{"created":"2023-06-26T11:00:01.061600+00:00","id":187,"links":{},"metadata":{"_buckets":{"deposit":"8414c93a-a19a-4408-ad4d-6625b959ca5a"},"_deposit":{"created_by":22,"id":"187","owners":[22],"pid":{"revision_id":0,"type":"depid","value":"187"},"status":"published"},"_oai":{"id":"oai:oist.repo.nii.ac.jp:00000187","sets":["7:1"]},"author_link":[],"control_number":"187","item_10006_creator_2":{"attribute_name":"著者","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"トーツ, マルト","creatorNameLang":"ja"}]}]},"item_10006_creator_3":{"attribute_name":"著者(英)","attribute_type":"creator","attribute_value_mlt":[{"creatorAffiliations":[{"affiliationNames":[{"affiliationNameLang":"en"}]}],"creatorNames":[{"creatorName":"Toots, Mart","creatorNameLang":"en"}]}]},"item_10006_date_granted_11":{"attribute_name":"Degree Conferral Date","attribute_value_mlt":[{"subitem_dategranted":"2017-07-18"}]},"item_10006_degree_grantor_9":{"attribute_name":"Degree Conferrral Institution","attribute_value_mlt":[{"subitem_degreegrantor":[{"subitem_degreegrantor_name":"Okinawa Institute of Science and Technology Graduate University"}],"subitem_degreegrantor_identifier":[{"subitem_degreegrantor_identifier_name":"38005","subitem_degreegrantor_identifier_scheme":"kakenhi"}]}]},"item_10006_degree_name_8":{"attribute_name":"Degree","attribute_value_mlt":[{"subitem_degreename":"Doctor of Philosophy"}]},"item_10006_description_7":{"attribute_name":"Abstract","attribute_value_mlt":[{"subitem_description":"The three-dimensional structure of a protein molecule, challenging to determine and close to impossible to predict, plays a key role in understanding protein function and has implications in drug design. When it comes to structure determination, there exist many complementary methods, each with their specific advantages and disadvantages. Most of those methods rely on a combined signal from thousands of individuals and cannot be used for directly reconstructing an actual 3d volume as it appears inside the sample.\n   This thesis focuses on developing the methodology and providing proof of concept for a novel approach in structure determination by reconstructing small protein nanocrystals via cryo-electron tomography. Real-space imaging gets past the phase problem that is a challenging companion of conventional diffraction-based methods. With electron tomography we can reconstruct and visualize a 3d nanocrystal in its entirety and study the properties of small biological crystal from a new perspective.\n   Being a relatively unexplored territory, nanocrystal tomography sets several challenges, such as creating nanocrystals small enough for imaging with transmission electron microscope and developing algorithms for going from a tilt-series to a 3d structure. For a proof of concept we create, image and reconstruct nanocrystals of hen egg white lysozyme that, having molecular weight of only 15 kDa, is generally considered unfeasible for electron tomography. Nanocrystals make finding and determining the relative orientations of the individual molecules possible, symmetry relations help reduce the effects of missing information, and by averaging we are able to reconstruct a molecular structure at a medium resolution of around 13 Å. Using Fourier Transform (FFT) we get a direct objective measure of the resolution of details within the reconstruction in the form of a diffraction pattern and show that in specific directions the resolution reaches as high as 7 Å in a single tomogram.\n   Additionally, this work explores two other tightly related ideas. First, we study the concept of extended field and show with extensive simulations that extending the reconstruction space in various regularized iterative reconstruction procedures helps reduce the overall error and prevent over-smoothing. Second, calculating FFT of an image comes at a computational cost, and when the image is not periodic, the discontinuity of the opposing edges causes undesirable strong artifacts in the FFT that could obstruct important details. In this project we implemented a simultaneous 2d FFT and edge artifact removal for real-time applications on a Field Programmable Gate Array (FPGA) reconfigurable computing system.","subitem_description_language":"en","subitem_description_type":"Other"}]},"item_10006_dissertation_number_12":{"attribute_name":"Degree Referral Number","attribute_value_mlt":[{"subitem_dissertationnumber":"甲第4号"}]},"item_10006_identifier_registration":{"attribute_name":"ID登録","attribute_value_mlt":[{"subitem_identifier_reg_text":"10.15102/1394.00000170","subitem_identifier_reg_type":"JaLC"}]},"item_10006_rights_13":{"attribute_name":"Copyright Information","attribute_value_mlt":[{"subitem_rights":"© 2017 The Author"}]},"item_10006_text_24":{"attribute_name":"Exam Date","attribute_value_mlt":[{"subitem_text_value":"2017-06-05"}]},"item_10006_version_type_18":{"attribute_name":"Version Format","attribute_value_mlt":[{"subitem_version_resource":"http://purl.org/coar/version/c_970fb48d4fbd8a85","subitem_version_type":"VoR"}]},"item_access_right":{"attribute_name":"アクセス権","attribute_value_mlt":[{"subitem_access_right":"open access","subitem_access_right_uri":"http://purl.org/coar/access_right/c_abf2"}]},"item_files":{"attribute_name":"ファイル情報","attribute_type":"file","attribute_value_mlt":[{"accessrole":"open_date","date":[{"dateType":"Available","dateValue":"2017-12-21"}],"displaytype":"detail","filename":"89.pdf","filesize":[{"value":"123.9 MB"}],"format":"application/pdf","licensetype":"license_note","mimetype":"application/pdf","url":{"label":"Full-Text","objectType":"fulltext","url":"https://oist.repo.nii.ac.jp/record/187/files/89.pdf"},"version_id":"ec83edc7-59be-4704-a70f-255512e74df7"},{"accessrole":"open_date","date":[{"dateType":"Available","dateValue":"2018-03-14"}],"displaytype":"detail","filename":"doc(3).pdf","filesize":[{"value":"42.9 kB"}],"format":"application/pdf","licensetype":"license_note","mimetype":"application/pdf","url":{"label":"Final Exam Abstract","objectType":"abstract","url":"https://oist.repo.nii.ac.jp/record/187/files/doc(3).pdf"},"version_id":"01ab1075-354b-42f8-99e6-673dafc06e83"}]},"item_language":{"attribute_name":"言語","attribute_value_mlt":[{"subitem_language":"eng"}]},"item_resource_type":{"attribute_name":"資源タイプ","attribute_value_mlt":[{"resourcetype":"doctoral thesis","resourceuri":"http://purl.org/coar/resource_type/c_db06"}]},"item_title":"低温電子線トモグラフィーによるタンパク質ナノ結晶の分子構造解析の可能性を探る","item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"低温電子線トモグラフィーによるタンパク質ナノ結晶の分子構造解析の可能性を探る","subitem_title_language":"ja"},{"subitem_title":"Exploring the Potential of Cryo-Electron Tomography on Protein Nanocrystals for Molecular Structure Determination","subitem_title_language":"en"}]},"item_type_id":"10006","owner":"22","path":["1"],"pubdate":{"attribute_name":"PubDate","attribute_value":"2017-12-21"},"publish_date":"2017-12-21","publish_status":"0","recid":"187","relation_version_is_last":true,"title":["低温電子線トモグラフィーによるタンパク質ナノ結晶の分子構造解析の可能性を探る"],"weko_creator_id":"22","weko_shared_id":-1},"updated":"2023-10-17T01:39:06.075981+00:00"}