京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第19958号 / 理博第4225号 / 新制||理||1607(附属図書館) / 33054 / 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 三木 邦夫, 教授 秋山 芳展 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Chemoreceptor dimers mediate bacterial chemotaxis through receptor arrays that form complexes with CheW and the kinase CheA. Both kinase activity and the rate of receptor methylation have been observed to change with receptor density in the signaling complexes of an assembled system. Receptor dimers play a structural and functional important role during the signaling process. The dimer is an established unit of a functional receptor array, but the exact packing arrangement of dimers in the signaling array is not known in detail. Two different models of the packing arrangement have been proposed, based on crystal structures of receptor cytoplasmic fragments: the trimer of dimers and hedgerow models. Here, we determine the importance of CF dimer organization on density dependence of kinase activity, receptor methylation, and we probe CF trimer organization by site-directed TMEA cross-linking. CF dimers were prepared by site-directed cysteine disulfide bond formation to test for a possible monomer-dimer equilibrium process in the density-dependence of kinase activity in the vesicle-assembled system. We found that density transition observed for CF4E is similar for both reduced and disulfide-linked CF, indicating that the CF is organized as dimers even at lower densities. CheR-catalyzed methylation experiment revealed that disulfide-linked CF dimers in solution are insufficient for efficient methylation, assembly of the CFs on a vesicle surface is required. CF trimers were trapped by the trifunctional crosslinker TMEA, but only with vesicle assembled CFs. TMEA crosslinking occurred between residues that were expected to form trimer, but also those that were not. The results provide evidence that CF behavior is highly dynamic in maleimide crosslinking reaction which conducted on vesicle assembled system.

Indiana University-Purdue University Indianapolis (IUPUI) / The information gained from sequencing of the human genome has begun to transform human biology and genetic medicine. The discovery of functionally important genetic variation lies at the heart of these endeavors, and there has been substantial progress in understanding the common patterns of single-nucleotide polymorphism (SNP) in humans- the most frequent type of variation in humans. Although more than 99% of human DNA sequences are the same across the population, variations in DNA sequence have a major impact on how we humans respond to disease; to environmental entities such as bacteria, viruses, toxins, and chemicals; and drugs and other therapies and thus studying differences between our genomes is vital. This makes SNPs as well other genetic variation data of great value for biomedical research and for developing pharmaceutical products or medical diagnostics. The goal of the project is to link genetic variation data to biological pathways and networks data, and also to clinical data for creating a framework for translational and systems biology studies. The study of the interactions between the components of biological systems and biological pathways has become increasingly important. It is known and accepted by scientists that it as important to study different biological entities as interacting systems, as in isolation. This project has ideas rooted in this thinking aiming at the integration of a genetic variation dataset with biological pathways dataset. Annotating genetic variation data with standardized disease notation is a very difficult yet important endeavor. One of the goals of this research is to identify whether informatics approaches can be applied to automatically annotate genetic variation data with a classification of diseases.

No description available.

No description available.

G protein signaling depends on the ability of the individual subunits of the G protein heterotrimer to assemble into a functional complex. Formation of the G protein βγ (Gβγ) dimer is particularly challenging because it is an obligate dimer in which the individual subunits are unstable on their own. Recent studies have revealed an intricate chaperone system that brings the Gβ and Gγ subunits together. This system includes the cytosolic chaperonin containing TCP-1 (CCT) and a co-chaperone phosducin-like protein 1 (PhLP1). Two key intermediates in the Gβγ assembly process, the Gβ-CCT and the PhLP1-Gβ-CCT complexes, were isolated and their structures determined by cryo-electron microscopy, chemical cross-linking coupled with mass spectrometry, and unnatural amino acid cross-linking. These structures show that Gβ interacts with CCT in a near-native state through interactions of the Gγ-binding region of Gβ with the CCTγ subunit. PhLP1 binding stabilizes the Gβ β-propeller, disrupting interactions with CCT and releasing a PhLP1-Gβ dimer for assembly with Gγ. We also investigated the role of CCT and PhLP1 in folding and assembling mTOR complexes, which regulate cell growth through phosphorylation. We found that the β-propeller protein mLST8 and one of its binding partners called raptor, which is a large protein in which one domain forms a β-propeller, both bind to CCT. PhLP1 forms a ternary complex with mLST8 and CCT and may play a co-chaperone role. Depletion of PhLP1 or CCT reduces assembly of mTOR complexes in the cell. Collectively, this report reveals diversity in the contributions of CCT to the formation of protein complexes in signaling pathways and presents a molecular mechanism of Gβ folding by CCT and PhLP1.

Today, paper and paperboard is an important part of the packaging industry, as well as natural part of our daily lives. The alternatives to paper and paperboard is often produced from nonrenewable sources such as petroleum and as demands on sustainability increase in the packaging sector, it gives paper a desirable advantage over plastics. To increase the use of paper, some of the limiting factors for paper needs to be overcome, such as its limited formability. One way to create a paper that can be formed in new ways is to imbibe the paper with an additive that makes its modulus changeable. This would make it possible to control the stiffness of the paper which would make it more formable. This have been the aim of this thesis. To create this formable paper four different approaches were used. Of these four, three included how paper can be treated with polyelectrolytes to be able to increase its modulus when stimuli are applied. The two first approaches were based on the layer-by-layer technique adsorbing alginate and cationic fibrils to form a layer that could be cross-linked, either on the surface of a film (the first approach) or in the network of fibres in a porous paper (the second approach). The last approach was to impregnate the papers with alginate. The results show that the first approach gave a too low adsorption of polyelectrolytes, why no difference could be detected. The second approach resulted in a higher adsorbed amount, but the effects were still too small. The third approach gave a paper which could, depending on the concentration of alginate, either increase or decrease its modulus when cross-linked. The last approach was to create a laminate, using unmodified fibers together with dialcohol cellulose fibres. This resulted in a paper that could be formed using heat and allowing the paper to cool down in the desirable form. In the curriculum for chemistry in Swedish high schools there is a paragraph that says that research in chemistry should be a part of the content the students learn. This is a challenge both to teachers and researchers. For teachers, to find research at an appropriate level and teach it in an understandable way. For researchers, to communicate the research so it is understandable for society. With this as a motivation, a second part of this thesis discuss the method flipped classroom in chemistry education at Swedish high schools. It was seen that from the teacher’s perspective, flipped classroom meant advantages that could be categorized into five categories. The categories that was found were Time to interact, Student responsibility, dialogue, laboratory work and understanding and using the language. / Pappers- och kartongindustrin är idag en viktig del av förpackningsindustrin. Alternativ till kartong är ofta producerat av icke-förnybara råvaror och idag när kraven på hållbarhet ökar ger detta kartong en fördel mot plast. För att öka användningsområdena för kartong så måste de begränsningar som materialet har idag övervinnas. Detta gäller till exempel formbarheten. Ett sätt att skapa kartong som kan bli format på nya sätt är att göra en additiv tillsats till papperet som har egenskapen att det kan variera sin styvhet. Detta skulle göra det möjligt att kontrollera papperets styvhet, vilket har varit målet för det här arbetet. Genom att använda fyra olika arbetssätt har denna egenskap försökts åstadkommas. Tre av arbetssätten har behandlat papper med polyelektrolyter vars E-modul kan ökas med hjälp av något stimuli. I de två första försöken applicerades polyelektrolyterna genom den så kallade lager-på-lager-tekniken, där alginat och katjoniska cellulosafibriller adsorberades, i första försöket på ytan av en film och i det andra på ytan av fibrerna i fibernätverket i ett poröst papper. I det tredje försöket impregnerades de orösa papperna med alginat. Resultatet från det första försöket var att adsorptionen inte gav någon effekt eftersom den absorberande mängden var för låg. I det andra försöket var adsorptionen högre men det påverkade inte de mekaniska egenskaperna nämnvärt. I det tredje försöket med impregnering så kunde en ändring av E-modulen observeras när systemet tvärbands. I det sista försöket användes en metod som byggde på laminering. Ett ark av modifierade fibrer guskades ihop med ett ark med dialkoholcellulosefibrer. De försök som gjordes tyder på att papperet kunde formas och kunde fås att behålla formen om det värmdes och kyldes i den önskade formen. I läroplanen för kemi på gymnasiet finns en paragraf som beskriver hur kemiundervisningen ska ha inslag av forskning. Detta är en utmaning för både lärare och forskare. Lärarnas utmaning består i att finna forskning på en bra nivå för eleverna och att förklara den på ett förståeligt sätt. För forskare består utmaningen i att kommunicera forskningen på ett förståeligt sätt till samhället. Med detta som motivering har detta arbete en utbildningsdel. I den har lärares perspektiv på metoden ”flipped classroom” i kemiklassrummet undersökts. Flipped classroom beskrevs ha styrkor och dessa kunde kategoriseras i fem kategorier. Kategorierna var tid för interaktion, elevens ansvar, dialog, laborationer och förstå och använda språket.

In this fast paced digital age, a vast amount of videos are produced every day, such as movies, TV programs, personal home videos, surveillance video, etc. This places a high demand for effective video data analysis and management techniques. In this dissertation, we have developed new techniques for segmentation, linking and understanding of video scenes. Firstly, we have developed a video scene segmentation framework that segments the video content into story units. Then, a linking method is designed to find the semantic correlation between video scenes/stories. Finally, to better understand the video content, we have developed a spatiotemporal attention detection model for videos. Our general framework for temporal scene segmentation, which is applicable to several video domains, is formulated in a statistical fashion and uses the Markov chain Monte Carlo (MCMC) technique to determine the boundaries between video scenes. In this approach, a set of arbitrary scene boundaries are initialized at random locations and are further automatically updated using two types of updates: diffusion and jumps. The posterior probability of the target distribution of the number of scenes and their corresponding boundary locations are computed based on the model priors and the data likelihood. Model parameter updates are controlled by the MCMC hypothesis ratio test, and samples are collected to generate the final scene boundaries. The major contribution of the proposed framework is two-fold: (1) it is able to find weak boundaries as well as strong boundaries, i.e., it does not rely on the fixed threshold; (2) it can be applied to different video domains. We have tested the proposed method on two video domains: home videos and feature films. On both of these domains we have obtained very accurate results, achieving on the average of 86% precision and 92% recall for home video segmentation, and 83% precision and 83% recall for feature films. The video scene segmentation process divides videos into meaningful units. These segments (or stories) can be further organized into clusters based on their content similarities. In the second part of this dissertation, we have developed a novel concept tracking method, which links news stories that focus on the same topic across multiple sources. The semantic linkage between the news stories is reflected in the combination of both their visual content and speech content. Visually, each news story is represented by a set of key frames, which may or may not contain human faces. The facial key frames are linked based on the analysis of the extended facial regions, and the non-facial key frames are correlated using the global matching. The textual similarity of the stories is expressed in terms of the normalized textual similarity between the keywords in the speech content of the stories. The developed framework has also been applied to the task of story ranking, which computes the interestingness of the stories. The proposed semantic linking framework and the story ranking method have both been tested on a set of 60 hours of open-benchmark video data (CNN and ABC news) from the TRECVID 2003 evaluation forum organized by NIST. Above 90% system precision has been achieved for the story linking task. The combination of both visual and speech cues has boosted the un-normalized recall by 15%. We have developed PEGASUS, a content based video retrieval system with fast speech and visual feature indexing and search. The system is available on the web: http://pegasus.cs.ucf.edu:8080/index.jsp. Given a video sequence, one important task is to understand what is present or what is happening in its content. To achieve this goal, target objects or activities need to be detected, localized and recognized in either the spatial and/or temporal domain. In the last portion of this dissertation, we present a visual attention detection method, which automatically generates the spatiotemporal saliency maps of input video sequences. The saliency map is later used in the detections of interesting objects and activities in videos by significantly narrowing the search range. Our spatiotemporal visual attention model generates the saliency maps based on both the spatial and temporal signals in the video sequences. In the temporal attention model, motion contrast is computed based on the planar motions (homography) between images, which are estimated by applying RANSAC on point correspondences in the scene. To compensate for the non-uniformity of the spatial distribution of interest-points, spanning areas of motion segments are incorporated in the motion contrast computation. In the spatial attention model, we have developed a fast method for computing pixel-level saliency maps using color histograms of images. Finally, a dynamic fusion technique is applied to combine both the temporal and spatial saliency maps, where temporal attention is dominant over the spatial model when large motion contrast exists, and vice versa. The proposed spatiotemporal attention framework has been extensively applied on multiple video sequences to highlight interesting objects and motions present in the sequences. We have achieved 82% user satisfactory rate on the point-level attention detection and over 92% user satisfactory rate on the object-level attention detection.

In manufacturing, requirements are an essential aspect of the development process. A requirements view provides a perspective on how requirements are incorporated into the design and architecture of a system. Requirements documents for different product versions at a company like Alstom contain operational scenarios and Given-When-Then requirements, a specific format for expressing functional requirements. Operational scenarios are examples of how the product will be used in real-world situations, and they can also be useful for identifying and specifying functional and nonfunctional requirements. Currently, operational scenarios are manually linked to Given-When-Then requirements. This thesis presents a conceptual design that streamlines the requirements engineering process and allows for easier linking operational scenarios to Given-When-Then requirements.

The primary objectives of this study were to develop an effective reactive extrusion process to produce granular phosphorylated pea starches with enhanced enzyme resistance, and examine the effects of bulk phosphorylation conditions on the morphology, physicochemical and functional properties of extruded pea starch phosphates. Two types of commercially available pea starches (NutriPea and Meelunie) were chosen as the research subjects in this study with differing native resistance. A number of methods including optical microscopy, SEM, ICP-OES, Englyst method, DSC and rapid visco analysis (RVA) were used to characterize the morphology and properties of extruded pea starches. The effects of feed formulations and extrusion conditions on phosphorus incorporation and Englyst digestion profiles were examined systemically. The results showed that phosphorus content and digestion profiles were highly dependent on the feed moisture. Enzyme resistance did not positively correlate with phosphorus content for extruded pea starch phosphates in contrast to their counterparts prepared by conventional aqueous slurry. This was because extrusion processing can markedly increase the susceptibility of pea starch granules to enzymatic digestion. Lower feed moisture content (40%) gave lower phosphorus content, significantly lower RDS content, and higher SDS and/or RS content. Bulk phosphorylation in the extruder resulted in decreased RS2 content but increased RS4 content. Screw geometry with excessive mixing index was not desirable in terms of producing resistant starch. High screw speeds (150rpm and 200rpm) and low feed rate (1.02kg/h) brought about higher yields of SDS and RS in spite of lower phosphorus incorporation. Reactive extrusion of pea starches under optimized conditions achieved a significant but moderate increase either in RS content (from 18.67% to 22.57% for NutriPea) or in SDS content (from 37.18% to 42.23% for Meelunie) compared to their native counterparts. However, RS and SDS content could not be improved simultaneously at least based on these pea starches and the reactive extrusion processes in this study. The optical and SEM micrographs confirmed that the granule integrity was largely retained after optimized reactive extrusion process. DSC thermograms found no significant correlation between gelatinization characteristics and Englyst digestion profiles. Evidenced by RVA pasting profiles, NutriPea pea starch phosphates exhibited enhanced thermal and shear stability in comparison to their native counterpart. A novel foaming injection technology of cross-linking reagents solution was pioneeringly introduced to uniformly coat all starch particles at the lowest moisture level possible during the continuous production of granular NutriPea pea starch phosphates. Yet, the resulting phosphorus incorporation was much lower than expected and would require further studies. / Thesis / Master of Applied Science (MASc) / The Canadian food industry is increasingly interested in the potential to probe new avenues to produce enzyme-resistant food starches from pulses starches. Although extrusion cooking is commonly used for manufacturing cereals, snacks and other food products, no research has been reported on using an extruder to rapidly produce resistant pulse starches for functional food ingredients. This study aimed to develop an effective reactive extrusion process to produce phosphate cross-linked pea starches with enhanced enzyme resistance (i.e., increased slowly digestible starch (SDS) and resistant starch (RS) content ) based on an examination of the effects of reaction conditions on the properties of extrusion products. Two types of commercially available pea starches, NutriPea and Meelunie, were chosen as subjects of the research. The cross-linked pea starches under optimized conditions achieved a significant but moderate increase either in RS content (for NutriPea) or in SDS content (for Meelunie) compared to their native counterparts. However, RS and SDS content could not be improved simultaneously at least based on these pea starches and the reactive extrusion processes in this study.