[ { "id": "https://thesis.library.caltech.edu/id/eprint/15157", "eprint_id": 15157, "rev_number": 37, "documents": [ { "id": "/id/document/138510", "doc_id": 138510, "rev_number": 4, "files": [ { "id": "/id/file/406015", "fileid": 406015, "datasetid": "document", "objectid": 138510, "filename": "Movie 4-S1.avi", "mime_type": "video/x-msvideo", "hash": "7a9a9856a86c0ed7d0cd3e338666b981", "hash_type": "MD5", "filesize": 44881324, "mtime": "2023-05-09 16:54:23", "url": "/15157/3/Movie 4-S1.avi" } ], "eprint_id": 15157, "pos": 3, "placement": 2, "mime_type": "video/x-msvideo", "format": "video/x-msvideo", "format_desc": "GVs' sensitivity to electron dosage", "language": "en", "security": "public", "license": "other", "main": "Movie 4-S1.avi", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/138511", "doc_id": 138511, "rev_number": 6, "files": [ { "id": "/id/file/406017", "fileid": 406017, "datasetid": "document", "objectid": 138511, "filename": "movie 5_S1.mp4", "mime_type": "video/mp4", "hash": "d90609fb366f61986a5cc40a77db2c9b", "hash_type": "MD5", "filesize": 30549007, "mtime": "2023-05-09 16:54:33", "url": "/15157/4/movie 5_S1.mp4" } ], "eprint_id": 15157, "pos": 4, "placement": 3, "mime_type": "video/mp4", "format": "video/mpeg", "format_desc": "Building an integrative model of the Legionella pneumonia Dot/Icm T4SS", "language": "en", "security": "public", "license": "other", "main": "movie 5_S1.mp4", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/138520", "doc_id": 138520, "rev_number": 5, "files": [ { "id": "/id/file/406051", "fileid": 406051, "datasetid": "document", "objectid": 138520, "filename": "PhD_thesis_final.pdf", "mime_type": "application/pdf", "hash": "b7ab1363052b7bbcfc0aacdc42054f53", "hash_type": "MD5", "filesize": 56663983, "mtime": "2023-05-09 17:47:09", "url": "/15157/5/PhD_thesis_final.pdf" } ], "eprint_id": 15157, "pos": 5, "placement": 1, "mime_type": "application/pdf", "format": "application/pdf", "language": "en", "security": "public", "license": "other", "main": "PhD_thesis_final.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final" }, { "id": "/id/document/138521", "doc_id": 138521, "rev_number": 3, "files": [ { "id": "/id/file/406053", "fileid": 406053, "datasetid": "document", "objectid": 138521, "filename": "PhD_thesis_final.docx", "mime_type": "application/vnd.openxmlformats-officedocument.wordprocessingml.document", "hash": "808af8ddadef65a73150140230af6796", "hash_type": "MD5", "filesize": 53610011, "mtime": "2023-05-09 17:47:19", "url": "/15157/6/PhD_thesis_final.docx" } ], "eprint_id": 15157, "pos": 6, "placement": 6, "mime_type": "application/vnd.openxmlformats-officedocument.wordprocessingml.document", "format": "application/msword", "format_desc": "Source file", "language": "en", "security": "internal", "license": "other", "main": "PhD_thesis_final.docx", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "archival" }, { "id": "/id/document/138524", "doc_id": 138524, "rev_number": 1, "files": [ { "id": "/id/file/406071", "fileid": 406071, "datasetid": "document", "objectid": 138524, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "5dd783cac836d6aa7338652c4804eddc", "hash_type": "MD5", "filesize": 42491, "mtime": "2023-05-09 17:57:38", "url": "/15157/7/indexcodes.txt" } ], "eprint_id": 15157, "pos": 7, "placement": 7, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/138520" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/138520" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/138520" } ] } }, { "id": "/id/document/138525", "doc_id": 138525, "rev_number": 1, "files": [ { "id": "/id/file/406072", "fileid": 406072, "datasetid": "document", "objectid": 138525, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "0a9599d38501ffd1c6b8aeeaba6464fd", "hash_type": "MD5", "filesize": 43903, "mtime": "2023-05-09 17:57:40", "url": "/15157/8/indexcodes.txt" } ], "eprint_id": 15157, "pos": 8, "placement": 8, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/msword to indexcodes", "language": "en", "security": "internal", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/138521" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/138521" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/138521" } ] } } ], "eprint_status": "archive", "userid": 12184, "dir": "disk0/00/01/51/57", "datestamp": "2023-05-15 20:20:42", "lastmod": "2023-05-22 20:33:41", "status_changed": "2023-05-15 20:20:42", "type": "thesis", "metadata_visibility": "show", "creators": { "items": [ { "email": "przemyslaw.dutka@gmail.com", "id": "Dutka-Przemys\u0142aw", "name": { "family": "Dutka", "given": "Przemys\u0142aw" }, "orcid": "0000-0003-3819-1618", "show_email": "NO" } ] }, "title": "Cryo-ET Reveals Molecular Details of Multi-Megadalton Bacterial Protein Complexes", "ispublished": "unpub", "full_text_status": "public", "keywords": "Gas vesicles, type IV secretion system, cryo-ET, integrative modeling, subtomogram averaging", "abstract": "
Cryo-electron tomography (cryo-ET) is a powerful method for investigating the 3D structure of intact cells, organelles, and complex protein macromolecules that cannot be crystallized or are too heterogenous for single-particle cryo-electron microscopy (cryo-EM). However, obtaining high- resolution cryo-ET structures for many biologically important targets is still a challenge. To address this challenge, cryo-ET can be combined with other methods, including X-ray crystallography, single-particle cryo-EM, structure predictions, cross-linking mass spectrometry, biochemistry, and evolutionary analysis to produce integrative models. Recently, with the development of AI-based tools such as AlphaFold2, structure prediction has played an increasingly important role in integrative modeling. The combination of cryo-ET and structure prediction in particular has provided unprecedented insights into the ultrastructure of cellular components. This thesis focuses on two bacterial multi-megadalton protein complexes which are difficult to study by classical structural biology approaches: gas vesicles (GVs) and the Legionella pneumophila Dot/Icm type IV secretion system (T4SS). GVs are gas-filled protein nanostructures that regulate the position of certain microorganisms in water and consequently their access to sunlight and nutrients. Here, we investigate the mechanical properties of GVs and reveal the molecular structure of GVs and its implication for the assembly mechanism. The Dot/Icm T4SS is a macromolecular complex formed by approximately 27 proteins, utilized by L. pneumophila to hijack the host cell's biology for its replication purposes. A nearly-complete integrative model of this complex provides crucial insights into its structural organization and its evolution from conjugation to secretion, as well as the transportation of substrates into the host cell.
", "date": "2023", "date_type": "degree", "id_number": "CaltechTHESIS:05092023-163511031", "refereed": "FALSE", "official_url": "https://resolver.caltech.edu/CaltechTHESIS:05092023-163511031", "related_url": { "items": [ { "description": "Article adapted for Chapter 2 (Measuring Gas Vesicle Dimensions by Electron Microscopy)", "type": "doi", "url": "https://doi.org/10.1002/pro.4056" }, { "description": "Article adapted for Chapter 3 (Geometric Effects in Gas Vesicle Buckling under Ultrasound)", "type": "doi", "url": "https://doi.org/10.1016/j.bpj.2022.09.004" }, { "description": "Article adapted for Chapter 4 (Structure of Anabaena Flos-Aquae Gas Vesicles Revealed by Cryo-ET)", "type": "doi", "url": "https://doi.org/10.1016/j.str.2023.03.011" }, { "description": "Article adapted for Chapter 5 (Structure and Function of the Dot/Icm T4SS)", "type": "doi", "url": "https://doi.org/10.1101/2023.03.22.533729" } ] }, "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "collection": "CaltechTHESIS", "reviewer": "Melissa Ray", "suggestions": "Released 2023-05-22. 1-week embargo until 22 May 2023.", "deposited_by": "Przemyslaw Dutka", "deposited_on": "2023-05-15 20:20:42", "doi": "10.7907/87jm-7v06", "divisions": { "items": [ "div_chem" ] }, "institution": "California Institute of Technology", "thesis_type": "phd", "thesis_advisor": { "items": [ { "email": "mikhail@caltech.edu", "id": "Shapiro-M-G", "name": { "family": "Shapiro", "given": "Mikhail G." }, "orcid": "0000-0002-0291-4215", "role": "advisor" }, { "email": "grant_jensen@byu.edu", "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864", "role": "co-advisor" } ] }, "thesis_committee": { "items": [ { "email": "dcrees@caltech.edu", "id": "Rees-D-C", "name": { "family": "Rees", "given": "Douglas C." }, "orcid": "0000-0003-4073-1185", "role": "chair" }, { "email": "mikhail@caltech.edu", "id": "Shapiro-M-G", "name": { "family": "Shapiro", "given": "Mikhail G." }, "orcid": "0000-0002-0291-4215", "role": "member" }, { "email": "grant_jensen@byu.edu", "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "orcid": "0000-0003-1556-4864", "role": "member" }, { "email": "phillips@pboc.caltech.edu", "id": "Phillips-R-B", "name": { "family": "Phillips", "given": "Robert B." }, "orcid": "0000-0003-3082-2809", "role": "member" } ] }, "thesis_degree": "PHD", "thesis_degree_grantor": "California Institute of Technology", "thesis_defense_date": "2023-04-28", "gradofc_approval_date": "2023-05-12", "review_status": "approved", "option_major": { "items": [ "biochem" ] }, "copyright_statement": "Author's Rights Authorization: I hereby certify that, if appropriate, I have obtained a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted here is the same as that approved by my advisory committee.\n\nI hereby grant to California Institute of Technology or its agents the non-exclusive license to archive and make accessible, under the conditions specified under \"Thesis Availability\" in this submission, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation, or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report.", "resource_type": "thesis", "pub_year": "2023", "author_list": "Dutka, Przemys\u0142aw", "advisor_list": "Shapiro, Mikhail G. and Jensen, Grant J.", "comittee_list": "Rees, Douglas C.; Shapiro, Mikhail G.; et el." }, { "id": "https://thesis.library.caltech.edu/id/eprint/13601", "eprint_id": 13601, "rev_number": 65, "documents": [ { "id": "/id/document/105146", "doc_id": 105146, "rev_number": 5, "files": [ { "id": "/id/file/321924", "fileid": 321924, "datasetid": "document", "objectid": 105146, "filename": "WeaverSJ_Thesis_20200109.pdf", "mime_type": "application/pdf", "hash": "351c88fddaa3608bd5b534cb929bbe05", "hash_type": "MD5", "filesize": 105266485, "mtime": "2020-01-09 17:58:39", "url": "/13601/25/WeaverSJ_Thesis_20200109.pdf" } ], "eprint_id": 13601, "pos": 25, "placement": 25, "mime_type": "application/pdf", "format": "application/pdf", "language": "en", "security": "public", "license": "other", "main": "WeaverSJ_Thesis_20200109.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final" }, { "id": "/id/document/105147", "doc_id": 105147, "rev_number": 2, "files": [ { "id": "/id/file/321926", "fileid": 321926, "datasetid": "document", "objectid": 105147, "filename": "lightbox.jpg", "mime_type": "image/png", "hash": "66f83b658c54b5cef11caa14adaed7e3", "hash_type": "MD5", "filesize": 26716, "mtime": "2020-01-09 17:58:55", "url": "/13601/26/lightbox.jpg" } ], "eprint_id": 13601, "pos": 26, "placement": 26, "mime_type": "image/png", "format": "other", "format_desc": "Thumbnails conversion from application/pdf to thumbnail_lightbox", "language": "en", "security": "public", "license": "other", "main": "lightbox.jpg", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/105146" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/105146" }, { "type": "http://eprints.org/relation/islightboxThumbnailVersionOf", "uri": "/id/document/105146" } ] } }, { "id": "/id/document/105148", "doc_id": 105148, "rev_number": 2, "files": [ { "id": "/id/file/321927", "fileid": 321927, "datasetid": "document", "objectid": 105148, "filename": "preview.png", "mime_type": "image/png", "hash": "58a418d02308d3b53f710fa35df84888", "hash_type": "MD5", "filesize": 41772, "mtime": "2020-01-09 17:58:58", "url": "/13601/27/preview.png" } ], "eprint_id": 13601, "pos": 27, "placement": 27, "mime_type": "image/png", "format": "other", "format_desc": "Thumbnail Documents conversion from application/pdf to thumbnail_preview", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/105146" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/105146" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/105146" } ] } }, { "id": "/id/document/105149", "doc_id": 105149, "rev_number": 2, "files": [ { "id": "/id/file/321928", "fileid": 321928, "datasetid": "document", "objectid": 105149, "filename": "medium.jpg", "mime_type": "image/png", "hash": "6051b4f99c3e98b45170082cdc9d5204", "hash_type": "MD5", "filesize": 6124, "mtime": "2020-01-09 17:59:01", "url": "/13601/28/medium.jpg" } ], "eprint_id": 13601, "pos": 28, "placement": 28, "mime_type": "image/png", "format": "other", "format_desc": "Thumbnails conversion from application/pdf to thumbnail_medium", "language": "en", "security": "public", "license": "other", "main": "medium.jpg", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/105146" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/105146" }, { "type": "http://eprints.org/relation/ismediumThumbnailVersionOf", "uri": "/id/document/105146" } ] } }, { "id": "/id/document/105150", "doc_id": 105150, "rev_number": 2, "files": [ { "id": "/id/file/321929", "fileid": 321929, "datasetid": "document", "objectid": 105150, "filename": "small.jpg", "mime_type": "image/png", "hash": "3ccbd8a7761bca8b01b676a459d9444b", "hash_type": "MD5", "filesize": 1561, "mtime": "2020-01-09 17:59:03", "url": "/13601/29/small.jpg" } ], "eprint_id": 13601, "pos": 29, "placement": 29, "mime_type": "image/png", "format": "other", "format_desc": "Thumbnails conversion from application/pdf to thumbnail_small", "language": "en", "security": "public", "license": "other", "main": "small.jpg", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/105146" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/105146" }, { "type": "http://eprints.org/relation/issmallThumbnailVersionOf", "uri": "/id/document/105146" } ] } }, { "id": "/id/document/105153", "doc_id": 105153, "rev_number": 6, "files": [ { "id": "/id/file/321934", "fileid": 321934, "datasetid": "document", "objectid": 105153, "filename": "20190315_SMovie1.mp4", "mime_type": "video/mp4", "hash": "322071a831abe7aa950e2c504625a674", "hash_type": "MD5", "filesize": 17344019, "mtime": "2020-01-09 18:02:31", "url": "/13601/31/20190315_SMovie1.mp4" } ], "eprint_id": 13601, "pos": 31, "placement": 31, "mime_type": "video/mp4", "format": "video/mpeg", "format_desc": "Supplemental Movie 1", "language": "en", "security": "public", "license": "other", "main": "20190315_SMovie1.mp4", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/105154", "doc_id": 105154, "rev_number": 7, "files": [ { "id": "/id/file/321936", "fileid": 321936, "datasetid": "document", "objectid": 105154, "filename": "20190315_SMovie2.mp4", "mime_type": "video/mp4", "hash": "18ebe99d324fcd1331915a7ade23f05d", "hash_type": "MD5", "filesize": 22554008, "mtime": "2020-01-09 18:02:37", "url": "/13601/32/20190315_SMovie2.mp4" } ], "eprint_id": 13601, "pos": 32, "placement": 32, "mime_type": "video/mp4", "format": "video/mpeg", "format_desc": "Supplemental Movie 2", "language": "en", "security": "public", "license": "other", "main": "20190315_SMovie2.mp4", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/105155", "doc_id": 105155, "rev_number": 6, "files": [ { "id": "/id/file/321938", "fileid": 321938, "datasetid": "document", "objectid": 105155, "filename": "20190315_SMovie3.mp4", "mime_type": "video/mp4", "hash": "bd4668d7d07a9dbcd6d89d184bb6a414", "hash_type": "MD5", "filesize": 6728498, "mtime": "2020-01-09 18:02:42", "url": "/13601/33/20190315_SMovie3.mp4" } ], "eprint_id": 13601, "pos": 33, "placement": 33, "mime_type": "video/mp4", "format": "video/mpeg", "format_desc": "Supplemental Movie 3", "language": "en", "security": "public", "license": "other", "main": "20190315_SMovie3.mp4", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/105316", "doc_id": 105316, "rev_number": 5, "files": [ { "id": "/id/file/322386", "fileid": 322386, "datasetid": "document", "objectid": 105316, "filename": "weaver-sara-6-month-request.pdf", "mime_type": "application/pdf", "hash": "ec2fee56bf7a39f93d2bca35c727b32c", "hash_type": "MD5", "filesize": 56583, "mtime": "2020-01-16 20:24:47", "url": "/13601/34/weaver-sara-6-month-request.pdf" } ], "eprint_id": 13601, "pos": 34, "placement": 2, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "Author 6-month request 2020-12-29", "language": "en", "security": "internal", "license": "other", "main": "weaver-sara-6-month-request.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "embargoform" }, { "id": "/id/document/105317", "doc_id": 105317, "rev_number": 2, "files": [ { "id": "/id/file/322388", "fileid": 322388, "datasetid": "document", "objectid": 105317, "filename": "lightbox.jpg", "mime_type": "image/png", "hash": "2047ac077acca70c26d10924485640cf", "hash_type": "MD5", "filesize": 71451, "mtime": "2020-01-16 20:25:03", "url": "/13601/35/lightbox.jpg" } ], "eprint_id": 13601, "pos": 35, "placement": 35, "mime_type": "image/png", "format": "other", "format_desc": "Thumbnails conversion from application/pdf to thumbnail_lightbox", "language": "en", "security": "internal", "license": "other", "main": "lightbox.jpg", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/105316" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/105316" }, { "type": "http://eprints.org/relation/islightboxThumbnailVersionOf", "uri": "/id/document/105316" } ] } }, { "id": "/id/document/105318", "doc_id": 105318, "rev_number": 2, "files": [ { "id": "/id/file/322389", "fileid": 322389, "datasetid": "document", "objectid": 105318, "filename": "preview.png", "mime_type": "image/png", "hash": "107ec3aaee46ec0ee81ba7a9a7178cba", "hash_type": "MD5", "filesize": 119839, "mtime": "2020-01-16 20:25:04", "url": "/13601/36/preview.png" } ], "eprint_id": 13601, "pos": 36, "placement": 36, "mime_type": "image/png", "format": "other", "format_desc": "Thumbnail Documents conversion from application/pdf to thumbnail_preview", "language": "en", "security": "internal", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/105316" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/105316" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/105316" } ] } }, { "id": "/id/document/105319", "doc_id": 105319, "rev_number": 2, "files": [ { "id": "/id/file/322390", "fileid": 322390, "datasetid": "document", "objectid": 105319, "filename": "medium.jpg", "mime_type": "image/png", "hash": "0c57bd436c99cc939a7801c61f30c11a", "hash_type": "MD5", "filesize": 14120, "mtime": "2020-01-16 20:25:04", "url": "/13601/37/medium.jpg" } ], "eprint_id": 13601, "pos": 37, "placement": 37, "mime_type": "image/png", "format": "other", "format_desc": "Thumbnails conversion from application/pdf to thumbnail_medium", "language": "en", "security": "internal", "license": "other", "main": "medium.jpg", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/105316" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/105316" }, { "type": "http://eprints.org/relation/ismediumThumbnailVersionOf", "uri": "/id/document/105316" } ] } }, { "id": "/id/document/105320", "doc_id": 105320, "rev_number": 2, "files": [ { "id": "/id/file/322391", "fileid": 322391, "datasetid": "document", "objectid": 105320, "filename": "small.jpg", "mime_type": "image/png", "hash": "9fec60b411c5d6a59cb1157fc902fb5e", "hash_type": "MD5", "filesize": 1649, "mtime": "2020-01-16 20:25:04", "url": "/13601/38/small.jpg" } ], "eprint_id": 13601, "pos": 38, "placement": 38, "mime_type": "image/png", "format": "other", "format_desc": "Thumbnails conversion from application/pdf to thumbnail_small", "language": "en", "security": "internal", "license": "other", "main": "small.jpg", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/105316" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/105316" }, { "type": "http://eprints.org/relation/issmallThumbnailVersionOf", "uri": "/id/document/105316" } ] } }, { "id": "/id/document/110323", "doc_id": 110323, "rev_number": 4, "files": [ { "id": "/id/file/337166", "fileid": 337166, "datasetid": "document", "objectid": 110323, "filename": "weaver-sara-release-permission.pdf", "mime_type": "application/pdf", "hash": "9336a89c0b3a57a7f687eeda1576bb49", "hash_type": "MD5", "filesize": 70709, "mtime": "2020-06-29 17:44:49", "url": "/13601/40/weaver-sara-release-permission.pdf" } ], "eprint_id": 13601, "pos": 40, "placement": 1, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "Author approval 2020-06-27", "language": "en", "security": "internal", "license": "other", "main": "weaver-sara-release-permission.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "release" }, { "id": "/id/document/110324", "doc_id": 110324, "rev_number": 2, "files": [ { "id": "/id/file/337168", "fileid": 337168, "datasetid": "document", "objectid": 110324, "filename": "lightbox.jpg", "mime_type": "image/png", "hash": "7fc3c183ed8f7e7a82c81a4252adf45b", "hash_type": "MD5", "filesize": 52114, "mtime": "2020-06-29 17:45:05", "url": "/13601/41/lightbox.jpg" } ], "eprint_id": 13601, "pos": 41, "placement": 41, "mime_type": "image/png", "format": "other", "format_desc": "Thumbnails conversion from application/pdf to thumbnail_lightbox", "language": "en", "security": "internal", "license": "other", "main": "lightbox.jpg", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/110323" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/110323" }, { "type": "http://eprints.org/relation/islightboxThumbnailVersionOf", "uri": "/id/document/110323" } ] } }, { "id": "/id/document/110325", "doc_id": 110325, "rev_number": 2, "files": [ { "id": "/id/file/337169", "fileid": 337169, "datasetid": "document", "objectid": 110325, "filename": "preview.png", "mime_type": "image/png", "hash": "5666f60b9c4eb8d80da03014a08fa85e", "hash_type": "MD5", "filesize": 75788, "mtime": "2020-06-29 17:45:06", "url": "/13601/42/preview.png" } ], "eprint_id": 13601, "pos": 42, "placement": 42, "mime_type": "image/png", "format": "other", "format_desc": "Thumbnail Documents conversion from application/pdf to thumbnail_preview", "language": "en", "security": "internal", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/110323" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/110323" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/110323" } ] } }, { "id": "/id/document/110326", "doc_id": 110326, "rev_number": 2, "files": [ { "id": "/id/file/337170", "fileid": 337170, "datasetid": "document", "objectid": 110326, "filename": "medium.jpg", "mime_type": "image/png", "hash": "86b886efefa2edf7447e1dd73d4df47a", "hash_type": "MD5", "filesize": 16899, "mtime": "2020-06-29 17:45:06", "url": "/13601/43/medium.jpg" } ], "eprint_id": 13601, "pos": 43, "placement": 43, "mime_type": "image/png", "format": "other", "format_desc": "Thumbnails conversion from application/pdf to thumbnail_medium", "language": "en", "security": "internal", "license": "other", "main": "medium.jpg", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/110323" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/110323" }, { "type": "http://eprints.org/relation/ismediumThumbnailVersionOf", "uri": "/id/document/110323" } ] } }, { "id": "/id/document/110327", "doc_id": 110327, "rev_number": 2, "files": [ { "id": "/id/file/337171", "fileid": 337171, "datasetid": "document", "objectid": 110327, "filename": "small.jpg", "mime_type": "image/png", "hash": "077407d5bdb57e3038c38f4d1d45ba17", "hash_type": "MD5", "filesize": 1781, "mtime": "2020-06-29 17:45:07", "url": "/13601/44/small.jpg" } ], "eprint_id": 13601, "pos": 44, "placement": 44, "mime_type": "image/png", "format": "other", "format_desc": "Thumbnails conversion from application/pdf to thumbnail_small", "language": "en", "security": "internal", "license": "other", "main": "small.jpg", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/110323" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/110323" }, { "type": "http://eprints.org/relation/issmallThumbnailVersionOf", "uri": "/id/document/110323" } ] } }, { "id": "/id/document/130896", "doc_id": 130896, "rev_number": 1, "files": [ { "id": "/id/file/376335", "fileid": 376335, "datasetid": "document", "objectid": 130896, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "43333aaf0c74439cf5344510014bf77a", "hash_type": "MD5", "filesize": 32507, "mtime": "2021-06-24 17:24:31", "url": "/13601/45/indexcodes.txt" } ], "eprint_id": 13601, "pos": 45, "placement": 45, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/105146" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/105146" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/105146" } ] } }, { "id": "/id/document/130897", "doc_id": 130897, "rev_number": 1, "files": [ { "id": "/id/file/376336", "fileid": 376336, "datasetid": "document", "objectid": 130897, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "2b6be37594522569b3aeb08d4558b006", "hash_type": "MD5", "filesize": 984, "mtime": "2021-06-24 17:24:31", "url": "/13601/46/indexcodes.txt" } ], "eprint_id": 13601, "pos": 46, "placement": 46, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "internal", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/105316" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/105316" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/105316" } ] } }, { "id": "/id/document/130898", "doc_id": 130898, "rev_number": 1, "files": [ { "id": "/id/file/376337", "fileid": 376337, "datasetid": "document", "objectid": 130898, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "7b574216e77253d9f293f99a1029426f", "hash_type": "MD5", "filesize": 873, "mtime": "2021-06-24 17:24:31", "url": "/13601/47/indexcodes.txt" } ], "eprint_id": 13601, "pos": 47, "placement": 47, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "internal", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/110323" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/110323" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/110323" } ] } } ], "eprint_status": "archive", "userid": 12072, "dir": "disk0/00/01/36/01", "datestamp": "2020-01-21 22:27:16", "lastmod": "2020-10-23 21:33:39", "status_changed": "2020-01-21 22:27:16", "type": "thesis", "metadata_visibility": "show", "creators": { "items": [ { "email": "sjw2132@gmail.com", "id": "Weaver-Sara-Jean", "name": { "family": "Weaver", "given": "Sara Jean" }, "orcid": "0000-0001-7753-6215", "show_email": "NO" } ] }, "title": "Visualizing Small Proteins with the cryoEM Platform and The Structure of the Vibrio cholerae Type IV Competence Pilus Secretin PilQ", "ispublished": "unpub", "full_text_status": "public", "keywords": "cryogenic electron microscopy, DARPin, Vibrio cholerae, secretin, PilQ", "abstract": "Solving protein structures by single-particle cryoelectron microscopy (cryo-EM) has become a crucial tool in structural biology. While exciting progress is being made toward the visualization of small macromolecules, the median protein size in both eukaryotes and bacteria is still beyond the reach of cryo-EM. To overcome this problem, we implemented a platform strategy in which a small protein target was rigidly attached to a large, symmetric base via a selectable adapter. Of our seven designs, the best construct used a designed ankyrin repeat protein (DARPin) rigidly fused to tetrameric rabbit muscle aldolase through a helical linker. The DARPin retained its ability to bind its target: GFP. We solved the structure of this complex to 3.0 \u00c5 resolution overall, with 5-8 \u00c5 resolution in the GFP region. As flexibility in the DARPin position limited the overall resolution of the target, we describe strategies to rigidify this element.
\r\n\r\nNatural competence is the process by which bacteria take up genetic material from their environment and integrate it into their genome using homologous recombination. In Vibrio cholerae, the Type IV competence pilus is thought to mediate DNA uptake by binding DNA and retracting back toward the cell. How the DNA enters the periplasm is unclear. One hypothesis suggests that the DNA-bound Type IV competence pilus retracts completely so that the DNA would pass through the outer membrane secretin pore (PilQ). PilQ is a 870 kDa outer membrane pore with C14 symmetry. Here, we purify the V. cholerae PilQ secretin from V. cholerae cells in amphipols for single particle cryogenic electron microscopy (cryoEM). We solve the structure to 3.0 \u00c5 and provide insight on the channel DNA may traverse through during uptake.
", "date": "2020", "date_type": "degree", "id_number": "CaltechTHESIS:12092019-141850032", "refereed": "FALSE", "official_url": "https://resolver.caltech.edu/CaltechTHESIS:12092019-141850032", "related_url": { "items": [ { "description": "Article adapted for Ch. 2", "type": "doi", "url": "https://doi.org/10.1101/455063(2018" } ] }, "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "collection": "CaltechTHESIS", "reviewer": "Kathy Johnson", "deposited_by": "Sara Weaver", "deposited_on": "2020-01-21 22:27:16", "doi": "10.7907/9B9V-PK08", "divisions": { "items": [ "div_chem" ] }, "institution": "California Institute of Technology", "thesis_type": "phd", "thesis_advisor": { "items": [ { "email": "jensen@caltech.edu", "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "role": "advisor" } ] }, "thesis_committee": { "items": [ { "email": "dcrees@caltech.edu", "id": "Rees-D-C", "name": { "family": "Rees", "given": "Douglas C." }, "role": "chair" }, { "email": "jensen@caltech.edu", "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "role": "member" }, { "email": "mikhail@caltech.edu", "id": "Shapiro-M-G", "name": { "family": "Shapiro", "given": "Mikhail G." }, "role": "member" }, { "email": "voorhees@caltech.edu", "id": "Voorhees-R-M", "name": { "family": "Voorhees", "given": "Rebecca M" }, "role": "member" } ] }, "thesis_degree": "PHD", "thesis_degree_grantor": "California Institute of Technology", "thesis_defense_date": "2019-11-22", "gradofc_approval_date": "2020-01-21", "review_status": "approved", "option_major": { "items": [ "chemistry" ] }, "copyright_statement": "Author's Rights Authorization: I hereby certify that, if appropriate, I have obtained a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted here is the same as that approved by my advisory committee.\n\nI hereby grant to California Institute of Technology or its agents the non-exclusive license to archive and make accessible, under the conditions specified under \"Thesis Availability\" in this submission, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation, or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report.", "resource_type": "thesis", "pub_year": "2020", "author_list": "Weaver, Sara Jean", "advisor_list": "Jensen, Grant J.", "comittee_list": "Rees, Douglas C.; Jensen, Grant J.; et el." }, { "id": "https://thesis.library.caltech.edu/id/eprint/7120", "eprint_id": 7120, "rev_number": 36, "documents": [ { "id": "/id/document/15012", "doc_id": 15012, "rev_number": 6, "files": [ { "id": "/id/file/98006", "fileid": 98006, "datasetid": "document", "objectid": 15012, "filename": "DobroThesis.pdf", "mime_type": "application/pdf", "filesize": 68450801, "mtime": "2012-12-26 04:44:14", "url": "/7120/1/DobroThesis.pdf" } ], "eprint_id": 7120, "pos": 1, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "Final Manuscript", "language": "en", "security": "public", "license": "other", "main": "DobroThesis.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/28117" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/28117" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/28117" } ] } }, { "id": "/id/document/15013", "doc_id": 15013, "rev_number": 5, "files": [ { "id": "/id/file/98007", "fileid": 98007, "datasetid": "document", "objectid": 15013, "filename": "Movie1-1.mov", "mime_type": "video/quicktime", "filesize": 58318439, "mtime": "2012-12-26 04:44:14", "url": "/7120/2/Movie1-1.mov" } ], "eprint_id": 7120, "pos": 2, "mime_type": "video/quicktime", "format": "video/quicktime", "format_desc": "Supplemental Movie 1.1", "language": "en", "security": "public", "license": "other", "main": "Movie1-1.mov", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/15014", "doc_id": 15014, "rev_number": 5, "files": [ { "id": "/id/file/98008", "fileid": 98008, "datasetid": "document", "objectid": 15014, "filename": "Movie1-2.mov", "mime_type": "video/quicktime", "filesize": 1256406, "mtime": "2012-12-26 04:44:14", "url": "/7120/3/Movie1-2.mov" } ], "eprint_id": 7120, "pos": 3, "mime_type": "video/quicktime", "format": "video/quicktime", "format_desc": "Supplemental Movie 1.2", "language": "en", "security": "public", "license": "other", "main": "Movie1-2.mov", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/15015", "doc_id": 15015, "rev_number": 5, "files": [ { "id": "/id/file/98009", "fileid": 98009, "datasetid": "document", "objectid": 15015, "filename": "Movie1-3.mov", "mime_type": "video/quicktime", "filesize": 2615186, "mtime": "2012-12-26 04:44:14", "url": "/7120/4/Movie1-3.mov" } ], "eprint_id": 7120, "pos": 4, "mime_type": "video/quicktime", "format": "video/quicktime", "format_desc": "Supplemental Movie 1.3", "language": "en", "security": "public", "license": "other", "main": "Movie1-3.mov", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/15016", "doc_id": 15016, "rev_number": 5, "files": [ { "id": "/id/file/98010", "fileid": 98010, "datasetid": "document", "objectid": 15016, "filename": "Movie1-4.mov", "mime_type": "video/quicktime", "filesize": 3820359, "mtime": "2012-12-26 04:44:14", "url": "/7120/5/Movie1-4.mov" } ], "eprint_id": 7120, "pos": 5, "mime_type": "video/quicktime", "format": "video/quicktime", "format_desc": "Supplemental Movie 1.4", "language": "en", "security": "public", "license": "other", "main": "Movie1-4.mov", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/15017", "doc_id": 15017, "rev_number": 5, "files": [ { "id": "/id/file/98011", "fileid": 98011, "datasetid": "document", "objectid": 15017, "filename": "Movie1-5.mov", "mime_type": "video/quicktime", "filesize": 43839003, "mtime": "2012-12-26 04:44:14", "url": "/7120/6/Movie1-5.mov" } ], "eprint_id": 7120, "pos": 6, "mime_type": "video/quicktime", "format": "video/quicktime", "format_desc": "Supplemental Movie 1.5", "language": "en", "security": "public", "license": "other", "main": "Movie1-5.mov", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/15020", "doc_id": 15020, "rev_number": 5, "files": [ { "id": "/id/file/98012", "fileid": 98012, "datasetid": "document", "objectid": 15020, "filename": "Movie2-1.mov", "mime_type": "video/quicktime", "filesize": 3354301, "mtime": "2012-12-26 04:44:14", "url": "/7120/7/Movie2-1.mov" } ], "eprint_id": 7120, "pos": 7, "mime_type": "video/quicktime", "format": "video/quicktime", "format_desc": "Supplemental Movie 2.1", "language": "en", "security": "public", "license": "other", "main": "Movie2-1.mov", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/15021", "doc_id": 15021, "rev_number": 5, "files": [ { "id": "/id/file/98013", "fileid": 98013, "datasetid": "document", "objectid": 15021, "filename": "Movie2-2.mov", "mime_type": "video/quicktime", "filesize": 5340784, "mtime": "2012-12-26 04:44:14", "url": "/7120/8/Movie2-2.mov" } ], "eprint_id": 7120, "pos": 8, "mime_type": "video/quicktime", "format": "video/quicktime", "format_desc": "Supplemental Movie 2.2", "language": "en", "security": "public", "license": "other", "main": "Movie2-2.mov", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/28117", "doc_id": 28117, "rev_number": 2, "files": [ { "id": "/id/file/98004", "fileid": 98004, "datasetid": "document", "objectid": 28117, "filename": "preview.png", "mime_type": "image/png", "hash": "640e22ab580374f1f6093bfcadd445c7", "hash_type": "MD5", "filesize": 40853, "mtime": "2012-12-26 04:44:14", "url": "/7120/9/preview.png" } ], "eprint_id": 7120, "pos": 9, "placement": 9, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "validuser", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/15012" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/15012" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/15012" } ] } }, { "id": "/id/document/127560", "doc_id": 127560, "rev_number": 1, "files": [ { "id": "/id/file/372996", "fileid": 372996, "datasetid": "document", "objectid": 127560, "filename": "indexcodes.txt", "mime_type": "text/x-c", "hash": "7d5393b1a43a618d0b612e7aef5b9f69", "hash_type": "MD5", "filesize": 35552, "mtime": "2021-06-24 01:51:47", "url": "/7120/10/indexcodes.txt" } ], "eprint_id": 7120, "pos": 10, "placement": 10, "mime_type": "text/x-c", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/15012" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/15012" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/15012" } ] } } ], "eprint_status": "archive", "userid": 8711, "dir": "disk0/00/00/71/20", "datestamp": "2012-06-08 21:37:33", "lastmod": "2019-10-03 23:56:26", "status_changed": "2012-06-08 21:37:33", "type": "thesis", "metadata_visibility": "show", "creators": { "items": [ { "email": "megandobro@gmail.com", "id": "Dobro-Megan-J", "name": { "family": "Dobro", "given": "Megan J." }, "show_email": "YES" } ] }, "title": "The Structural Biology of HIV Budding and Maturation", "ispublished": "unpub", "full_text_status": "public", "keywords": "HIV, ESCRT, electron cryotomography, EM, tomography, archaea, cell division", "abstract": "The Human Immunodeficiency Virus (HIV) depends on the ability to exit infected cells, mature into an infectious state, and infect new host cells. The structural details of exiting and maturation (known as the \"late stage events\") remain elusive, but further understanding could lead to new therapies. HIV exits cells by hijacking a host cellular complex called ESCRT (Endosomal Sorting Complex Required for Transport), which evolved to constrict membranes in multivesicular body formation and cytokinesis. Electron cryotomography (ECT) was used to gain three-dimensional images of ESCRT in several contexts, including the physiological system of archaeal cell division. This study provided insight into the monomer interactions in the complex and led to a molecular mechanism of membrane constriction.
\r\n\r\nHIV is released from the cell as an immature particle with the main structural protein, Gag, forming a spherical shell around the RNA genome and enzymes. Gag is then cleaved into several proteins that refold and assemble into the conical capsid that is characteristic of the mature, infectious particle. The capsid is typically a closed cone, but unclosed varieties provide insight to the mechanism of assembly. By combining ECT, computer simulations, and fluorescence light microscopy, we analyzed features of unclosed capsids that suggest a \"curling sheet\" model of capsid assembly. These studies not only provided novel insight into the late stages of the HIV life cycle, but also contributed to the methods used by electron microscopists and researchers of HIV.
\r\n", "date": "2012", "date_type": "degree", "id_number": "CaltechTHESIS:06012012-133153407", "refereed": "FALSE", "official_url": "https://resolver.caltech.edu/CaltechTHESIS:06012012-133153407", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "collection": "CaltechTHESIS", "reviewer": "Kathy Johnson", "deposited_by": "Megan Dobro", "deposited_on": "2012-06-08 21:37:33", "doi": "10.7907/X6XW-5303", "divisions": { "items": [ "div_biol" ] }, "institution": "California Institute of Technology", "thesis_type": "phd", "thesis_advisor": { "items": [ { "email": "jensen@caltech.edu", "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "role": "advisor" } ] }, "thesis_committee": { "items": [ { "email": "bjorkman@caltech.edu", "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "role": "chair" }, { "email": "dchan@caltech.edu", "id": "Chan-D-C", "name": { "family": "Chan", "given": "David C." }, "role": "member" }, { "email": "sefraser@caltech.edu", "id": "Fraser-S-E", "name": { "family": "Fraser", "given": "Scott E." }, "role": "member" }, { "email": "jensen@caltech.edu", "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "role": "member" } ] }, "thesis_degree": "PHD", "thesis_degree_grantor": "California Institute of Technology", "thesis_defense_date": "2012-05-14", "gradofc_approval_date": "2012-06-08", "thesis_awards": "Graduate Dean's Award for Outstanding Community Service, 2012", "review_status": "approved", "option_major": { "items": [ "biology" ] }, "copyright_statement": "Author's Rights Authorization: I hereby certify that, if appropriate, I have obtained a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted here is the same as that approved by my advisory committee.\n\nI hereby grant to California Institute of Technology or its agents the non-exclusive license to archive and make accessible, under the conditions specified under \"Thesis Availability\" in this submission, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation, or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report.", "resource_type": "thesis", "pub_year": "2012", "author_list": "Dobro, Megan J.", "advisor_list": "Jensen, Grant J.", "comittee_list": "Bjorkman, Pamela J.; Chan, David C.; et el." }, { "id": "https://thesis.library.caltech.edu/id/eprint/5245", "eprint_id": 5245, "rev_number": 49, "documents": [ { "id": "/id/document/8380", "doc_id": 8380, "rev_number": 4, "files": [ { "id": "/id/file/51998", "fileid": 51998, "datasetid": "document", "objectid": 8380, "filename": "00Title.pdf", "mime_type": "application/pdf", "filesize": 280689, "mtime": "2012-12-26 03:16:52", "url": "/5245/1/00Title.pdf" } ], "eprint_id": 5245, "pos": 1, "placement": 2, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "00Title.pdf", "language": "en", "security": "public", "license": "other", "main": "00Title.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/24839" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/24839" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/24839" } ] } }, { "id": "/id/document/8381", "doc_id": 8381, "rev_number": 4, "files": [ { "id": "/id/file/52002", "fileid": 52002, "datasetid": "document", "objectid": 8381, "filename": "01Introduction.pdf", "mime_type": "application/pdf", "filesize": 1040015, "mtime": "2012-12-26 03:16:52", "url": "/5245/2/01Introduction.pdf" } ], "eprint_id": 5245, "pos": 2, "placement": 3, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "01Introduction.pdf", "language": "en", "security": "public", "license": "other", "main": "01Introduction.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/24840" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/24840" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/24840" } ] } }, { "id": "/id/document/8382", "doc_id": 8382, "rev_number": 4, "files": [ { "id": "/id/file/52006", "fileid": 52006, "datasetid": "document", "objectid": 8382, "filename": "02Peach.pdf", "mime_type": "application/pdf", "filesize": 2288404, "mtime": "2012-12-26 03:16:52", "url": "/5245/3/02Peach.pdf" } ], "eprint_id": 5245, "pos": 3, "placement": 4, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "02Peach.pdf", "language": "en", "security": "public", "license": "other", "main": "02Peach.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/24841" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/24841" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/24841" } ] } }, { "id": "/id/document/8383", "doc_id": 8383, "rev_number": 4, "files": [ { "id": "/id/file/52010", "fileid": 52010, "datasetid": "document", "objectid": 8383, "filename": "03Prec.pdf", "mime_type": "application/pdf", "filesize": 3939550, "mtime": "2012-12-26 03:16:53", "url": "/5245/4/03Prec.pdf" } ], "eprint_id": 5245, "pos": 4, "placement": 5, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "03Prec.pdf", "language": "en", "security": "public", "license": "other", "main": "03Prec.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/24842" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/24842" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/24842" } ] } }, { "id": "/id/document/8384", "doc_id": 8384, "rev_number": 4, "files": [ { "id": "/id/file/52014", "fileid": 52014, "datasetid": "document", "objectid": 8384, "filename": "04Conclusion.pdf", "mime_type": "application/pdf", "filesize": 99842, "mtime": "2012-12-26 03:16:53", "url": "/5245/5/04Conclusion.pdf" } ], "eprint_id": 5245, "pos": 5, "placement": 6, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "04Conclusion.pdf", "language": "en", "security": "public", "license": "other", "main": "04Conclusion.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/24843" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/24843" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/24843" } ] } }, { "id": "/id/document/8385", "doc_id": 8385, "rev_number": 4, "files": [ { "id": "/id/file/52018", "fileid": 52018, "datasetid": "document", "objectid": 8385, "filename": "05Appendix.pdf", "mime_type": "application/pdf", "filesize": 994548, "mtime": "2012-12-26 03:16:53", "url": "/5245/6/05Appendix.pdf" } ], "eprint_id": 5245, "pos": 6, "placement": 7, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "05Appendix.pdf", "language": "en", "security": "public", "license": "other", "main": "05Appendix.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/24844" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/24844" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/24844" } ] } }, { "id": "/id/document/8386", "doc_id": 8386, "rev_number": 5, "files": [ { "id": "/id/file/52022", "fileid": 52022, "datasetid": "document", "objectid": 8386, "filename": "PeterLeongThesis.pdf", "mime_type": "application/pdf", "filesize": 7198483, "mtime": "2012-12-26 03:16:54", "url": "/5245/7/PeterLeongThesis.pdf" } ], "eprint_id": 5245, "pos": 7, "placement": 1, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "Full thesis", "language": "en", "security": "public", "license": "other", "main": "PeterLeongThesis.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/24845" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/24845" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/24845" } ] } }, { "id": "/id/document/8761", "doc_id": 8761, "rev_number": 4, "files": [ { "id": "/id/file/204728", "fileid": 204728, "datasetid": "document", "objectid": 8761, "filename": "Access_to_your_thesis.txt", "mime_type": "text/plain", "filesize": 973, "mtime": "2016-08-22 21:18:03", "url": "/5245/8/Access_to_your_thesis.txt" } ], "eprint_id": 5245, "pos": 8, "format": "text/plain", "format_desc": "author ok 2009", "language": "en", "security": "internal", "license": "other", "main": "Access_to_your_thesis.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "release" }, { "id": "/id/document/24839", "doc_id": 24839, "rev_number": 2, "files": [ { "id": "/id/file/51996", "fileid": 51996, "datasetid": "document", "objectid": 24839, "filename": "preview.png", "mime_type": "image/png", "hash": "f501463663a6b75e74551fbc306ea9bd", "hash_type": "MD5", "filesize": 15227, "mtime": "2012-12-26 03:16:51", "url": "/5245/9/preview.png" } ], "eprint_id": 5245, "pos": 9, "placement": 9, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/8380" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/8380" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/8380" } ] } }, { "id": "/id/document/24840", "doc_id": 24840, "rev_number": 2, "files": [ { "id": "/id/file/52000", "fileid": 52000, "datasetid": "document", "objectid": 24840, "filename": "preview.png", "mime_type": "image/png", "hash": "3551123844651544856d4f7dc53c5738", "hash_type": "MD5", "filesize": 25916, "mtime": "2012-12-26 03:16:52", "url": "/5245/10/preview.png" } ], "eprint_id": 5245, "pos": 10, "placement": 10, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/8381" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/8381" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/8381" } ] } }, { "id": "/id/document/24841", "doc_id": 24841, "rev_number": 2, "files": [ { "id": "/id/file/52004", "fileid": 52004, "datasetid": "document", "objectid": 24841, "filename": "preview.png", "mime_type": "image/png", "hash": "e5b8effe433446ca5451aeefcea6ac13", "hash_type": "MD5", "filesize": 17292, "mtime": "2012-12-26 03:16:52", "url": "/5245/11/preview.png" } ], "eprint_id": 5245, "pos": 11, "placement": 11, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/8382" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/8382" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/8382" } ] } }, { "id": "/id/document/24842", "doc_id": 24842, "rev_number": 2, "files": [ { "id": "/id/file/52008", "fileid": 52008, "datasetid": "document", "objectid": 24842, "filename": "preview.png", "mime_type": "image/png", "hash": "2ef13976a3465ab92da2566c591edf63", "hash_type": "MD5", "filesize": 17253, "mtime": "2012-12-26 03:16:53", "url": "/5245/12/preview.png" } ], "eprint_id": 5245, "pos": 12, "placement": 12, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/8383" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/8383" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/8383" } ] } }, { "id": "/id/document/24843", "doc_id": 24843, "rev_number": 2, "files": [ { "id": "/id/file/52012", "fileid": 52012, "datasetid": "document", "objectid": 24843, "filename": "preview.png", "mime_type": "image/png", "hash": "5e9c38c509844df99d4630f98022de11", "hash_type": "MD5", "filesize": 27668, "mtime": "2012-12-26 03:16:53", "url": "/5245/13/preview.png" } ], "eprint_id": 5245, "pos": 13, "placement": 13, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/8384" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/8384" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/8384" } ] } }, { "id": "/id/document/24844", "doc_id": 24844, "rev_number": 2, "files": [ { "id": "/id/file/52016", "fileid": 52016, "datasetid": "document", "objectid": 24844, "filename": "preview.png", "mime_type": "image/png", "hash": "dbcc47362aaaa4266723cedace79f6bd", "hash_type": "MD5", "filesize": 25161, "mtime": "2012-12-26 03:16:53", "url": "/5245/14/preview.png" } ], "eprint_id": 5245, "pos": 14, "placement": 14, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/8385" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/8385" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/8385" } ] } }, { "id": "/id/document/24845", "doc_id": 24845, "rev_number": 2, "files": [ { "id": "/id/file/52020", "fileid": 52020, "datasetid": "document", "objectid": 24845, "filename": "preview.png", "mime_type": "image/png", "hash": "f501463663a6b75e74551fbc306ea9bd", "hash_type": "MD5", "filesize": 15227, "mtime": "2012-12-26 03:16:54", "url": "/5245/15/preview.png" } ], "eprint_id": 5245, "pos": 15, "placement": 15, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/8386" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/8386" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/8386" } ] } }, { "id": "/id/document/125162", "doc_id": 125162, "rev_number": 1, "files": [ { "id": "/id/file/370595", "fileid": 370595, "datasetid": "document", "objectid": 125162, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "8c18b0ce48be8bef29d166f48ce00e2f", "hash_type": "MD5", "filesize": 3364, "mtime": "2021-06-24 00:02:46", "url": "/5245/16/indexcodes.txt" } ], "eprint_id": 5245, "pos": 16, "placement": 16, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/8380" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/8380" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/8380" } ] } }, { "id": "/id/document/125163", "doc_id": 125163, "rev_number": 1, "files": [ { "id": "/id/file/370596", "fileid": 370596, "datasetid": "document", "objectid": 125163, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "9147e21ff85f430924b7e6f2aead7b12", "hash_type": "MD5", "filesize": 11588, "mtime": "2021-06-24 00:02:47", "url": "/5245/17/indexcodes.txt" } ], "eprint_id": 5245, "pos": 17, "placement": 17, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/8381" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/8381" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/8381" } ] } }, { "id": "/id/document/125164", "doc_id": 125164, "rev_number": 1, "files": [ { "id": "/id/file/370597", "fileid": 370597, "datasetid": "document", "objectid": 125164, "filename": "indexcodes.txt", "mime_type": "text/x-c", "hash": "6f17a79887a4d17398da36fee73591e6", "hash_type": "MD5", "filesize": 10190, "mtime": "2021-06-24 00:02:47", "url": "/5245/18/indexcodes.txt" } ], "eprint_id": 5245, "pos": 18, "placement": 18, "mime_type": "text/x-c", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/8382" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/8382" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/8382" } ] } }, { "id": "/id/document/125165", "doc_id": 125165, "rev_number": 1, "files": [ { "id": "/id/file/370598", "fileid": 370598, "datasetid": "document", "objectid": 125165, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "ea76db431640ff243e9bb06383a48c38", "hash_type": "MD5", "filesize": 9237, "mtime": "2021-06-24 00:02:47", "url": "/5245/19/indexcodes.txt" } ], "eprint_id": 5245, "pos": 19, "placement": 19, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/8383" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/8383" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/8383" } ] } }, { "id": "/id/document/125166", "doc_id": 125166, "rev_number": 1, "files": [ { "id": "/id/file/370599", "fileid": 370599, "datasetid": "document", "objectid": 125166, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "937001aad67535a881d0b44abcd89c86", "hash_type": "MD5", "filesize": 2265, "mtime": "2021-06-24 00:02:48", "url": "/5245/20/indexcodes.txt" } ], "eprint_id": 5245, "pos": 20, "placement": 20, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/8384" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/8384" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/8384" } ] } }, { "id": "/id/document/125167", "doc_id": 125167, "rev_number": 1, "files": [ { "id": "/id/file/370600", "fileid": 370600, "datasetid": "document", "objectid": 125167, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "4bf13feb23595f58e335e4335eaee029", "hash_type": "MD5", "filesize": 3662, "mtime": "2021-06-24 00:02:48", "url": "/5245/21/indexcodes.txt" } ], "eprint_id": 5245, "pos": 21, "placement": 21, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/8385" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/8385" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/8385" } ] } }, { "id": "/id/document/125168", "doc_id": 125168, "rev_number": 1, "files": [ { "id": "/id/file/370601", "fileid": 370601, "datasetid": "document", "objectid": 125168, "filename": "indexcodes.txt", "mime_type": "text/x-c", "hash": "1206561f48bbcbe605ae26509ada06ce", "hash_type": "MD5", "filesize": 22151, "mtime": "2021-06-24 00:02:48", "url": "/5245/22/indexcodes.txt" } ], "eprint_id": 5245, "pos": 22, "placement": 22, "mime_type": "text/x-c", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/8386" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/8386" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/8386" } ] } }, { "id": "/id/document/125169", "doc_id": 125169, "rev_number": 1, "files": [ { "id": "/id/file/370602", "fileid": 370602, "datasetid": "document", "objectid": 125169, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "21ba1ef388193c47f6e0d41ccb3cb87e", "hash_type": "MD5", "filesize": 492, "mtime": "2021-06-24 00:02:48", "url": "/5245/23/indexcodes.txt" } ], "eprint_id": 5245, "pos": 23, "placement": 23, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from text/plain to indexcodes", "language": "en", "security": "internal", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/8761" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/8761" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/8761" } ] } } ], "eprint_status": "archive", "userid": 2, "dir": "disk0/00/00/52/45", "datestamp": "2008-08-13", "lastmod": "2020-12-18 02:39:04", "status_changed": "2009-11-10 21:38:56", "type": "thesis", "metadata_visibility": "show", "creators": { "items": [ { "email": "peter.a.leong@gmail.com", "id": "Leong-Peter-Anthony", "name": { "family": "Leong", "given": "Peter Anthony" }, "show_email": "YES" } ] }, "title": "Computational Challenges in High-Resolution Cryo-Electron Microscopy", "ispublished": "unpub", "full_text_status": "public", "keywords": "Cryo-Electron Microscopy; Depth of Field; Distributed Computation; Ewald Sphere Curvature; Parallel Computation; Three-Dimensional Reconstruction", "abstract": "To avoid the challenges of crystallization and the size limitations of NMR, it has long been hoped that single-particle cryo-electron microscopy (cryo-EM) would eventually yield atomically interpretable reconstructions. For the most favorable class of specimens (large icosahedral viruses), two of the key obstacles are the large computational requirements of high-resolution reconstructions and the curvature of the Ewald sphere, which leads to a breakdown of the projection theorem used by conventional 3D reconstruction programs. Here, two solutions to these obstacles are presented.
\r\n\r\nFirst, a simple distributed processing system named Peach was developed to meet the rising computational demands of modern structural biology (and other) laboratories without additional expense by using existing hardware resources more efficiently. A central server distributes jobs to idle workstations in such a way that each computer is used maximally, but without disturbing intermittent interactive users. As compared to other distributed systems, Peach is simple, easy to install, easy to administer, easy to use, scalable, and robust. While it was designed to queue and distribute large numbers of small tasks to participating computers, it can also be used to send single jobs automatically to the fastest currently available computer and/or survey the activity of an entire laboratory's computers. Tests of robustness and scalability are reported, as are three specific cryo-EM applications where Peach enabled projects that would not otherwise have been feasible without an expensive, dedicated cluster.
\r\n\r\nSecond, an iterative refinement reconstruction algorithm, Prec, is described that overcomes the curvature of the Ewald sphere resolution limitation by averaging information from images recorded from different points of view, as are present in typical micrographs. Prec was implemented in the popular software packages IMIRS, EMAN, and Bsoft. In preliminary tests with both simple and multi-slice simulated images, Prec overcame the curvature problem even in the presence of noise. Prec was then used to refine the three recently published, ~ 4 \u00c5 resolution, icosahedral virus reconstructions from experimental cryo-EM images, but unfortunately no significant improvements in resolution were realized. Further simulations showed that limitations other than the Ewald sphere curvature problem must still be dominant in these experimental studies.
\r\n", "date": "2009", "date_type": "degree", "id_number": "CaltechETD:etd-08072008-171049", "refereed": "FALSE", "official_url": "https://resolver.caltech.edu/CaltechETD:etd-08072008-171049", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "collection": "CaltechTHESIS", "reviewer": "Kathy Johnson", "deposited_by": "Imported from ETD-db", "deposited_on": "2008-08-13", "doi": "10.7907/GJKS-2P80", "divisions": { "items": [ "div_eng" ] }, "institution": "California Institute of Technology", "thesis_type": "phd", "thesis_advisor": { "items": [ { "email": "jensen@caltech.edu", "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "role": "advisor" } ] }, "thesis_committee": { "items": [ { "email": "sefraser@caltech.edu", "id": "Fraser-S-E", "name": { "family": "Fraser", "given": "Scott E." }, "role": "chair" }, { "email": "dcrees@caltech.edu", "id": "Rees-D-C", "name": { "family": "Rees", "given": "Douglas C." }, "role": "member" }, { "email": "jensen@caltech.edu", "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "role": "member" }, { "email": "phillips@pboc.caltech.edu", "id": "Phillips-R-B", "name": { "family": "Phillips", "given": "Robert B." }, "role": "member" }, { "email": "Hong.Zhou@UCLA.edu", "id": "Zhou-Z-Hong", "name": { "family": "Zhou", "given": "Z. Hong" }, "role": "member" }, { "email": "btf@caltech.edu", "id": "Fultz-B-T", "name": { "family": "Fultz", "given": "Brent T." }, "role": "member" } ] }, "thesis_degree": "PHD", "thesis_degree_grantor": "California Institute of Technology", "thesis_submitted_date": "2008-08-07", "thesis_defense_date": "2008-08-04", "thesis_approved_date": "2008-08-13", "gradofc_approval_date": "2008-08-11", "review_status": "approved", "option_major": { "items": [ "appliedphys" ] }, "copyright_statement": "I hereby certify that, if appropriate, I have obtained a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee.\n\nI hereby grant to California Institute of Technology or its agents the non-exclusive\nlicense to archive and make accessible, under the conditions specified below,\nmy thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report.", "resource_type": "thesis", "pub_year": "2009", "author_list": "Leong, Peter Anthony", "advisor_list": "Jensen, Grant J.", "comittee_list": "Fraser, Scott E.; Rees, Douglas C.; et el." }, { "id": "https://thesis.library.caltech.edu/id/eprint/1921", "eprint_id": 1921, "rev_number": 92, "documents": [ { "id": "/id/document/3306", "doc_id": 3306, "rev_number": 7, "files": [ { "id": "/id/file/19718", "fileid": 19718, "datasetid": "document", "objectid": 3306, "filename": "Chapter3_SuppMovie.mov", "mime_type": "video/quicktime", "filesize": 65393500, "mtime": "2012-12-26 02:44:11", "url": "/1921/1/Chapter3_SuppMovie.mov" } ], "eprint_id": 1921, "pos": 1, "placement": 11, "mime_type": "video/quicktime", "format": "video/quicktime", "format_desc": "Chapter3_SuppMovie.mov", "language": "en", "security": "public", "license": "other", "main": "Chapter3_SuppMovie.mov", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/3307", "doc_id": 3307, "rev_number": 9, "files": [ { "id": "/id/file/19719", "fileid": 19719, "datasetid": "document", "objectid": 3307, "filename": "Chapter4_SuppMovie1.mov", "mime_type": "video/quicktime", "filesize": 45707444, "mtime": "2012-12-26 02:44:11", "url": "/1921/2/Chapter4_SuppMovie1.mov" } ], "eprint_id": 1921, "pos": 2, "placement": 12, "mime_type": "video/quicktime", "format": "video/quicktime", "format_desc": "Chapter4_SuppMovie1.mov", "language": "en", "security": "public", "license": "other", "main": "Chapter4_SuppMovie1.mov", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/3308", "doc_id": 3308, "rev_number": 8, "files": [ { "id": "/id/file/19720", "fileid": 19720, "datasetid": "document", "objectid": 3308, "filename": "Chapter4_SuppMovie2.mov", "mime_type": "video/quicktime", "filesize": 29408580, "mtime": "2012-12-26 02:44:11", "url": "/1921/3/Chapter4_SuppMovie2.mov" } ], "eprint_id": 1921, "pos": 3, "placement": 13, "mime_type": "video/quicktime", "format": "video/quicktime", "format_desc": "Chapter4_SuppMovie2.mov", "language": "en", "security": "public", "license": "other", "main": "Chapter4_SuppMovie2.mov", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/3309", "doc_id": 3309, "rev_number": 12, "files": [ { "id": "/id/file/19721", "fileid": 19721, "datasetid": "document", "objectid": 3309, "filename": "Chapter4_SuppMovie3.mov", "mime_type": "video/quicktime", "filesize": 5569732, "mtime": "2012-12-26 02:44:11", "url": "/1921/4/Chapter4_SuppMovie3.mov" } ], "eprint_id": 1921, "pos": 4, "placement": 14, "mime_type": "video/quicktime", "format": "video/quicktime", "format_desc": "Chapter4_SuppMovie3.mov", "language": "en", "security": "public", "license": "other", "main": "Chapter4_SuppMovie3.mov", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/3310", "doc_id": 3310, "rev_number": 12, "files": [ { "id": "/id/file/19722", "fileid": 19722, "datasetid": "document", "objectid": 3310, "filename": "Chapter4_SuppMovie4.mov", "mime_type": "video/quicktime", "filesize": 35025160, "mtime": "2012-12-26 02:44:11", "url": "/1921/5/Chapter4_SuppMovie4.mov" } ], "eprint_id": 1921, "pos": 5, "placement": 15, "mime_type": "video/quicktime", "format": "video/quicktime", "format_desc": "Chapter4_SuppMovie4.mov", "language": "en", "security": "public", "license": "other", "main": "Chapter4_SuppMovie4.mov", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/3311", "doc_id": 3311, "rev_number": 12, "files": [ { "id": "/id/file/19723", "fileid": 19723, "datasetid": "document", "objectid": 3311, "filename": "Chapter4_SuppMovie5.mov", "mime_type": "video/quicktime", "filesize": 13206416, "mtime": "2012-12-26 02:44:11", "url": "/1921/6/Chapter4_SuppMovie5.mov" } ], "eprint_id": 1921, "pos": 6, "placement": 16, "mime_type": "video/quicktime", "format": "video/quicktime", "format_desc": "Chapter4_SuppMovie5.mov", "language": "en", "security": "public", "license": "other", "main": "Chapter4_SuppMovie5.mov", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/3312", "doc_id": 3312, "rev_number": 13, "files": [ { "id": "/id/file/19724", "fileid": 19724, "datasetid": "document", "objectid": 3312, "filename": "Chapter5_SuppMovie.mpg", "mime_type": "video/mpeg", "filesize": 20727666, "mtime": "2012-12-26 02:44:11", "url": "/1921/7/Chapter5_SuppMovie.mpg" } ], "eprint_id": 1921, "pos": 7, "placement": 17, "mime_type": "video/mpeg", "format": "video/mpeg", "format_desc": "Chapter5_SuppMovie.mpg", "language": "en", "security": "public", "license": "other", "main": "Chapter5_SuppMovie.mpg", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "supplemental" }, { "id": "/id/document/3313", "doc_id": 3313, "rev_number": 5, "files": [ { "id": "/id/file/19728", "fileid": 19728, "datasetid": "document", "objectid": 3313, "filename": "GEMurphy_EntireThesis.pdf", "mime_type": "application/pdf", "filesize": 17586889, "mtime": "2012-12-26 02:44:12", "url": "/1921/8/GEMurphy_EntireThesis.pdf" } ], "eprint_id": 1921, "pos": 8, "placement": 1, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "GEMurphy_EntireThesis.pdf", "language": "en", "security": "public", "license": "other", "main": "GEMurphy_EntireThesis.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/19997" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/19997" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/19997" } ] } }, { "id": "/id/document/3314", "doc_id": 3314, "rev_number": 15, "files": [ { "id": "/id/file/19732", "fileid": 19732, "datasetid": "document", "objectid": 3314, "filename": "GEM_AppendixA.pdf", "mime_type": "application/pdf", "filesize": 2560522, "mtime": "2012-12-26 02:44:13", "url": "/1921/9/GEM_AppendixA.pdf" } ], "eprint_id": 1921, "pos": 9, "placement": 9, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "GEM_AppendixA.pdf", "language": "en", "security": "public", "license": "other", "main": "GEM_AppendixA.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/19998" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/19998" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/19998" } ] } }, { "id": "/id/document/3315", "doc_id": 3315, "rev_number": 15, "files": [ { "id": "/id/file/19736", "fileid": 19736, "datasetid": "document", "objectid": 3315, "filename": "GEM_AppendixB.pdf", "mime_type": "application/pdf", "filesize": 1439637, "mtime": "2012-12-26 02:44:13", "url": "/1921/10/GEM_AppendixB.pdf" } ], "eprint_id": 1921, "pos": 10, "placement": 10, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "GEM_AppendixB.pdf", "language": "en", "security": "public", "license": "other", "main": "GEM_AppendixB.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/19999" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/19999" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/19999" } ] } }, { "id": "/id/document/3316", "doc_id": 3316, "rev_number": 7, "files": [ { "id": "/id/file/19740", "fileid": 19740, "datasetid": "document", "objectid": 3316, "filename": "GEM_Chapter1.pdf", "mime_type": "application/pdf", "filesize": 1196261, "mtime": "2012-12-26 02:44:13", "url": "/1921/11/GEM_Chapter1.pdf" } ], "eprint_id": 1921, "pos": 11, "placement": 3, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "GEM_Chapter1.pdf", "language": "en", "security": "public", "license": "other", "main": "GEM_Chapter1.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/20000" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/20000" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/20000" } ] } }, { "id": "/id/document/3317", "doc_id": 3317, "rev_number": 7, "files": [ { "id": "/id/file/19744", "fileid": 19744, "datasetid": "document", "objectid": 3317, "filename": "GEM_Chapter2.pdf", "mime_type": "application/pdf", "filesize": 2268204, "mtime": "2012-12-26 02:44:14", "url": "/1921/12/GEM_Chapter2.pdf" } ], "eprint_id": 1921, "pos": 12, "placement": 4, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "GEM_Chapter2.pdf", "language": "en", "security": "public", "license": "other", "main": "GEM_Chapter2.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/20001" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/20001" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/20001" } ] } }, { "id": "/id/document/3318", "doc_id": 3318, "rev_number": 7, "files": [ { "id": "/id/file/19748", "fileid": 19748, "datasetid": "document", "objectid": 3318, "filename": "GEM_Chapter3.pdf", "mime_type": "application/pdf", "filesize": 2904990, "mtime": "2012-12-26 02:44:14", "url": "/1921/13/GEM_Chapter3.pdf" } ], "eprint_id": 1921, "pos": 13, "placement": 5, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "GEM_Chapter3.pdf", "language": "en", "security": "public", "license": "other", "main": "GEM_Chapter3.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/20002" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/20002" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/20002" } ] } }, { "id": "/id/document/3319", "doc_id": 3319, "rev_number": 8, "files": [ { "id": "/id/file/19752", "fileid": 19752, "datasetid": "document", "objectid": 3319, "filename": "GEM_Chapter4.pdf", "mime_type": "application/pdf", "filesize": 2582222, "mtime": "2012-12-26 02:44:14", "url": "/1921/14/GEM_Chapter4.pdf" } ], "eprint_id": 1921, "pos": 14, "placement": 6, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "GEM_Chapter4.pdf", "language": "en", "security": "public", "license": "other", "main": "GEM_Chapter4.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/20003" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/20003" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/20003" } ] } }, { "id": "/id/document/3320", "doc_id": 3320, "rev_number": 9, "files": [ { "id": "/id/file/19756", "fileid": 19756, "datasetid": "document", "objectid": 3320, "filename": "GEM_Chapter5.pdf", "mime_type": "application/pdf", "filesize": 3563533, "mtime": "2012-12-26 02:44:15", "url": "/1921/15/GEM_Chapter5.pdf" } ], "eprint_id": 1921, "pos": 15, "placement": 7, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "GEM_Chapter5.pdf", "language": "en", "security": "public", "license": "other", "main": "GEM_Chapter5.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/20004" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/20004" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/20004" } ] } }, { "id": "/id/document/3321", "doc_id": 3321, "rev_number": 9, "files": [ { "id": "/id/file/19760", "fileid": 19760, "datasetid": "document", "objectid": 3321, "filename": "GEM_Chapter6.pdf", "mime_type": "application/pdf", "filesize": 956365, "mtime": "2012-12-26 02:44:15", "url": "/1921/16/GEM_Chapter6.pdf" } ], "eprint_id": 1921, "pos": 16, "placement": 8, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "GEM_Chapter6.pdf", "language": "en", "security": "public", "license": "other", "main": "GEM_Chapter6.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/20005" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/20005" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/20005" } ] } }, { "id": "/id/document/3322", "doc_id": 3322, "rev_number": 5, "files": [ { "id": "/id/file/19764", "fileid": 19764, "datasetid": "document", "objectid": 3322, "filename": "GEM_FrontMatter.pdf", "mime_type": "application/pdf", "filesize": 338755, "mtime": "2012-12-26 02:44:15", "url": "/1921/17/GEM_FrontMatter.pdf" } ], "eprint_id": 1921, "pos": 17, "placement": 2, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "GEM_FrontMatter.pdf", "language": "en", "security": "public", "license": "other", "main": "GEM_FrontMatter.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/20006" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/20006" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/20006" } ] } }, { "id": "/id/document/15796", "doc_id": 15796, "rev_number": 3, "files": [ { "id": "/id/file/202120", "fileid": 202120, "datasetid": "document", "objectid": 15796, "filename": "thesis_release_request_for_Gavin_Erick_Murphy_(2007)_nov_2012.txt", "mime_type": "text/plain", "filesize": 1448, "mtime": "2016-08-22 21:15:20", "url": "/1921/18/thesis_release_request_for_Gavin_Erick_Murphy_(2007)_nov_2012.txt" } ], "eprint_id": 1921, "pos": 18, "format": "text/plain", "format_desc": "release request nov 2012", "language": "en", "security": "internal", "license": "other", "main": "thesis_release_request_for_Gavin_Erick_Murphy_(2007)_nov_2012.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "release" }, { "id": "/id/document/15917", "doc_id": 15917, "rev_number": 3, "files": [ { "id": "/id/file/202122", "fileid": 202122, "datasetid": "document", "objectid": 15917, "filename": "Re_thesis_release_request_for_Gavin_Erick_Murphy_(2007)__advisor_ok_nov2012.txt", "mime_type": "text/plain", "filesize": 2250, "mtime": "2016-08-22 21:15:20", "url": "/1921/19/Re_thesis_release_request_for_Gavin_Erick_Murphy_(2007)__advisor_ok_nov2012.txt" } ], "eprint_id": 1921, "pos": 19, "format": "text/plain", "format_desc": " advisor ok nov2012", "language": "en", "security": "internal", "license": "other", "main": "Re_thesis_release_request_for_Gavin_Erick_Murphy_(2007)__advisor_ok_nov2012.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "release" }, { "id": "/id/document/16301", "doc_id": 16301, "rev_number": 3, "files": [ { "id": "/id/file/202123", "fileid": 202123, "datasetid": "document", "objectid": 16301, "filename": "Murphy_Gavin_Erick_2007.PDF", "mime_type": "application/pdf", "filesize": 44891, "mtime": "2016-08-22 21:15:20", "url": "/1921/20/Murphy_Gavin_Erick_2007.PDF" } ], "eprint_id": 1921, "pos": 20, "format": "application/pdf", "language": "en", "security": "internal", "license": "other", "main": "Murphy_Gavin_Erick_2007.PDF", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "approvalform" }, { "id": "/id/document/19997", "doc_id": 19997, "rev_number": 2, "files": [ { "id": "/id/file/19726", "fileid": 19726, "datasetid": "document", "objectid": 19997, "filename": "preview.png", "mime_type": "image/png", "hash": "84eea260f581a12b7b07b3eeef0855cd", "hash_type": "MD5", "filesize": 18271, "mtime": "2012-12-26 02:44:11", "url": "/1921/21/preview.png" } ], "eprint_id": 1921, "pos": 21, "placement": 21, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3313" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/3313" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3313" } ] } }, { "id": "/id/document/19998", "doc_id": 19998, "rev_number": 2, "files": [ { "id": "/id/file/19730", "fileid": 19730, "datasetid": "document", "objectid": 19998, "filename": "preview.png", "mime_type": "image/png", "hash": "8ffc374f9d35e2deb1ed0093703159a2", "hash_type": "MD5", "filesize": 23006, "mtime": "2012-12-26 02:44:12", "url": "/1921/22/preview.png" } ], "eprint_id": 1921, "pos": 22, "placement": 22, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3314" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/3314" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3314" } ] } }, { "id": "/id/document/19999", "doc_id": 19999, "rev_number": 2, "files": [ { "id": "/id/file/19734", "fileid": 19734, "datasetid": "document", "objectid": 19999, "filename": "preview.png", "mime_type": "image/png", "hash": "22b698dddb865c9dc85d990237546422", "hash_type": "MD5", "filesize": 19909, "mtime": "2012-12-26 02:44:13", "url": "/1921/23/preview.png" } ], "eprint_id": 1921, "pos": 23, "placement": 23, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3315" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/3315" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3315" } ] } }, { "id": "/id/document/20000", "doc_id": 20000, "rev_number": 2, "files": [ { "id": "/id/file/19738", "fileid": 19738, "datasetid": "document", "objectid": 20000, "filename": "preview.png", "mime_type": "image/png", "hash": "335aeb93eba9e97ac7ced78c828bb2e2", "hash_type": "MD5", "filesize": 28636, "mtime": "2012-12-26 02:44:13", "url": "/1921/24/preview.png" } ], "eprint_id": 1921, "pos": 24, "placement": 24, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3316" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/3316" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3316" } ] } }, { "id": "/id/document/20001", "doc_id": 20001, "rev_number": 2, "files": [ { "id": "/id/file/19742", "fileid": 19742, "datasetid": "document", "objectid": 20001, "filename": "preview.png", "mime_type": "image/png", "hash": "965f0c87a2e70540f77aa8d36dea190c", "hash_type": "MD5", "filesize": 20641, "mtime": "2012-12-26 02:44:13", "url": "/1921/25/preview.png" } ], "eprint_id": 1921, "pos": 25, "placement": 25, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3317" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/3317" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3317" } ] } }, { "id": "/id/document/20002", "doc_id": 20002, "rev_number": 2, "files": [ { "id": "/id/file/19746", "fileid": 19746, "datasetid": "document", "objectid": 20002, "filename": "preview.png", "mime_type": "image/png", "hash": "f6bfbcd27f0451be03c9e9001486e97b", "hash_type": "MD5", "filesize": 19594, "mtime": "2012-12-26 02:44:14", "url": "/1921/26/preview.png" } ], "eprint_id": 1921, "pos": 26, "placement": 26, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3318" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/3318" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3318" } ] } }, { "id": "/id/document/20003", "doc_id": 20003, "rev_number": 2, "files": [ { "id": "/id/file/19750", "fileid": 19750, "datasetid": "document", "objectid": 20003, "filename": "preview.png", "mime_type": "image/png", "hash": "d7e55745fb77576ea30f1c1c5f2b6ac1", "hash_type": "MD5", "filesize": 18437, "mtime": "2012-12-26 02:44:14", "url": "/1921/27/preview.png" } ], "eprint_id": 1921, "pos": 27, "placement": 27, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3319" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/3319" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3319" } ] } }, { "id": "/id/document/20004", "doc_id": 20004, "rev_number": 2, "files": [ { "id": "/id/file/19754", "fileid": 19754, "datasetid": "document", "objectid": 20004, "filename": "preview.png", "mime_type": "image/png", "hash": "bcceee151a5f3ab22c051044265da4b8", "hash_type": "MD5", "filesize": 14050, "mtime": "2012-12-26 02:44:15", "url": "/1921/28/preview.png" } ], "eprint_id": 1921, "pos": 28, "placement": 28, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3320" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/3320" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3320" } ] } }, { "id": "/id/document/20005", "doc_id": 20005, "rev_number": 2, "files": [ { "id": "/id/file/19758", "fileid": 19758, "datasetid": "document", "objectid": 20005, "filename": "preview.png", "mime_type": "image/png", "hash": "c65944a952b354e8cef5763755dd24c9", "hash_type": "MD5", "filesize": 6851, "mtime": "2012-12-26 02:44:15", "url": "/1921/29/preview.png" } ], "eprint_id": 1921, "pos": 29, "placement": 29, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3321" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/3321" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3321" } ] } }, { "id": "/id/document/20006", "doc_id": 20006, "rev_number": 2, "files": [ { "id": "/id/file/19762", "fileid": 19762, "datasetid": "document", "objectid": 20006, "filename": "preview.png", "mime_type": "image/png", "hash": "84eea260f581a12b7b07b3eeef0855cd", "hash_type": "MD5", "filesize": 18271, "mtime": "2012-12-26 02:44:15", "url": "/1921/30/preview.png" } ], "eprint_id": 1921, "pos": 30, "placement": 30, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3322" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/3322" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3322" } ] } }, { "id": "/id/document/121608", "doc_id": 121608, "rev_number": 1, "files": [ { "id": "/id/file/367000", "fileid": 367000, "datasetid": "document", "objectid": 121608, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "f676179c9f698122a5b94a1e39f158e3", "hash_type": "MD5", "filesize": 36074, "mtime": "2021-06-23 21:30:54", "url": "/1921/31/indexcodes.txt" } ], "eprint_id": 1921, "pos": 31, "placement": 31, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3313" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3313" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/3313" } ] } }, { "id": "/id/document/121609", "doc_id": 121609, "rev_number": 1, "files": [ { "id": "/id/file/367001", "fileid": 367001, "datasetid": "document", "objectid": 121609, "filename": "indexcodes.txt", "mime_type": "text/x-c", "hash": "626eacd1994353457cad7e606cd84eb7", "hash_type": "MD5", "filesize": 10467, "mtime": "2021-06-23 21:30:54", "url": "/1921/32/indexcodes.txt" } ], "eprint_id": 1921, "pos": 32, "placement": 32, "mime_type": "text/x-c", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3314" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3314" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/3314" } ] } }, { "id": "/id/document/121610", "doc_id": 121610, "rev_number": 1, "files": [ { "id": "/id/file/367002", "fileid": 367002, "datasetid": "document", "objectid": 121610, "filename": "indexcodes.txt", "mime_type": "text/x-c", "hash": "51b6f85da5081f210d1b29f92bc02a98", "hash_type": "MD5", "filesize": 9381, "mtime": "2021-06-23 21:30:55", "url": "/1921/33/indexcodes.txt" } ], "eprint_id": 1921, "pos": 33, "placement": 33, "mime_type": "text/x-c", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3315" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3315" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/3315" } ] } }, { "id": "/id/document/121611", "doc_id": 121611, "rev_number": 1, "files": [ { "id": "/id/file/367003", "fileid": 367003, "datasetid": "document", "objectid": 121611, "filename": "indexcodes.txt", "mime_type": "text/x-c", "hash": "b1306af45e36e59ac58604815ca78e86", "hash_type": "MD5", "filesize": 11697, "mtime": "2021-06-23 21:30:55", "url": "/1921/34/indexcodes.txt" } ], "eprint_id": 1921, "pos": 34, "placement": 34, "mime_type": "text/x-c", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3316" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3316" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/3316" } ] } }, { "id": "/id/document/121612", "doc_id": 121612, "rev_number": 1, "files": [ { "id": "/id/file/367004", "fileid": 367004, "datasetid": "document", "objectid": 121612, "filename": "indexcodes.txt", "mime_type": "text/x-c", "hash": "80eddc4a35652a5beaadb25b5aa82c19", "hash_type": "MD5", "filesize": 10906, "mtime": "2021-06-23 21:30:55", "url": "/1921/35/indexcodes.txt" } ], "eprint_id": 1921, "pos": 35, "placement": 35, "mime_type": "text/x-c", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3317" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3317" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/3317" } ] } }, { "id": "/id/document/121613", "doc_id": 121613, "rev_number": 1, "files": [ { "id": "/id/file/367005", "fileid": 367005, "datasetid": "document", "objectid": 121613, "filename": "indexcodes.txt", "mime_type": "text/x-c", "hash": "5903dfe862de78d196103832247cd91d", "hash_type": "MD5", "filesize": 9494, "mtime": "2021-06-23 21:30:55", "url": "/1921/36/indexcodes.txt" } ], "eprint_id": 1921, "pos": 36, "placement": 36, "mime_type": "text/x-c", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3318" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3318" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/3318" } ] } }, { "id": "/id/document/121614", "doc_id": 121614, "rev_number": 1, "files": [ { "id": "/id/file/367006", "fileid": 367006, "datasetid": "document", "objectid": 121614, "filename": "indexcodes.txt", "mime_type": "text/x-c", "hash": "d41910daa527120b96c378f4f07513aa", "hash_type": "MD5", "filesize": 11322, "mtime": "2021-06-23 21:30:56", "url": "/1921/37/indexcodes.txt" } ], "eprint_id": 1921, "pos": 37, "placement": 37, "mime_type": "text/x-c", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3319" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3319" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/3319" } ] } }, { "id": "/id/document/121615", "doc_id": 121615, "rev_number": 1, "files": [ { "id": "/id/file/367007", "fileid": 367007, "datasetid": "document", "objectid": 121615, "filename": "indexcodes.txt", "mime_type": "text/x-c", "hash": "779469bc35412d230b090e8b8506ab19", "hash_type": "MD5", "filesize": 8230, "mtime": "2021-06-23 21:30:56", "url": "/1921/38/indexcodes.txt" } ], "eprint_id": 1921, "pos": 38, "placement": 38, "mime_type": "text/x-c", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3320" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3320" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/3320" } ] } }, { "id": "/id/document/121616", "doc_id": 121616, "rev_number": 1, "files": [ { "id": "/id/file/367008", "fileid": 367008, "datasetid": "document", "objectid": 121616, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "6ddbeb64a2e25695f7a68d151a7b2a1f", "hash_type": "MD5", "filesize": 5980, "mtime": "2021-06-23 21:30:56", "url": "/1921/39/indexcodes.txt" } ], "eprint_id": 1921, "pos": 39, "placement": 39, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3321" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3321" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/3321" } ] } }, { "id": "/id/document/121617", "doc_id": 121617, "rev_number": 1, "files": [ { "id": "/id/file/367009", "fileid": 367009, "datasetid": "document", "objectid": 121617, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "b43eb0a0e5222a37345d95b2f8462138", "hash_type": "MD5", "filesize": 3615, "mtime": "2021-06-23 21:30:56", "url": "/1921/40/indexcodes.txt" } ], "eprint_id": 1921, "pos": 40, "placement": 40, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/3322" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/3322" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/3322" } ] } }, { "id": "/id/document/121618", "doc_id": 121618, "rev_number": 1, "files": [ { "id": "/id/file/367010", "fileid": 367010, "datasetid": "document", "objectid": 121618, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "16d55bca8799e112aec8a4fa27c51344", "hash_type": "MD5", "filesize": 860, "mtime": "2021-06-23 21:30:56", "url": "/1921/41/indexcodes.txt" } ], "eprint_id": 1921, "pos": 41, "placement": 41, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from text/plain to indexcodes", "language": "en", "security": "internal", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/15796" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/15796" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/15796" } ] } }, { "id": "/id/document/121619", "doc_id": 121619, "rev_number": 1, "files": [ { "id": "/id/file/367011", "fileid": 367011, "datasetid": "document", "objectid": 121619, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "b7dff0fadb0503e7a947bfec7264302b", "hash_type": "MD5", "filesize": 1114, "mtime": "2021-06-23 21:30:56", "url": "/1921/42/indexcodes.txt" } ], "eprint_id": 1921, "pos": 42, "placement": 42, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from text/plain to indexcodes", "language": "en", "security": "internal", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/15917" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/15917" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/15917" } ] } } ], "eprint_status": "archive", "userid": 2, "dir": "disk0/00/00/19/21", "datestamp": "2007-05-29", "lastmod": "2020-02-25 22:22:53", "status_changed": "2009-09-25 02:19:53", "type": "thesis", "metadata_visibility": "show", "creators": { "items": [ { "email": "gavinmster@gmail.com", "id": "Murphy-Gavin-Erick", "name": { "family": "Murphy", "given": "Gavin Erick" }, "show_email": "NO" } ] }, "title": "Cryoelectron Tomography of Bacteria and their Macromolecular Machines", "ispublished": "unpub", "full_text_status": "public", "keywords": "2-oxoglutarate dehydrogenase; Caulobacter crescentus; dual-axis; electron cryotomography; flagellar motor; Hylemonella gracilis; in situ; Pyruvate dehydrogenase; surface structures; tomography; Treponema primitia; ultrastructure; Vibrio cholerae", "abstract": "Cryoelectron tomography (CET) fills a glaring gap in the imaging capabilities of biology by reconstructing cells to medium resolution. The technique was applied in three areas to understand biology\u2019s macromolecular machines: (1) the quaternary structure of the octahedrally-cored E. coli pyruvate dehydrogenase (PDHC) and 2-oxoglutarate dehydrogenase (OGDHC) complexes in vitro; (2) the ultrastructure of the spirochete Treponema primitia; and (3) the structure of the in situ flagellar motors from T. primitia, Hylemonella gracilis, Caulobacter crescentus, and Vibrio cholerae. Whereas the complexes PDHC and OGDHC were thought to have their subunit proteins E1 and E3 bound directly to the octahedral E2 core\u2014the so-called face/edge model\u2014it was discovered that the subunits are flexibly tethered 11 nm from the corners of the core. Several novel structures were discovered in the spirochete T. primitia. Spirochetes are spiral-shaped cells that propel themselves with periplasmic, not external, flagella. Bowl-shaped structures dot its surface and hook-like appendages that form arcades stripe the length of the cell. Fibrils extend from its cell tips that might help attach the cells to surfaces. Inside the periplasm, porous, cone-shaped structures reside at each cell tip and a second periplasmic layer undergirds its outer membrane, which might prevent the periplasmic flagella from rupturing the cell. Previous imaging of the flagellar motor produced either high-resolution reconstructions of the purified basal body removed from its context or low-resolution images of the in situ motor. Our in situ 3-D reconstructions described for the first time the structure of the stators, the membrane embedded component that spins the rotor. Novel shapes were discovered that indicate there are various attachments and versions of the flagellar motor that were never expected.", "date": "2007", "date_type": "degree", "id_number": "CaltechETD:etd-05212007-162731", "refereed": "FALSE", "official_url": "https://resolver.caltech.edu/CaltechETD:etd-05212007-162731", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "collection": "CaltechTHESIS", "reviewer": "Kathy Johnson", "deposited_by": "Imported from ETD-db", "deposited_on": "2007-05-29", "doi": "10.7907/517B-0Z68", "divisions": { "items": [ "div_biol" ] }, "institution": "California Institute of Technology", "thesis_type": "phd", "thesis_advisor": { "items": [ { "email": "jensen@caltech.edu", "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "role": "advisor" } ] }, "thesis_committee": { "items": [ { "email": "bjorkman@caltech.edu", "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "role": "chair" }, { "email": "jensen@caltech.edu", "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "role": "member" }, { "email": "jleadbetter@caltech.edu", "id": "Leadbetter-J-R", "name": { "family": "Leadbetter", "given": "Jared R." }, "role": "member" }, { "email": "melowitz@caltech.edu", "id": "Elowitz-M-B", "name": { "family": "Elowitz", "given": "Michael B." }, "role": "member" } ] }, "thesis_degree": "PHD", "thesis_degree_grantor": "California Institute of Technology", "thesis_submitted_date": "2007-05-21", "thesis_defense_date": "2007-05-04", "thesis_approved_date": "2007-05-29", "gradofc_approval_date": "2007-05-30", "thesis_awards": "Lawrence L. and Audrey W. Ferguson Prize, 2007.", "review_status": "approved", "option_major": { "items": [ "biochem" ] }, "copyright_statement": "I hereby certify that, if appropriate, I have obtained a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee.\n\nI hereby grant to California Institute of Technology or its agents the non-exclusive\nlicense to archive and make accessible, under the conditions specified below,\nmy thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report.", "resource_type": "thesis", "pub_year": "2007", "author_list": "Murphy, Gavin Erick", "advisor_list": "Jensen, Grant J.", "comittee_list": "Bjorkman, Pamela J.; Jensen, Grant J.; et el." }, { "id": "https://thesis.library.caltech.edu/id/eprint/1802", "eprint_id": 1802, "rev_number": 39, "documents": [ { "id": "/id/document/2928", "doc_id": 2928, "rev_number": 7, "files": [ { "id": "/id/file/201747", "fileid": 201747, "datasetid": "document", "objectid": 2928, "filename": "Part1_Title.pdf", "mime_type": "application/pdf", "filesize": 268270, "mtime": "2016-08-22 21:15:07", "url": "/1802/1/Part1_Title.pdf" } ], "eprint_id": 1802, "pos": 1, "placement": 2, "format": "application/pdf", "format_desc": "Part1_Title.pdf", "language": "en", "security": "validuser", "license": "other", "main": "Part1_Title.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/73021" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/73021" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/73021" } ] } }, { "id": "/id/document/2929", "doc_id": 2929, "rev_number": 6, "files": [ { "id": "/id/file/17819", "fileid": 17819, "datasetid": "document", "objectid": 2929, "filename": "Part2_Introduction.pdf", "mime_type": "application/pdf", "filesize": 495899, "mtime": "2012-12-26 02:42:06", "url": "/1802/2/Part2_Introduction.pdf" } ], "eprint_id": 1802, "pos": 2, "placement": 3, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "Part2_Introduction.pdf", "language": "en", "security": "public", "license": "other", "main": "Part2_Introduction.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/19646" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/19646" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/19646" } ] } }, { "id": "/id/document/2930", "doc_id": 2930, "rev_number": 6, "files": [ { "id": "/id/file/17823", "fileid": 17823, "datasetid": "document", "objectid": 2930, "filename": "Part3_M_pneumoniae.pdf", "mime_type": "application/pdf", "filesize": 2240425, "mtime": "2012-12-26 02:42:07", "url": "/1802/3/Part3_M_pneumoniae.pdf" } ], "eprint_id": 1802, "pos": 3, "placement": 4, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "Part3_M_pneumoniae.pdf", "language": "en", "security": "public", "license": "other", "main": "Part3_M_pneumoniae.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/19647" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/19647" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/19647" } ] } }, { "id": "/id/document/2931", "doc_id": 2931, "rev_number": 6, "files": [ { "id": "/id/file/201761", "fileid": 201761, "datasetid": "document", "objectid": 2931, "filename": "Part4_O_tauri.pdf", "mime_type": "application/pdf", "filesize": 5534425, "mtime": "2016-08-22 21:15:07", "url": "/1802/4/Part4_O_tauri.pdf" } ], "eprint_id": 1802, "pos": 4, "placement": 5, "format": "application/pdf", "format_desc": "Part4_O_tauri.pdf", "language": "en", "security": "public", "license": "other", "main": "Part4_O_tauri.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/73022" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/73022" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/73022" } ] } }, { "id": "/id/document/2932", "doc_id": 2932, "rev_number": 6, "files": [ { "id": "/id/file/201767", "fileid": 201767, "datasetid": "document", "objectid": 2932, "filename": "Part5_Conclusion.pdf", "mime_type": "application/pdf", "filesize": 69909, "mtime": "2016-08-22 21:15:08", "url": "/1802/5/Part5_Conclusion.pdf" } ], "eprint_id": 1802, "pos": 5, "placement": 6, "format": "application/pdf", "format_desc": "Part5_Conclusion.pdf", "language": "en", "security": "public", "license": "other", "main": "Part5_Conclusion.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/73023" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/73023" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/73023" } ] } }, { "id": "/id/document/2933", "doc_id": 2933, "rev_number": 6, "files": [ { "id": "/id/file/201775", "fileid": 201775, "datasetid": "document", "objectid": 2933, "filename": "Part6_Vitrobot.pdf", "mime_type": "application/pdf", "filesize": 193423, "mtime": "2016-08-22 21:15:08", "url": "/1802/6/Part6_Vitrobot.pdf" } ], "eprint_id": 1802, "pos": 6, "placement": 7, "format": "application/pdf", "format_desc": "Part6_Vitrobot.pdf", "language": "en", "security": "public", "license": "other", "main": "Part6_Vitrobot.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/73024" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/73024" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/73024" } ] } }, { "id": "/id/document/2934", "doc_id": 2934, "rev_number": 5, "files": [ { "id": "/id/file/201782", "fileid": 201782, "datasetid": "document", "objectid": 2934, "filename": "Whole_thesis.pdf", "mime_type": "application/pdf", "filesize": 8785409, "mtime": "2016-08-22 21:15:08", "url": "/1802/7/Whole_thesis.pdf" } ], "eprint_id": 1802, "pos": 7, "placement": 1, "format": "application/pdf", "format_desc": "Whole_thesis.pdf", "language": "en", "security": "public", "license": "other", "main": "Whole_thesis.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/73025" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/73025" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/73025" } ] } }, { "id": "/id/document/16035", "doc_id": 16035, "rev_number": 4, "files": [ { "id": "/id/file/201783", "fileid": 201783, "datasetid": "document", "objectid": 16035, "filename": "Henderson_Gregory_P_2007.PDF", "mime_type": "application/pdf", "filesize": 43814, "mtime": "2016-08-22 21:15:09", "url": "/1802/8/Henderson_Gregory_P_2007.PDF" } ], "eprint_id": 1802, "pos": 8, "placement": 6, "format": "application/pdf", "language": "en", "security": "internal", "license": "other", "main": "Henderson_Gregory_P_2007.PDF", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "approvalform" }, { "id": "/id/document/19646", "doc_id": 19646, "rev_number": 2, "files": [ { "id": "/id/file/17817", "fileid": 17817, "datasetid": "document", "objectid": 19646, "filename": "preview.png", "mime_type": "image/png", "hash": "f3ad0078a6560a469d8114024e720757", "hash_type": "MD5", "filesize": 24980, "mtime": "2012-12-26 02:42:06", "url": "/1802/9/preview.png" } ], "eprint_id": 1802, "pos": 9, "placement": 9, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "validuser", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/2929" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/2929" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/2929" } ] } }, { "id": "/id/document/19647", "doc_id": 19647, "rev_number": 2, "files": [ { "id": "/id/file/17821", "fileid": 17821, "datasetid": "document", "objectid": 19647, "filename": "preview.png", "mime_type": "image/png", "hash": "f76b58251991a40262cbdef201e0222b", "hash_type": "MD5", "filesize": 16959, "mtime": "2012-12-26 02:42:06", "url": "/1802/10/preview.png" } ], "eprint_id": 1802, "pos": 10, "placement": 10, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "validuser", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/2930" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/2930" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/2930" } ] } }, { "id": "/id/document/73021", "doc_id": 73021, "rev_number": 2, "files": [ { "id": "/id/file/201745", "fileid": 201745, "datasetid": "document", "objectid": 73021, "filename": "preview.png", "mime_type": "image/png", "hash": "db07a16be7909ff1b67afc45ba9b45a8", "hash_type": "MD5", "filesize": 8842, "mtime": "2016-08-22 21:15:07", "url": "/1802/13/preview.png" } ], "eprint_id": 1802, "pos": 13, "placement": 13, "format": "image/png", "language": "en", "security": "internal", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/2928" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/2928" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/2928" } ] } }, { "id": "/id/document/73022", "doc_id": 73022, "rev_number": 2, "files": [ { "id": "/id/file/201756", "fileid": 201756, "datasetid": "document", "objectid": 73022, "filename": "preview.png", "mime_type": "image/png", "hash": "cd25eb824af72a5d0c5d9faf753b741a", "hash_type": "MD5", "filesize": 12721, "mtime": "2016-08-22 21:15:07", "url": "/1802/14/preview.png" } ], "eprint_id": 1802, "pos": 14, "placement": 14, "format": "image/png", "language": "en", "security": "internal", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/2931" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/2931" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/2931" } ] } }, { "id": "/id/document/73023", "doc_id": 73023, "rev_number": 2, "files": [ { "id": "/id/file/201766", "fileid": 201766, "datasetid": "document", "objectid": 73023, "filename": "preview.png", "mime_type": "image/png", "hash": "7606a6fc194c2dfe10129fdffcdc7238", "hash_type": "MD5", "filesize": 32647, "mtime": "2016-08-22 21:15:08", "url": "/1802/15/preview.png" } ], "eprint_id": 1802, "pos": 15, "placement": 15, "format": "image/png", "language": "en", "security": "internal", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/2932" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/2932" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/2932" } ] } }, { "id": "/id/document/73024", "doc_id": 73024, "rev_number": 2, "files": [ { "id": "/id/file/201773", "fileid": 201773, "datasetid": "document", "objectid": 73024, "filename": "preview.png", "mime_type": "image/png", "hash": "92db61bac182502168419e248d8ff41f", "hash_type": "MD5", "filesize": 19801, "mtime": "2016-08-22 21:15:08", "url": "/1802/16/preview.png" } ], "eprint_id": 1802, "pos": 16, "placement": 16, "format": "image/png", "language": "en", "security": "internal", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/2933" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/2933" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/2933" } ] } }, { "id": "/id/document/73025", "doc_id": 73025, "rev_number": 2, "files": [ { "id": "/id/file/201780", "fileid": 201780, "datasetid": "document", "objectid": 73025, "filename": "preview.png", "mime_type": "image/png", "hash": "db07a16be7909ff1b67afc45ba9b45a8", "hash_type": "MD5", "filesize": 8842, "mtime": "2016-08-22 21:15:08", "url": "/1802/17/preview.png" } ], "eprint_id": 1802, "pos": 17, "placement": 17, "format": "image/png", "language": "en", "security": "internal", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/2934" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/2934" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/2934" } ] } }, { "id": "/id/document/76935", "doc_id": 76935, "rev_number": 3, "files": [ { "id": "/id/file/217983", "fileid": 217983, "datasetid": "document", "objectid": 76935, "filename": "Henderson To students and advisors of currently full or partially wi...pdf", "mime_type": "application/pdf", "hash": "d68e1f9b0ff0535c6baa58cb701948e7", "hash_type": "MD5", "filesize": 150493, "mtime": "2017-03-15 21:13:15", "url": "/1802/18/Henderson To students and advisors of currently full or partially wi...pdf" } ], "eprint_id": 1802, "pos": 18, "placement": 18, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "Policy email sent 02272017", "language": "en", "security": "internal", "license": "other", "main": "Henderson To students and advisors of currently full or partially wi...pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "other" }, { "id": "/id/document/76936", "doc_id": 76936, "rev_number": 2, "files": [ { "id": "/id/file/217985", "fileid": 217985, "datasetid": "document", "objectid": 76936, "filename": "lightbox.jpg", "mime_type": "image/png", "hash": "5813ea2818222bae7d50d0b21ee7eadd", "hash_type": "MD5", "filesize": 83749, "mtime": "2017-03-15 21:13:43", "url": "/1802/19/lightbox.jpg" } ], "eprint_id": 1802, "pos": 19, "placement": 19, "mime_type": "image/png", "format": "other", "format_desc": "Thumbnails conversion from application/pdf to thumbnail_lightbox", "language": "en", "security": "internal", "license": "other", "main": "lightbox.jpg", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/76935" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/76935" }, { "type": "http://eprints.org/relation/islightboxThumbnailVersionOf", "uri": "/id/document/76935" } ] } }, { "id": "/id/document/76937", "doc_id": 76937, "rev_number": 2, "files": [ { "id": "/id/file/217986", "fileid": 217986, "datasetid": "document", "objectid": 76937, "filename": "preview.png", "mime_type": "image/png", "hash": "a8b815b910cac1a23d9d3608fd851045", "hash_type": "MD5", "filesize": 136303, "mtime": "2017-03-15 21:13:44", "url": "/1802/20/preview.png" } ], "eprint_id": 1802, "pos": 20, "placement": 20, "mime_type": "image/png", "format": "other", "format_desc": "Thumbnail Documents conversion from application/pdf to thumbnail_preview", "language": "en", "security": "internal", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/76935" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/76935" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/76935" } ] } }, { "id": "/id/document/76938", "doc_id": 76938, "rev_number": 2, "files": [ { "id": "/id/file/217987", "fileid": 217987, "datasetid": "document", "objectid": 76938, "filename": "medium.jpg", "mime_type": "image/png", "hash": "6c076769bb316b0c639e886ec307c05e", "hash_type": "MD5", "filesize": 12271, "mtime": "2017-03-15 21:13:44", "url": "/1802/21/medium.jpg" } ], "eprint_id": 1802, "pos": 21, "placement": 21, "mime_type": "image/png", "format": "other", "format_desc": "Thumbnails conversion from application/pdf to thumbnail_medium", "language": "en", "security": "internal", "license": "other", "main": "medium.jpg", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/76935" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/76935" }, { "type": "http://eprints.org/relation/ismediumThumbnailVersionOf", "uri": "/id/document/76935" } ] } }, { "id": "/id/document/76939", "doc_id": 76939, "rev_number": 2, "files": [ { "id": "/id/file/217988", "fileid": 217988, "datasetid": "document", "objectid": 76939, "filename": "small.jpg", "mime_type": "image/png", "hash": "701db8a45222a06738c651e727794a88", "hash_type": "MD5", "filesize": 1921, "mtime": "2017-03-15 21:13:45", "url": "/1802/22/small.jpg" } ], "eprint_id": 1802, "pos": 22, "placement": 22, "mime_type": "image/png", "format": "other", "format_desc": "Thumbnails conversion from application/pdf to thumbnail_small", "language": "en", "security": "internal", "license": "other", "main": "small.jpg", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/76935" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/76935" }, { "type": "http://eprints.org/relation/issmallThumbnailVersionOf", "uri": "/id/document/76935" } ] } }, { "id": "/id/document/121259", "doc_id": 121259, "rev_number": 1, "files": [ { "id": "/id/file/366651", "fileid": 366651, "datasetid": "document", "objectid": 121259, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "0f4b02b3a91a1e0d5c93909d80fd182c", "hash_type": "MD5", "filesize": 3236, "mtime": "2021-06-23 21:22:04", "url": "/1802/23/indexcodes.txt" } ], "eprint_id": 1802, "pos": 23, "placement": 23, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "validuser", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/2928" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/2928" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/2928" } ] } }, { "id": "/id/document/121260", "doc_id": 121260, "rev_number": 1, "files": [ { "id": "/id/file/366652", "fileid": 366652, "datasetid": "document", "objectid": 121260, "filename": "indexcodes.txt", "mime_type": "text/x-c", "hash": "cc513ffa9ccba74f18ec7048296b1930", "hash_type": "MD5", "filesize": 11243, "mtime": "2021-06-23 21:22:04", "url": "/1802/24/indexcodes.txt" } ], "eprint_id": 1802, "pos": 24, "placement": 24, "mime_type": "text/x-c", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/2929" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/2929" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/2929" } ] } }, { "id": "/id/document/121261", "doc_id": 121261, "rev_number": 1, "files": [ { "id": "/id/file/366653", "fileid": 366653, "datasetid": "document", "objectid": 121261, "filename": "indexcodes.txt", "mime_type": "text/x-c", "hash": "c9fe4763e81cd44ad9f36fb4e5948f84", "hash_type": "MD5", "filesize": 10681, "mtime": "2021-06-23 21:22:04", "url": "/1802/25/indexcodes.txt" } ], "eprint_id": 1802, "pos": 25, "placement": 25, "mime_type": "text/x-c", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/2930" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/2930" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/2930" } ] } }, { "id": "/id/document/121262", "doc_id": 121262, "rev_number": 1, "files": [ { "id": "/id/file/366654", "fileid": 366654, "datasetid": "document", "objectid": 121262, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "e33e5a301ead8df5a4de6c223ead2a14", "hash_type": "MD5", "filesize": 16394, "mtime": "2021-06-23 21:22:04", "url": "/1802/26/indexcodes.txt" } ], "eprint_id": 1802, "pos": 26, "placement": 26, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/2931" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/2931" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/2931" } ] } }, { "id": "/id/document/121263", "doc_id": 121263, "rev_number": 1, "files": [ { "id": "/id/file/366655", "fileid": 366655, "datasetid": "document", "objectid": 121263, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "212970928c63c4e74367fb3f0635513d", "hash_type": "MD5", "filesize": 1392, "mtime": "2021-06-23 21:22:04", "url": "/1802/27/indexcodes.txt" } ], "eprint_id": 1802, "pos": 27, "placement": 27, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/2932" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/2932" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/2932" } ] } }, { "id": "/id/document/121264", "doc_id": 121264, "rev_number": 1, "files": [ { "id": "/id/file/366656", "fileid": 366656, "datasetid": "document", "objectid": 121264, "filename": "indexcodes.txt", "mime_type": "text/x-c", "hash": "8fc1b977780ef86d8ab05541b09aa1dc", "hash_type": "MD5", "filesize": 9373, "mtime": "2021-06-23 21:22:05", "url": "/1802/28/indexcodes.txt" } ], "eprint_id": 1802, "pos": 28, "placement": 28, "mime_type": "text/x-c", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/2933" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/2933" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/2933" } ] } }, { "id": "/id/document/121265", "doc_id": 121265, "rev_number": 1, "files": [ { "id": "/id/file/366657", "fileid": 366657, "datasetid": "document", "objectid": 121265, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "ea8a0c335839963769203434a3e74860", "hash_type": "MD5", "filesize": 30584, "mtime": "2021-06-23 21:22:05", "url": "/1802/29/indexcodes.txt" } ], "eprint_id": 1802, "pos": 29, "placement": 29, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/2934" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/2934" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/2934" } ] } }, { "id": "/id/document/121266", "doc_id": 121266, "rev_number": 1, "files": [ { "id": "/id/file/366658", "fileid": 366658, "datasetid": "document", "objectid": 121266, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "4e1bf20c643356ae713809e0be24b820", "hash_type": "MD5", "filesize": 1140, "mtime": "2021-06-23 21:22:05", "url": "/1802/30/indexcodes.txt" } ], "eprint_id": 1802, "pos": 30, "placement": 30, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "internal", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/76935" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/76935" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/76935" } ] } } ], "eprint_status": "archive", "userid": 2, "dir": "disk0/00/00/18/02", "datestamp": "2007-05-16", "lastmod": "2020-02-22 00:52:26", "status_changed": "2009-09-25 02:15:32", "type": "thesis", "metadata_visibility": "show", "creators": { "items": [ { "email": "gphenderson@mednet.ucla.edu", "id": "Henderson-Gregory-Philip", "name": { "family": "Henderson", "given": "Gregory Philip" }, "orcid": "0000-0002-6035-0817", "show_email": "NO" } ] }, "title": "Ultrastructural Studies of Two Model Minimal Cells by Electron Cryotomography", "ispublished": "unpub", "full_text_status": "public", "keywords": "electron cryotomography; Mycoplasma pneumoniae; Ostreococcus tauri", "abstract": "While most motile bacteria propel themselves with flagella, other mechanisms have been described including retraction of surface-attached pili, secretion of polysaccharides, or movement of motors along surface protein tracks. These have been referred to collectively as forms of \"gliding\" motility. Despite being simultaneously one of the smallest and simplest of all known cells, Mycoplasma pneumoniae builds a surprisingly large and complex cell extension known as the attachment organelle that enables it to glide. Here, three-dimensional images of the attachment organelle were produced with unprecedented clarity and authenticity using state-of-the-art electron cryotomography. The attachment organelle was seen to contain a multi-subunit, jointed, dynamic motor much larger than a flagellar basal body and comparable in complexity. A new model for its function is proposed wherein inchworm-like conformational changes of its electron-dense core are leveraged against a cytoplasmic anchor and transmitted to the surface through layered adhesion proteins.
\r\n\r\nThe hallmark of eukaryotic cells is their segregation of key biological functions into discrete, membrane-bound organelles. Creating accurate models of their ultrastructural complexity has been difficult in part because of the limited resolution of light microscopy and the artifact-prone nature of conventional electron microscopy. Here we explored the potential of the emerging technology electron cryotomography to produce three-dimensional images of an entire eukaryotic cell in a near-native state. Ostreococcus tauri was chosen as the specimen because as a unicellular picoplankton with just one copy of each organelle, it is the smallest known eukaryote and was therefore likely to yield the highest resolution images. Whole cells were imaged at various stages of the cell cycle, yielding 3-D reconstructions of complete chloroplasts, mitochondria, endoplasmic reticula, Golgi bodies, peroxisomes, microtubules, and putative ribosome distributions in-situ. Surprisingly, the nucleus was seen to open long before mitosis, and while one microtubule (or two in some predivisional cells) were consistently present, no mitotic spindle was ever observed, prompting speculation that a single microtubule might be sufficient to segregate multiple chromosomes.
", "date": "2007", "date_type": "degree", "id_number": "CaltechETD:etd-05142007-131453", "refereed": "FALSE", "official_url": "https://resolver.caltech.edu/CaltechETD:etd-05142007-131453", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "collection": "CaltechTHESIS", "reviewer": "Kathy Johnson", "suggestions": "Released to public view 01292018 // Partially withheld: full thesis and ch.1,4-6. Partially Restricted to campus: ch. 2-3. // 03152017: Released and Restricted to Caltech community only until 15 September 2017.", "deposited_by": "Imported from ETD-db", "deposited_on": "2007-05-16", "doi": "10.7907/HK2B-CT58", "divisions": { "items": [ "div_biol" ] }, "institution": "California Institute of Technology", "thesis_type": "phd", "thesis_advisor": { "items": [ { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "role": "advisor" } ] }, "thesis_committee": { "items": [ { "email": "bjorkman@caltech.edu", "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "role": "chair" }, { "email": "dcrees@caltech.edu", "id": "Rees-D-C", "name": { "family": "Rees", "given": "Douglas C." }, "role": "member" }, { "email": "jensen@caltech.edu", "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "role": "member" }, { "email": "jleadbetter@caltech.edu", "id": "Leadbetter-J-R", "name": { "family": "Leadbetter", "given": "Jared R." }, "role": "member" }, { "email": "sefraser@caltech.edu", "id": "Fraser-S-E", "name": { "family": "Fraser", "given": "Scott E." }, "role": "member" } ] }, "thesis_degree": "PHD", "thesis_degree_grantor": "California Institute of Technology", "thesis_submitted_date": "2007-05-14", "thesis_defense_date": "2007-05-02", "thesis_approved_date": "2007-05-16", "gradofc_approval_date": "2007-05-15", "review_status": "approved", "option_major": { "items": [ "biology" ] }, "copyright_statement": "I hereby certify that, if appropriate, I have obtained a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee.\n\nI hereby grant to California Institute of Technology or its agents the non-exclusive\nlicense to archive and make accessible, under the conditions specified below,\nmy thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report.", "resource_type": "thesis", "pub_year": "2007", "author_list": "Henderson, Gregory Philip", "advisor_list": "Jensen, Grant J.", "comittee_list": "Bjorkman, Pamela J.; Rees, Douglas C.; et el." }, { "id": "https://thesis.library.caltech.edu/id/eprint/2459", "eprint_id": 2459, "rev_number": 10, "documents": [ { "id": "/id/document/4692", "doc_id": 4692, "rev_number": 2, "files": [ { "id": "/id/file/27028", "fileid": 27028, "datasetid": "document", "objectid": 4692, "filename": "JB_thesis.pdf", "mime_type": "application/pdf", "filesize": 26747160, "mtime": "2012-12-26 02:51:45", "url": "/2459/1/JB_thesis.pdf" } ], "eprint_id": 2459, "pos": 1, "mime_type": "application/pdf", "format": "application/pdf", "format_desc": "JB_thesis.pdf", "language": "en", "security": "public", "license": "other", "main": "JB_thesis.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "final", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/21247" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/21247" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/21247" } ] } }, { "id": "/id/document/13964", "doc_id": 13964, "rev_number": 4, "files": [ { "id": "/id/file/203469", "fileid": 203469, "datasetid": "document", "objectid": 13964, "filename": "Benjamin_Jordan_20060001.pdf", "mime_type": "application/pdf", "filesize": 587405, "mtime": "2016-08-22 21:16:05", "url": "/2459/2/Benjamin_Jordan_20060001.pdf" } ], "eprint_id": 2459, "pos": 2, "format": "application/pdf", "language": "en", "security": "internal", "license": "other", "main": "Benjamin_Jordan_20060001.pdf", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "content": "approvalform", "relation": { "items": [ { "type": "http://eprints.org/relation/hasVolatileVersion", "uri": "/id/document/73085" }, { "type": "http://eprints.org/relation/haspreviewThumbnailVersion", "uri": "/id/document/73085" }, { "type": "http://eprints.org/relation/hasVersion", "uri": "/id/document/73085" } ] } }, { "id": "/id/document/21247", "doc_id": 21247, "rev_number": 2, "files": [ { "id": "/id/file/27026", "fileid": 27026, "datasetid": "document", "objectid": 21247, "filename": "preview.png", "mime_type": "image/png", "hash": "93099aec79a977b8a7c052cb412240da", "hash_type": "MD5", "filesize": 10784, "mtime": "2012-12-26 02:51:45", "url": "/2459/3/preview.png" } ], "eprint_id": 2459, "pos": 3, "placement": 3, "mime_type": "image/png", "format": "image/png", "language": "en", "security": "public", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/4692" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/4692" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/4692" } ] } }, { "id": "/id/document/73085", "doc_id": 73085, "rev_number": 2, "files": [ { "id": "/id/file/203467", "fileid": 203467, "datasetid": "document", "objectid": 73085, "filename": "preview.png", "mime_type": "image/png", "hash": "c1ef17dd1a5b750b42705b1c42b7371a", "hash_type": "MD5", "filesize": 182350, "mtime": "2016-08-22 21:16:05", "url": "/2459/5/preview.png" } ], "eprint_id": 2459, "pos": 5, "placement": 5, "format": "image/png", "language": "en", "security": "internal", "license": "other", "main": "preview.png", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/13964" }, { "type": "http://eprints.org/relation/ispreviewThumbnailVersionOf", "uri": "/id/document/13964" }, { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/13964" } ] } }, { "id": "/id/document/122952", "doc_id": 122952, "rev_number": 1, "files": [ { "id": "/id/file/368352", "fileid": 368352, "datasetid": "document", "objectid": 122952, "filename": "indexcodes.txt", "mime_type": "text/x-c", "hash": "8de469c9d0cec47887500a7f5ebbd0d5", "hash_type": "MD5", "filesize": 27938, "mtime": "2021-06-23 22:12:34", "url": "/2459/6/indexcodes.txt" } ], "eprint_id": 2459, "pos": 6, "placement": 6, "mime_type": "text/x-c", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "public", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/4692" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/4692" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/4692" } ] } }, { "id": "/id/document/122953", "doc_id": 122953, "rev_number": 1, "files": [ { "id": "/id/file/368353", "fileid": 368353, "datasetid": "document", "objectid": 122953, "filename": "indexcodes.txt", "mime_type": "text/plain", "hash": "f26781d21f9a23cb9c45e0405488c217", "hash_type": "MD5", "filesize": 1355, "mtime": "2021-06-23 22:12:34", "url": "/2459/7/indexcodes.txt" } ], "eprint_id": 2459, "pos": 7, "placement": 7, "mime_type": "text/plain", "format": "other", "format_desc": "Generate index codes conversion from application/pdf to indexcodes", "language": "en", "security": "internal", "license": "other", "main": "indexcodes.txt", "media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/13964" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/13964" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/13964" } ] } } ], "eprint_status": "archive", "userid": 2, "dir": "disk0/00/00/24/59", "datestamp": "2006-06-05", "lastmod": "2020-03-30 20:54:55", "status_changed": "2009-09-25 02:38:30", "type": "thesis", "metadata_visibility": "show", "creators": { "items": [ { "email": "jordan.benjamin@gmail.com", "id": "Benjamin-Schooler-Jordan", "name": { "family": "Benjamin Schooler", "given": "Jordan" }, "orcid": "0000-0002-4328-7254", "show_email": "YES" } ] }, "title": "Structural Studies of Human Immunodeficiency Virus Type I by CryoElectron Tomography", "ispublished": "unpub", "full_text_status": "public", "keywords": "AIDS; capsid structure; cryo-electron tomography; electron microscopy; fullerene cone; HIV; lentivirus; retrovirus", "abstract": "Gag, the major structural component of the type 1 human immunodeficiency virus (HIV-1), comprises the matrix (MA), capsid (CA), nucleocapsid (NC), and p6 proteins, as well as the SP1 and SP2 spacer peptides. In the immature HIV-1 virion, the domains of Gag are arranged radially with the amino-terminus of MA at the membrane. Mature viral particles are formed when Gag is proteolytically cleaved, allowing CA to reassemble into the viral core, which contains NC bound to genomic RNA. While the structures of nearly every HIV-1 protein are known in atomic detail from X-ray crystallography and NMR spectroscopy, many questions remain about the intermolecular interactions in both the immature and mature particles.
\r\n\r\nWe have obtained three-dimensional structures of individual immature and mature HIV-1 virus-like particles by cryoelectron tomography. Reconstructions of the mature particles revealed diverse core morphologies with a preference for conical shapes consistent with 5,7 fullerene cones. Uniform positioning of the wide end of the cores and an internal density likely to be the NC/RNA complex were also observed, as were multiple and nested viral cores. Our results support the fullerene cone model for the core structure and suggest that specific interactions may occur between the CA, MA, and NC layers in the mature virion. These experiments also aided the characterization of a new cryostage allowing routine collection of dual-axis tomograms.
\r\n\r\nTomograms of the immature virions revealed patches of hexagonally ordered Gag molecules interspersed with regions of disordered or absent Gag. We developed novel tools for analysis of locally ordered lattices embedded in curved structures, including a method for locating and averaging the Gag unit cell in situ. The unit cell average revealed that the CA domains and the SP1 spacer peptides were organized in a hexagonal lattice with ring-to-ring spacing of 8 nm in the CA layer and 7.5 nm in SP1. No regular lattice was found in the MA or NC layers. Based on the averaged Gag unit cell, we proposed a pseudoatomic model for the CA and SP1 domains in the immature virion.
\r\n", "date": "2006", "date_type": "degree", "id_number": "CaltechETD:etd-06052006-124843", "refereed": "FALSE", "official_url": "https://resolver.caltech.edu/CaltechETD:etd-06052006-124843", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "collection": "CaltechTHESIS", "reviewer": "Kathy Johnson", "suggestions": "\"Note also that I have changed my last name since then due to marriage: \r\nJordan Benjamin Schooler\r\n3338-2L Circle Brook Dr\r\nRoanoke, VA 24018\"\r\n", "deposited_by": "Imported from ETD-db", "deposited_on": "2006-06-05", "doi": "10.7907/HM3M-HZ81", "divisions": { "items": [ "div_biol" ] }, "institution": "California Institute of Technology", "thesis_type": "phd", "thesis_advisor": { "items": [ { "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "role": "advisor" } ] }, "thesis_committee": { "items": [ { "email": "bjorkman@caltech.edu", "id": "Bjorkman-P-J", "name": { "family": "Bjorkman", "given": "Pamela J." }, "role": "chair" }, { "email": "evroth@caltech.edu", "id": "Rothenberg-E-V", "name": { "family": "Rothenberg", "given": "Ellen V." }, "role": "member" }, { "email": "jensen@caltech.edu", "id": "Jensen-G-J", "name": { "family": "Jensen", "given": "Grant J." }, "role": "member" }, { "email": "sefraser@caltech.edu", "id": "Fraser-S-E", "name": { "family": "Fraser", "given": "Scott E." }, "role": "member" } ] }, "thesis_degree": "PHD", "thesis_degree_grantor": "California Institute of Technology", "thesis_submitted_date": "2006-06-05", "thesis_defense_date": "2006-05-23", "thesis_approved_date": "2006-06-05", "review_status": "approved", "option_major": { "items": [ "biology" ] }, "copyright_statement": "I hereby certify that, if appropriate, I have obtained a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee.\n\nI hereby grant to California Institute of Technology or its agents the non-exclusive\nlicense to archive and make accessible, under the conditions specified below,\nmy thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report.", "resource_type": "thesis", "pub_year": "2006", "author_list": "Benjamin Schooler, Jordan", "advisor_list": "Jensen, Grant J.", "comittee_list": "Bjorkman, Pamela J.; Rothenberg, Ellen V.; et el." } ]