京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第22719号 / 理博第4628号 / 新制||理||1665(附属図書館) / 京都大学大学院理学研究科化学専攻 / (主査)教授 杉山 弘, 教授 深井 周也, 教授 秋山 芳展 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Understanding the cellular membrane interaction with membrane active biomolecules and antimicrobial agents provides an insight in their working mechanism. Here, we studied the effect of antimicrobial agents; a recently developed peptidomimetics E107-3 and colistin as well as the N-terminal helix H0, of Endophilin A1 on the lipid bilayer. It is important to discern the interaction mechanism of antimicrobial peptides with lipid membranes in battling multidrug resistant bacterial pathogens. We study the modification of structural and mechanical properties with a recently reported peptidomimetic on lipid bilayer. The compound referred to as E107-3 is synthesized based on the acylated reduced amide scaffold and has been shown to exhibit good antimicrobial potency. This compound increases lipid bilayer permeability as indicated by our vesicle leakage essay. Micropipette aspiration experiment shows that exposure of GUV to the compound causes the protrusion length Lp to spontaneously increase and then decrease, followed by GUV rupture. Solution atomic force microscopy (AFM) is used to visualize lipid bilayer structural modulation within a nanoscopic regime. This compound induces nanoscopic heterogeneous structures rather than pore like structures as produced by melittin. Finally, we use AFM-based force spectroscopy to study the impact of the compound on lipid bilayer’s mechanical properties. With the incremental addition of this compound, we found the bilayer puncture force decreases moderately and a 39% decrease of the bilayer area compressibility modulus KA. To explain our experimental data, we propose a membrane interaction model encompassing disruption of lipid chain packing and extraction of lipid molecules. The later action mode is supported by our observation of a double-bilayer structure in the presence of fusogenic calcium ions. Polyanionic Lipopolysaccharides LPS are important in regulating the permeability of outer membrane (OM) of gram-negative bacteria. To initiate the bactericidal activity of polymyxins, it is essential to impair the LPS-enriched OM. Here, we study the mechanism of membrane permeability caused by colistin (Polymyxin E) of LPS/phospholipid bilayers. Our vesicle leakage experiment showed that colistin binding enhanced bilayer permeability; the maximum increase in the bilayer permeability was positively correlated with the LPS fraction. Addition of magnesium ions abolished the effect of LPS in enhancing bilayer permeabilization. Solution atomic force microscopy (AFM) measurements on planar lipid bilayers shows the formation of nano- and macro clusters which protruded from the bilayer by ~2nm. Moreover, increasing the fraction of LPS or colistin enhances the formation of clusters but inhibits by magnesium ions addition. To explain our experimental data, we proposed a lipid-clustering model where colistin binds to LPS to form large-scale complexes segregated from zwitterionic phospholipids. The discontinuity (and thickness mismatch) at the edge of LPS-colistin clusters will create a passage that allows solutes to permeate through. The proposed model is consistent with all data obtained from our leakage and AFM experiments. Our results of LPS-dependent membrane restructuring provided useful insights into the mechanism that could be used by polymyxins in impairing the permeability barrier of the OM of Gram-negative bacteria. Also, we studied the effect of helix H0 of a membrane modification inducing protein endophilin, on planar bilayer. We obtained transmembrane defects on the bilayer when scanned.with AFM.

The thesis is focused on the physics of magnetic nanoparticles (NPs), starting from the solution of magnetic structure, internal alignment within the single particle and role of interactions and particle structure in magnetic response of systems of the NPs. Moreover, the macroscopic arrangement of the NPs and its effect on the properties of system containing the NPs are discussed. The work brings several new results and concepts, such as the solution of magnetic structure of the ε-Fe2O3 phase, methods of proper detection and description of magnetic metal catalyst in carbon nanotubes and role of the NP arrangement and their effect on graphene placed on the top of substrates decorated with the NPs. 1

Kenaf fiber is increasingly getting the attention of the industries due to its excellent mechanical properties, feasibility, growth rate, and ease of cultivation. On the other hand, cellulose nanofibril is one of the important building blocks of all the bast fibers which significantly contributes to their mechanical properties. However, most of the studies in the literature have estimated the value of axial elastic modulus for fiber-bundles which has some unavoidable issues resulting in incorrect modulus. Moreover, the transverse elastic modulus is another important parameter that also needs to be studied. Hence, to compensate for the gap in the literature, a single unit of both kenaf microfiber and cellulose nanofibril have been subjected to nanomechanical characterization to analyze their surface morphology and determine their elastic modulus in the axial and transverse direction. The experiments also pave to a protocol to characterize micro and nanofibrils nanomechanically and determine their elastic moduli.

No description available.

Amyloid aggregation involves the spontaneous formation of fibers from misfolded proteins. This process requires low energy input, results in robust fibers, and is thus of interest from a materials manufacturing perspective. The effect of glutamine content and hydrophobicity of template peptides on amyloid aggregation of a template-peptide system involving myoglobin was studied at near-physiological conditions by Fourier transform infrared spectroscopy, atomic force microscopy, field emission scanning electron microscopy, and nanoindentation. Hydrophobic interactions were found to be important for controlled hierarchical fiber growth via a cooperative mechanism, with the largest effect in myoglobin mixtures. Hydrophobic packing increased for most systems as aggregation progressed. The largest changes in structure occurred upon drying. When myoglobin was present with the highest glutamine-containing template (P7), the high glutamine peptide was not effective as a template, since it appeared to prefer self-catalysis. A low level of glutamine in some unordered templates was insufficient for amyloid development. However, templating was more important in glutamine-free templates mixed with myoglobin, which formed fibers with a surprisingly high elastic modulus. This may have been due to template patterning. Nanoindentation results confirmed that glutamine blocks were not necessary for strong intermolecular interactions and cooperative fibril formation. / Master of Science

In this project, we focus on developing a method to produce synthetic spider silk thin films. Using these films we optimized mechanical properties, lowered cost, and improved the environmental impact using different processing methods. Applications for spider silk films are broad, ranging from physical protection to biocompatible materials. This project was designed to improve mechanical properties and production methods of films made from synthetic forms of MaSp1 and MaSp2 from the dragline silk of Nephila clavipes. We have increased the mechanical stress (200 MPa) to more than 4 times that of similar products with elongations as high as 35%. The films have also been analyzed using NMR, XRD, and AFM or SEM showing that the secondary structure in as-poured films is mainly alpha-helical and after processing this structure turns to an aligned betasheet formation similar to that in spider silk fibers.

Listeria monocytogenes is a major concern for the food industry. It is one of the major agents causing listeriosis. The objective of the first part of this study is to evaluate the effect of hydration level on attached listeria monocytogenes on stainless steel/High density polyethylene transferred to food products. Attached cells were prepared on stainless steel/High density polyethylene. Transfer experiments were conducted from inoculated surface material slides to cold smoked salmon fillets. This experiment was repeated 6 times. The results were analyzed with an analysis of variance by SAS. The differences between the different RH% and surface conditions were not statistically significant. There was variability in between packages, brands and over the course of storage after opening, and likely contributed to the variability of transfer observed in this set of experiments. The objective of the second part of the research is to study the effect of hydration level on the detachment of Listeria monocytogenes biofilm growing on stainless steel by using Atomic force microscope. Biofilms were grown on stainless steel in drip flow bioreactor at 32 °C for 72 h. Then biofilms were equilibrated over saturated salt solution at 20 °C for 48 h before the Atomic Force Microscope experiment. The results showed that cohesive energy value of the biofilm increased with biofilm depth. Only square shaped displaced 2.5X2.5 μm region were visualized after serious of raster scanning under high load which means that moisture condition of Listeria monocytogenes biofilm can significantly affect the cohesiveness between of Listeria monocytogenes biofilm.

No description available.

In this thesis I am presenting a detailed study to optimize the deposition of magnetic molecules and gold nanoparticles in atomically flat surfaces by self-assembling them from solution. Epitaxially grown and atomically flat gold surface on mica is used as substrate for this study. These surfaces have roughness of the order one tenth of a nanometer and are perfect to image molecules and nanoparticles in the 1-10 nanometers range. The purpose of these studies is to find the suitable parameters and conditions necessary to deposit a monolayer of nano-substance on chips containing gold nanowires which will eventually be used to form single electron transistors by electromigration breaking of the nanowire. Maximization of the covered surface area is crucial to optimize the yield of finding a molecule/nanoparticle near the gap formed in the nanowire after electromigration breaking. Coverage of the surface by molecules/nanoparticles mainly depends on the deposition time and concentration of the solution used for the self-assembly. Deposition of the samples under study was done for different solution concentrations and deposition times until a self-assembly monolayer covering most of the surface area is obtained. Imaging of the surfaces after deposition was done by tapping-mode AFM. Analysis of the AFM images was performed and deposition parameters (i.e. coverage or molecule/particle size distribution) were obtained. The subjects of this investigation were a molecular polyoxometalate, a single-molecule magnet and functionalized gold nanoparticles. The obtained results agree with the structure of each of the studied systems. Using the optimized deposition parameters found in this investigation, single-electron transport measurements have been carried out. Preliminary results indicate the right choice of the deposition parameters.