{"id":3769,"date":"2022-10-04T18:08:00","date_gmt":"2022-10-04T16:08:00","guid":{"rendered":"https:\/\/equipes.lps.u-psud.fr\/sobio\/?p=3769"},"modified":"2022-12-15T10:10:29","modified_gmt":"2022-12-15T09:10:29","slug":"phd-defense-of-mohamad-harastani","status":"publish","type":"post","link":"https:\/\/equipes.lps.u-psud.fr\/sobio\/phd-defense-of-mohamad-harastani\/","title":{"rendered":"PhD defense of Mohamad Harastani"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\">Mohamad HARASTANI has defended his PhD thesis entitled \u201cImage analysis method development for in vitro and in situ cryo electron tomography studies of conformational variability of biomolecular complexes: case of nucleosome structural and dynamics studies\u201d, under the supervision of Slavica JONIC (IMPMC, Sorbonne Universit\u00e9) and Am\u00e9lie LEFORESTIER.<\/p>\n\n\n\n<div class=\"wp-block-columns is-layout-flex wp-container-core-columns-is-layout-7387b849 wp-block-columns-is-layout-flex\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<figure class=\"wp-block-image size-full is-resized\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-content\/uploads\/sites\/10\/2022\/12\/MH_PhD22-2.jpg\" alt=\"\" class=\"wp-image-3772\" width=\"406\" height=\"462\" srcset=\"https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-content\/uploads\/sites\/10\/2022\/12\/MH_PhD22-2.jpg 672w, https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-content\/uploads\/sites\/10\/2022\/12\/MH_PhD22-2-263x300.jpg 263w\" sizes=\"auto, (max-width: 406px) 100vw, 406px\" \/><\/figure>\n<\/div>\n\n\n\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow\">\n<figure class=\"wp-block-image size-large is-resized\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-content\/uploads\/sites\/10\/2022\/12\/Capture-decran-2022-12-15-a-10.03.11-1024x827.png\" alt=\"\" class=\"wp-image-3775\" width=\"386\" height=\"312\" srcset=\"https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-content\/uploads\/sites\/10\/2022\/12\/Capture-decran-2022-12-15-a-10.03.11-1024x827.png 1024w, https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-content\/uploads\/sites\/10\/2022\/12\/Capture-decran-2022-12-15-a-10.03.11-300x242.png 300w, https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-content\/uploads\/sites\/10\/2022\/12\/Capture-decran-2022-12-15-a-10.03.11-768x620.png 768w, https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-content\/uploads\/sites\/10\/2022\/12\/Capture-decran-2022-12-15-a-10.03.11.png 1152w\" sizes=\"auto, (max-width: 386px) 100vw, 386px\" \/><figcaption class=\"wp-element-caption\">Illustration of HEMNMA-3D use with <em>in situ<\/em> cryo-ET nucleosome dataset (Harastani, M., Eltsov, M., Leforestier, A., &amp; Jonic, S. (2021). Hemnma-3d: Cryo electron tomography method based on normal mode analysis to study continuous conformational variability of macromolecular complexes. <em>Frontiers in molecular biosciences<\/em>, 317).<\/figcaption><\/figure>\n<\/div>\n<\/div>\n\n\n\n<p class=\"wp-block-paragraph\">This thesis presents the first two cryo-electron tomography (cryo-ET) data processing methods that address continuous conformational variability of biomolecules, HEMNMA-3D and TomoFlow. HEMNMA-3D analyses experimental data with motion directions simulated by Normal Mode Analysis, and allows the discovery of a large range of biomolecular motions hidden in the data. However, HEMNMA-3D depends on this prior (simulated motion directions), making it prone to misinterpretation and bias when misused. TomoFlow extracts movements from the data without prior information using a computer vision technique called the Optical Flow. Therefore, it is less prone to misinterpretation and misuse. However, when it encounters large motion magnitudes, it results in a smooth and downscaled version of the actual biomolecular motion. HEMNMA-3D and TomoFlow have different mathematical models, but both are able to explore biomolecular conformational landscapes and are superior to classification. HEMNMA-3D and TomoFlow are validated on synthetic datasets. The two methods are applied on experimental cryo-ET data of nucleosome conformational variability, a specially challenging object in situ. They show coherent results, shedding insight into the conformational variability of nucleosomes in situ, in line with preliminary and theoretical analyses. Based on this, they are also expected to be useful for conformational studies of other biomolecular complexes in vitro and in situ. The software of HEMNMA-3D and TomoFlow is publicly available, as part of the cryo-ET data processing pipeline of the open-source software package ContinuousFlex, which is currently a plugin of Scipion software, extensively used in the field, and uses Scipion\u2019s backend software Xmipp.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Mohamad HARASTANI has defended his PhD thesis entitled \u201cImage analysis method development for in vitro and in situ cryo electron tomography studies of conformational variability of biomolecular complexes: case of &#8230;<\/p>\n","protected":false},"author":21,"featured_media":3772,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-3769","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-news"],"_links":{"self":[{"href":"https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-json\/wp\/v2\/posts\/3769","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-json\/wp\/v2\/users\/21"}],"replies":[{"embeddable":true,"href":"https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-json\/wp\/v2\/comments?post=3769"}],"version-history":[{"count":3,"href":"https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-json\/wp\/v2\/posts\/3769\/revisions"}],"predecessor-version":[{"id":3776,"href":"https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-json\/wp\/v2\/posts\/3769\/revisions\/3776"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-json\/wp\/v2\/media\/3772"}],"wp:attachment":[{"href":"https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-json\/wp\/v2\/media?parent=3769"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-json\/wp\/v2\/categories?post=3769"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/equipes.lps.u-psud.fr\/sobio\/wp-json\/wp\/v2\/tags?post=3769"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}