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Comparison of Molecular Structures of Protofibrils and Mature Fibrils Formed by Residues 113-127 of Syrian Hamster Prion Protein
No full text類澱粉樣纖維 (amyloid fibril) 是由錯誤折疊之蛋白質聚集而成，傳染性海綿樣腦病變 (TSE) 即為類澱粉樣纖維或其先驅物造成的疾病之一。普昂蛋白 (Prion protein,PrP) 正是引發傳染性海綿樣腦病的主因，當有致病性的普昂蛋白 (PrPSc) 存在，會誘使其他正常的普昂蛋白 (PrPC) 轉變為致病性結構，PrPSc單體通過分子間氫鍵與凡德瓦力作用而聚集成類澱粉樣纖維沉積於患者腦中，傷害患者的神經系統。探討類澱粉樣纖維的分子結構對於了解其致病機制甚至是找出治療方法十分重要，但類澱粉樣纖維為不溶性的非晶型物質，難以用一般解析蛋白質分子結構的液態核磁共振與X光繞射偵測，所以目前固態核磁共振技術仍是分析類澱粉樣纖維結構的最佳方法。 在論文中我們針對敘利亞倉鼠普昂蛋白第113至127的胜肽片段(Ac-AGAAAAGAVVGGLGG-NH2, SHaPrP113-127)進行研究，探討胜肽在培養過程中的分子結構。我們利用ThT螢光吸收、穿透式電子顯微鏡以及原子力顯微鏡辨識纖維分子的生成與構形，發現SHaPrP113-127在純化後已具備纖維絲狀形貌，也具有ThT螢光吸收特性，其纖維寬度約12 nm，高度約1 nm，長度約100 nm，邊界並不明顯。經培養後的成熟纖維其寬度及高度與未培養者相似，唯長度略長，約300 nm，並且ThT螢光吸收較強，顯示其結構較為完整。接著利用固態核磁共振去偵測培養前後的分子結構，透過二級化學位移可以確定培養前後都是β-strand結構，同時可由13C線寬得知SHaPrP113-127纖維分子從115到120殘基位置結構較規則。實驗結果比較發現，培養之後的成熟纖維有明顯的steric zipper結構，未培養的樣品則沒有此特性。由實驗數據我們可以推測結構不完全的原纖絲(protofibril)應是形成單層β-sheet結構後，再以層與層之間side chain的疏水作用力形成zipper結構。配合紅外線光譜之鑑定，得到β-sheet是反向平行排列。最後以分子動態計算 (MD simulation)，得到SHaPrP113-127類澱粉樣纖維的分子結構模型。Amyloid fibrils are ordered aggregates of misfolded proteins, which associated with many neurodisorder diseases. Transmissible spongiform encephalopathy (TSE) is one of these fatal diseases. It is suggested that TSE is caused by the conversion of prion protein from its normal cellular form (cellular prion protein, PrPC) to the disease-specific form (scrapie prion protein, PrPSc).The presence of PrPSc will induce the misfolding of other PrPC to PrPSc, existing in the form of amyloid fibrils and damaging the nervous system of the victims. To elucidate the mechanism and pathways of fibril formation and to find the therapy, it is very important to analyze the molecular structure of amyloid fibrils. However, because amyloid fibrils are insoluble in most buffers and are non-crystalline, it is difficult to use conventional experimental techniques such as solution-state NMR or X-ray to obtain the detailed structure of amyloid fibrils. Solid state NMR spectroscopy is a unique method that can provide high-resolution, site-specific structural constraints for amyloid fibrils. In this thesis, we report the results of ThT fluorescence, TEM, AFM, FTIR, and solid-state NMR (SSNMR) data for protofibrils and mature fibrils formed by residues 113-127 of the Syrian hamster prion protein (SHaPrP113-127, Ac-AGAAAAGAVVGGLGG-NH2). We found that after purification, SHaPrP113-127 peptides have already had short fibrillar structure, and also an enhanced fluorescence upon binding to ThT. These properties confirm that the SHaPrP113-127 peptides right after purification are in protofibrillar state. After incubation, the length of the mature fibrils becomes longer and the intensity of the ThT fluorescence becomes significantly enhanced. The mature fibrils in general have a length over 300 nm, a width of 12 nm, and a height of 1 nm. From the chemical shift and the linewidth data obtained from SSNMR measurements, the β-sheet structure formed in both protofibrils and mature fibrils have significant ordered structure from the residue 115 to 120. Our data reveal that the molecular structure of mature fibrils adopts the motif of steric zipper, whereas, the structure of protofibrils dose not. From the FTIR spectra, the β-strands within each layer are anti-parallel. Consequently, a molecular model for the fibrils was constructed by molecular dynamics simulations incorporated with structural constraints obtained from solid-state NMR measurements. We suppose that the process of fibril formation takes the following pathway. First, monomeric SHaPrP113-127 molecules self-assemble into single layer that is predominated by anti-parallel β-sheet. After that, two layers mate tightly and form the steric zipper by the hydrophobic interaction of side chains.第一章 序論 1-1 類澱粉樣纖維 1-2 普昂蛋白簡介 4-3 普昂蛋白結構異變 7-4 偵測類澱粉樣纖維分子結構 12-4-1 紅外線光譜 13-4-2 圓二色光譜 15-4-3 固態核磁共振 17-5 研究動機 19-6 參考文獻 20二章 核磁共振基本原理 26-1 引言 26-2 核磁共振基本原理 26-2-1 核自旋（Nuclear spin） 26-2-2 自旋弛豫（Relaxation） 29-2-3 NMR訊號 33-2-4 NMR系統中的作用力 34-2-5 二維核磁共振光譜 39-3 固態核磁共振（Solid state NMR） 41-3-1 魔術角旋轉（Magic angle spinning, MAS） 42-3-2 去耦合 (Decoupling) 43-3-3交叉極化（Cross-polarization, CP） 44-3-4回耦（recoupling） 46-4 固態核磁共振對於偵測蛋白質二級結構的應用 48-5 小結 51-6 參考文獻 51三章、合成與鑑定 54-1 材料與儀器 54-1-1化學藥品 54-1-2 使用儀器型號一覽表 56-2 胜肽樣品的製備 57-2-1 固相胜肽合成 57-2-2 胜肽樣品的純化 62-2-3胜肽樣品的鑑定 63-3 SHaPrP113-127類澱粉樣蛋白纖維的備製 65-4 類澱粉樣蛋白纖維的鑑定 66-4-1 ThT（Thioflavin-T） 螢光吸收 67-4-2 穿透式電子顯微鏡 (TEM) 69-4-3 原子力顯微鏡 (AFM) 70-5 類澱粉樣纖維分子結構的鑑定 70-5-1 固態核磁共振 71-5-2 紅外光吸收光譜（FT-IR） 72-6 固態核磁共振光譜 72-6-1 13C-H交叉極化魔角旋轉光譜 72-6-2 fpRFDR-CT光譜 73-6-3 fpRFDR 2D 74-6-4 DARR (Dipolar assisted rotational resonance) 74-7 參考文獻： 75四章 實驗結果與討論 78-1 胜肽的純化與鑑定 78-2 類澱粉樣纖維分子的鑑定 80-2-1 穿透式電子顯微鏡 80-2-2 ThT螢光吸收 82-2-3 原子力顯微鏡 83-3 建構SHaPrP113-127形成類澱粉樣纖維的分子模型 85-3-1 13C-13C同核相關二維譜 86-3-2 Steric Zipper 91-3-3 FT-IR實驗結果93-3-4 SHaPrP113-127分子間結構（Intermolecular Structure）96-3-5分子模型之建構 105-4 與SHaPrP109-122以及HuPrP106-126之類澱粉樣纖維分子結構比較 110-5 參考文獻 112五章 總結與未來展望 115-1 論文總結 115-2 未來展望 11
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Molecular Structure of Amyloid Fibrils Formed by Residues 127 to 147 of the Human Prion Protein
No full textDispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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