "run and reverse". We observed the swimming traces of monotrichously flagellated Vibrio alginolyticus cells and examined the relationship between the swimming pattern and the sense of progress. Swimming in regions other than a solid surface was confirmed to be linear run and reverse. Near a solid surface, the traces consisted of "run and arc"; the cells were found to curve sharply during backward swimming, while they progressed linearly during forward swimming. The "run and arc" swimming pattern may play an important role in the chemotaxis strategy of marine bacteria at solid surfaces.

Adaptation, Physiological↗

PubMed2004

Dermatitis due to epiregulin deficiency and a critical role of epiregulin in immune-related responses of keratinocyte and macrophage.

Epidermal growth factor (EGF) family members, including epiregulin (EP), play a fundamental role in epithelial tissues; however, their roles in immune responses and the physiological role of EP remain to be elucidated. The skin has a versatile system of immune surveillance. Biologically active IL-1alpha is released to extracellular space upon damage from keratinocytes and is a major player in skin inflammation. Here, we show that EP is expressed not only in keratinocytes but also in tissue-resident macrophages, and that EP-deficient (EP(-/-)) mice develop chronic dermatitis. Wound healing in the skin in EP(-/-) mice was not impaired in vivo, nor was the growth rate of keratinocytes from EP(-/-) mice different from that of WT mice in vitro. Of interest is that in WT keratinocytes, both IL-1alpha and the secreted form of EP induced down-regulation of IL-18 mRNA expression, which overexpression in the epidermis was reported to induce skin inflammation in mice, whereas the down-regulation of IL-18 induced by IL-1alpha was impaired in EP(-/-) keratinocytes. Although bone marrow transfer experiments indicated that EP deficiency in non-bone-marrow-derived cells is essential for the development of dermatitis, production of proinflammatory cytokines by EP(-/-) macrophages in response to Toll-like receptor agonists was much lower, compared with WT macrophages, whose dysfunction in EP(-/-) macrophages was not compensated by the addition of the secreted form of EP. These findings, taken together, suggested that EP plays a critical role in immune/inflammatory-related responses of keratinocytes and macrophages at the barrier from the outside milieu and that the secreted and membrane-bound forms of EP have distinct functions.

Animals↗

PubMed2004

Forced rotation of Na+-driven flagellar motor in a coupling ion-free environment.

Rotational characteristics of Na+-driven flagellar motor in the presence and absence of coupling ion were analyzed by electrorotation method. The motor rotated spontaneously in the presence of Na+, and the rotation accelerated or decelerated following the direction of the applied external torque. The spontaneous motor rotation was inhibited by removal of external Na+, however, the motor could be forcibly rotated by relatively small external torque applied by the electrorotation apparatus. The observed characteristic of the motor was completely different from that of ATP-driven motor systems, which form rigor bond when their energy source, ATP, is absent. The internal resistance of the flagellar motor increased significantly when the coupling ion could not access the inside of the motor, suggesting that the interaction between the rotor and the stator is changed by the binding of the coupling ion to the internal sites of the motor.

Bacillus↗

PubMed2004

Inducible costimulator-dependent IL-10 production by regulatory T cells specific for self-antigen.

In this study, we investigated the relationship between the expression levels of self-antigen and the function of self-reactive T cells in the periphery. To this end, we used two rat insulin promoter-ovalbumin (RIP-OVA) transgenic mice (RIP-OVA(high), RIP-OVA(low)) in which was produced only in pancreatic beta-islet cells. The OVA-producing transgenic mice were crossed to DO.11.10 (DO) mice expressing a T cell antigen receptor specific for OVA(323-339). The responsiveness of peripheral CD4(+) T cells in the double transgenic mice was examined. We demonstrated that hyporesponsive but highly IL-10-producing T cells were developed in DO x OVA(high) mice only, not in DO x OVA(low) mice. These IL-10-producing T cells exhibited regulatory activity both in in vitro and in vivo experiments. Moreover, these IL-10-producing regulatory T (Tr) cells expressed high levels of inducible costimulator (ICOS) before in vitro stimulation. Blockade of ICOS-signaling inhibited the production of IL-10 and abrogated the inhibitory function of these Tr cells. Thus, these results suggested that the development of IL-10-producing Tr cells depends on the expression levels of self-antigen in vivo and that ICOS signal plays a critical role in immune regulation by IL-10-producing Tr cells in self-tolerance.

Animals↗

PubMed2004

Molecular basis of antigen recognition by insulin specific T cell receptor.

The TCR alpha/beta chains recognize antigen peptides bound to the groove of the MHC class II molecule. The crystal structure analyses of the TCR/peptide/MHC class II complexes have revealed that the Valpha chains play a significant role in antigen recognition. However, molecular details which amino acid residues of the Valpha chain are able to contribute to fine antigen specificity are not clearly understood. Previously, we have classified a panel of T hybrids specific for insulin isotypes from different species of animals into four groups based on response profiles to these antigens. In particular, the group III (pork insulin > or = beef insulin hierarchy of responsiveness) and IV (pork insulin >> beef insulin hierarchy of responsiveness) T hybrids are interesting, since these TCR alpha/beta chains with marked different antigen specificities demonstrate identical gene usages and very similar sequences. To specifically address the molecular requirements for insulin recognition by TCR, the TCR alpha and beta chain genes from these group III and IV T hybrids were transfected into 58 alpha-beta- T hybrid. The experiments suggested that CDR3alpha dictates the fine antigen specificity. Then, we have introduced a series of mutations into position 95 of CDR3alpha. The mutation experiments clearly indicated that position 95alpha determines the antigen specificity of the group III and IV T hybrids.

Amino Acid Sequence↗

PubMed2004

Effects of acetic acid treatment on plant chromosome structures analyzed by atomic force microscopy.

Acetic acid treatment has been frequently used to remove cellular contaminants from plant chromosome samples for structural analyses by scanning electron microscopy and atomic force microscopy (AFM). We evaluated the effects of various concentrations of acetic acid treatments on barley chromosome structures by using AFM. The long-term 45% acetic acid treatment significantly damaged the chromosome structures, although the treatment effectively removed the cellular contaminants. On the other hand, the treatment with 15% acetic acid could not obtain sufficiently clean chromosome samples and the chromosome surface structures could not be observed. In contrast, we obtained clean chromosome preparation without severe damage by using an intermediate concentration (30%) of acetic acid treatment. In the centromeric region, we could observe fiber structures with a width of 100 nm, which were composed of ca. 50-nm granules and aligned to the axes of chromosomes. Thus, AFM analysis of chromosomes appropriately treated with acetic acid will provide important insights into the organization of higher-order structures of plant chromosomes.

Acetic Acid↗

PubMed2004

Numerical analysis of the depletion zone formation around a growing protein crystal.

It is expected that a protein depletion zone and an impurity depletion zone are formed around a crystal during protein crystal growth if the diffusion field around the crystal is not disturbed. The growth rate of the crystal may be decreased and the impurity uptake may be suppressed to result in highly ordered crystals if these zones are not disturbed. It is well known that a microgravity environment can reduce convective fluid motion, and this is thought to disturb the depletion zones. Therefore, we expect that crystals grown in space can attain better quality than those grown on the ground. In this study, we estimate the depletion zone formation numerically and discuss the results of crystallization in space experiments. In case of alpha-amylase, most of the crystals form a cluster-like morphology on the ground using PEG 8000 as a precipitant. However, in space, we have obtained a single and high-quality crystal grown from the same sample compositions. We have measured the viscosity of the solution, the diffusion coefficient, and the growth rate of protein crystals on the ground. Applying numerical analysis to these values a significant depletion zone was expected to form mainly due to higher values of the viscosity. This might be one of the main reasons for better quality single crystals grown in space, where the depletion zone is thought to remain undisturbed. For protein crystallization experiments, salts are widely used as a precipitant. However, in that case, reduced concentration depletion zone effects can be expected because of a low viscosity. Therefore, if it is possible to increase the viscosity of the protein solution by means of an additive, the depletion zone formation effect would be enhanced to provide a technique that would be especially effective in space.

Aspergillus oryzae↗

PubMed2004

The crystal structure of human dipeptidyl peptidase IV (DPPIV) complex with diprotin A.

Dipeptidyl peptidase IV (DPPIV) is a serine protease, a member of the prolyl oligopeptidase (POP) family, and has been implicated in several diseases. Therefore, it seems important to develop selective inhibitors for human DPPIV (hDPPIV) that are able to control the biological function of hDPPIV. In order to elucidate the binding mode and substrate specificity, we determined the crystal structure complex of hDPPIV and diprotin A (IIe-Pro-IIe), a slowly hydrolyzed substrate of hDPPIV, at 2.2 A resolution. In this paper, we discuss the molecular interaction mechanism of diprotin A with hDPPIV based on the X-ray crystal structure.

Binding Sites↗

PubMed2003

A simplified counter diffusion method combined with a 1D simulation program for optimizing crystallization conditions.

We developed a new protein crystallization method has been developed using a simplified counter-diffusion method for optimizing crystallization condition. It is composed of only a single capillary, the gel in the silicon tube and the screw-top test tube, which are readily available in the laboratory. The one capillary can continuously scan a wide range of crystallization conditions (combination of the concentrations of the precipitant and the protein) unless crystallization occurs, which means that it corresponds to many drops in the vapor-diffusion method. The amount of the precipitant and the protein solutions can be much less than in conventional methods. In this study, lysozyme and alpha-amylase were used as model proteins for demonstrating the efficiency of this method. In addition, one-dimensional (1-D) simulations of the crystal growth were performed based on the 1-D diffusion model. The optimized conditions can be applied to the initial crystallization conditions for both other counter-diffusion methods with the Granada Crystallization Box (GCB) and for the vapor-diffusion method after some modification.

Capillary Action↗

PubMed2003

Scanning Near-field Optical/Atomic Force Microscopy detection of fluorescence in situ hybridization signals beyond the optical limit.

Fluorescence in situ hybridization (FISH) is widely used in molecular biological study. However, high-resolution analysis of fluorescent signals is theoretically limited by the 300-nm resolution optical limit of light microscopy. As an alternative to detection by light microscopy, we used Scanning Near-field Optical/Atomic Force Microscopy (SNOM/AFM), which can simultaneously obtain topographic and fluorescent images with nanometer-scale resolution. In this study, we demonstrated high-resolution SNOM/AFM imaging of barley chromosome (Hordeum vulgare, cv. Minorimugi) FISH signals using telomeric DNA probes. Besides detecting the granular structures on chromosomes in a topographic image, we clearly detected fluorescent signals in telomeric regions with low-magnification imaging. The high-resolution analysis suggested that one of the telomeric signals could be observed by expanded imaging as two fluorescent regions separated by approximately 250 nm. This result indicated that the fluorescent signals beyond the optical limit were detected with higher resolution scanning by SNOM/AFM.

Chromosomes↗

PubMed2003

Transfer-printing of highly aligned DNA nanowires.

We developed a simple method of reproducibly creating highly aligned DNA nanowires without any surface modifications or special equipment. Stretched DNA molecules initially present on the PDMS sheet were transferred onto another surface using transfer-printing (TP). Fluorescent microscopic and atomic force microscopic images revealed that many DNA molecules were highly aligned on surfaces after TP. Furthermore, it was also possible to realize the two-dimensional assembly of DNA nanowires by repeating TP.

Bacteriophage lambda↗

PubMed2003

The structure and function of human dipeptidyl peptidase IV, possessing a unique eight-bladed beta-propeller fold.

Dipeptidyl peptidase IV (DPPIV) is a serine protease, a member of the prolyl oligopeptidase (POP) family, and has been implicated in several diseases. Therefore, the development of DPPIV selective inhibitors, which are able to control the biological function of DPPIV, is important. We determined the crystal structure of human DPPIV at 2.6A resolution. The molecule consists of a unique eight-bladed beta-propeller domain in the N-terminal region and a serine protease domain in the C-terminal region. Also, the large "cave" structure, which is thought to control the access of the substrate, is found on the side of the beta-propeller fold. Comparison of the overall amino acid sequence between human DPPIV and POP shows low homology (12.9%). In this paper, we report the structure of human DPPIV, especially focusing on a unique eight-bladed beta-propeller domain. We also discuss the way for the access of the substrate to this domain.

Amino Acid Sequence↗

PubMed2003

Crystallization and preliminary X-ray study of human dipeptidyl peptidase IV (DPPIV).

Human DPPIV has been expressed in the baculovirus system and purified and crystallized using the hanging-drop method. A crystal was obtained from 180 mM Gly-NaOH buffer pH 9.5 containing 18% PEG 4000 and 180 mM sodium acetate. The crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 118.04, b = 125.92, c = 136.84 A, and diffracts beyond 2.6 A resolution. There are two molecules per asymmetric unit, indicating a solvent content of 57.6%.

Cloning, Molecular↗

PubMed2003

Hierarchical chromatin structure of Schizosaccharomyces pombe revealed by atomic force microscopy.

Many structural studies on higher eukaryotic chromatin have been carried out, but chromatin structure in fungi remains unclear. Schizosaccharomyces pombe has been used for investigations of chromosome function; however, the structural details of S. pombe chromatin have not been clarified owing to its small nucleus. We used atomic force microscopy for nano-scale imaging of chromatin isolated from S. pombe. Topographic images indicated that nuclear chromatin contained at least three hierarchical structures: large-scale chromatin fibers, spherical domains in the fibers, and nodules in the domains. The average diameters of the domain and the nodule were 363 +/- 85.2 nm and 46.2 +/- 9.30 nm. Each structure comprising the hierarchy was similar to higher eukaryotic chromatin thus far observed, despite definite differences in chromatin organization at the nucleosomal level. The presence of histone H1 suggested that there might be an alternative to compensate for histone H1 lacking in S. pombe.

Cell Cycle↗

PubMed2003

Atomic force microscopy study of chromosome surface structure changed by protein extraction.

We applied atomic force microscopy (AFM) to investigate the surface structure of barley chromosome in combination with a chemical treatment method. As a result, we have obtained high-resolution topographic images of granular structures with a diameter of ca. 50 nm on the surface of critical-point dried metaphase chromosomes. Treatment with 2M NaCl significantly modified the chromosome surface structure: surface roughness was increased and chromosome thickness was decreased. The NaCl treatment extracted two major proteins with molecular weights of 4000 and 20,000 Da. These proteins might be belonging to non-histone protein families that do not contain any aromatic amino acid. The results demonstrate the advantage of the combined method of high-resolution AFM imaging and chemical treatments for understanding nano-scale surface structures of the chromosome.

Chromosome Structures↗

PubMed2003

Analysis by atomic force microscopy of morphological changes in barley chromosomes during FISH treatment.

We employed atomic force microscopy (AFM) to examine structural changes in barley chromosomes during the four steps of standard FISH processes. Rehydration and dehydration with alcohol accompanying RNase treatment increased chromosome arm width and decreased chromosome height about 50%. Subsequent heat denaturation reduced chromosome height further. These three-dimensional structural changes of the chromosomes were substantial, but the FISH signal produced by the hybridization of fluorescent probes was clear when observed by a fluorescence microscope. In higher-magnification images, we observed granular structures considered to represent the chromatin fiber on the surface of the chromosomes in each FISH protocol step. These our results indicate that FISH treatments result in severe damage of the three-dimensional higher-order structures of the chromosomes, although nano-structures, such as nucleosome and chromatin fibers, remain intact and relatively unaffected.

Artifacts↗

PubMed2003

Method for patterning stretched DNA molecules on mica surfaces by soft lithography.

Lambda DNA was stretched and patterned on mica surface using soft lithography. A highly diluted solution of amino propyl trimethoxy silane in hexane was deposited on a line patterned polydimethylsiloxane (PDMS) stamp. The functionalized stamp was then used to pick up DNA by molecular combing while the line patterns are parallel to the liquid surface. The stamp was then microcontact printed on freshly cleaved mica. We successfully obtained stretched DNA pattern on mica surface. DNA was found to be stretched in patterns perpendicular to those carved on the stamp. The stretched DNA population was large enough to be used for molecular biology mapping studies. Furthermore, the possibility of locating stretched DNA molecules in the desired position by stamping makes this method a good candidate for assembling non-semiconductor molecular devices.

Aluminum Silicates↗

PubMed2003

[First domestic production of transaminase assay reagents].

Ultraviolet absorption has continued to improve and has become a commonly used method. The development of automated instruments has also contributed to its use, making the Reitman-Frankel Method retire from the prominent stage it once occupied. While the Camen Method was indicated to be short of substrates, it is now used after incorporating improvements proposed from various countries, including the JSCC recommendation from Japan, as a titration method for the enzyme reference materials. The JSCC Common Standards Method was further provisioned through detailed examinations ot its reagents and processes, and is utilized under strict conditions. Standardization has thus evolved from more technique to what includes reference materials.

Drug Industry↗