{"id":70,"date":"2024-04-05T14:40:16","date_gmt":"2024-04-05T21:40:16","guid":{"rendered":"https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/?page_id=70"},"modified":"2024-12-13T13:08:37","modified_gmt":"2024-12-13T21:08:37","slug":"research","status":"publish","type":"page","link":"https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/research\/","title":{"rendered":"Research"},"content":{"rendered":"\n<style type=\"text\/css\" data-created_by=\"avia_inline_auto\" id=\"style-css-av-lwhaqou1-bd1c5ba6562012bd456c403a1553a954\">\n\n@media only screen and (min-width: 990px){ \n#top .avia-slideshow .av-slideshow-caption.av-lwhaqou1-bd1c5ba6562012bd456c403a1553a954__0 .avia-caption-content{\nfont-size:35px;\n}\n#top .avia-slideshow .av-slideshow-caption.av-lwhaqou1-bd1c5ba6562012bd456c403a1553a954__0 .avia-caption-content p{\nfont-size:35px;\n}\n}\n\n@media only screen and (min-width: 768px) and (max-width: 989px){ \n#top .avia-slideshow .av-slideshow-caption.av-lwhaqou1-bd1c5ba6562012bd456c403a1553a954__0 .avia-caption-content{\nfont-size:35px;\n}\n#top .avia-slideshow .av-slideshow-caption.av-lwhaqou1-bd1c5ba6562012bd456c403a1553a954__0 .avia-caption-content p{\nfont-size:35px;\n}\n}\n\n@media only screen and (min-width: 480px) and (max-width: 767px){ \n#top .avia-slideshow .av-slideshow-caption.av-lwhaqou1-bd1c5ba6562012bd456c403a1553a954__0 .avia-caption-content{\nfont-size:30px;\n}\n#top .avia-slideshow .av-slideshow-caption.av-lwhaqou1-bd1c5ba6562012bd456c403a1553a954__0 .avia-caption-content p{\nfont-size:30px;\n}\n}\n\n@media only screen and (max-width: 479px){ \n#top .avia-slideshow .av-slideshow-caption.av-lwhaqou1-bd1c5ba6562012bd456c403a1553a954__0 .avia-caption-content{\nfont-size:24px;\n}\n#top .avia-slideshow .av-slideshow-caption.av-lwhaqou1-bd1c5ba6562012bd456c403a1553a954__0 .avia-caption-content p{\nfont-size:24px;\n}\n}\n<\/style>\n<div  class='avia-slideshow av-lwhaqou1-bd1c5ba6562012bd456c403a1553a954 avia-slideshow-featured av_slideshow avia-slide-slider  avia-builder-el-0  el_before_av_three_fifth  avia-builder-el-first  av-slideshow-ui av-control-default av-slideshow-manual av-loop-once av-loop-manual-endless av-default-height-applied avia-slideshow-1' data-slideshow-options=\"{&quot;animation&quot;:&quot;slide&quot;,&quot;autoplay&quot;:false,&quot;loop_autoplay&quot;:&quot;once&quot;,&quot;interval&quot;:5,&quot;loop_manual&quot;:&quot;manual-endless&quot;,&quot;autoplay_stopper&quot;:false,&quot;noNavigation&quot;:false,&quot;bg_slider&quot;:false,&quot;keep_padding&quot;:false,&quot;hoverpause&quot;:false,&quot;show_slide_delay&quot;:0}\"  itemprop=\"image\" itemscope=\"itemscope\" itemtype=\"https:\/\/schema.org\/ImageObject\" ><ul class='avia-slideshow-inner ' style='padding-bottom: 28.666666666667%;'><li  class='avia-slideshow-slide av-lwhaqou1-bd1c5ba6562012bd456c403a1553a954__0  av-single-slide slide-1 slide-odd'><div data-rel='slideshow-1' class='avia-slide-wrap '   ><div class='av-slideshow-caption av-lwhaqou1-bd1c5ba6562012bd456c403a1553a954__0 avia-caption'><div class=\"avia-inner-caption\"><div class='avia-caption-content '  itemprop=\"description\" ><p>Research<\/p>\n<\/div><\/div><\/div><img decoding=\"async\" fetchpriority=\"high\" class=\"wp-image-441 avia-img-lazy-loading-not-441\"  src=\"https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/pMYB36_H2B_3xYFP_tile3_root3-copy-1500x430.jpg\" width=\"1500\" height=\"430\" title='pMYB36_H2B_3xYFP_tile3_root3 copy' alt=''  itemprop=\"thumbnailUrl\"   \/><\/div><\/li><\/ul><\/div>\n<div  class='flex_column av-1c93a-a5093380c14facdd8f1407a759a20587 av_three_fifth  avia-builder-el-1  el_after_av_slideshow  el_before_av_two_fifth  first flex_column_div  '     ><section  class='av_textblock_section av-m2thdazg-1eb6be90be7baafb5e3d925b9c271805 '   itemscope=\"itemscope\" itemtype=\"https:\/\/schema.org\/CreativeWork\" ><div class='avia_textblock'  itemprop=\"text\" ><p><span style=\"font-size: 14pt;font-family: arial, helvetica, sans-serif\"><span style=\"font-weight: 400\">In plants, embryo formation produces a rudimentary body consisting of a root, stem, and a few leaves. The body plan is elaborated post-embryonically by the branching of roots and shoots. Aboveground, intricate molecular networks regulate shoot development and the formation of new organs, such as flowers, in response to intrinsic and extrinsic cues. However, below the ground, comparatively less is known about root system development. <\/span><\/span><\/p>\n<p><span style=\"font-size: 14pt;font-family: arial, helvetica, sans-serif\"><span style=\"font-weight: 400\">Roots and their responses to environmental stimuli are critical for plant health and productivity. Root systems are also a tractable model to investigate fundamental principles underlying organ neogenesis. <\/span><span style=\"font-weight: 400\">Research on root development may therefore have broad implications for critical topics ranging from organ and tissue regeneration to modulating plant architecture and resilience in the face of climate change.<\/span><span style=\"font-weight: 400\">\u00a0<\/span><\/span><\/p>\n<\/div><\/section><\/div><div  class='flex_column av-1426m-ca6dfb7bf9b6fd2b2569f01620b95a29 av_two_fifth  avia-builder-el-3  el_after_av_three_fifth  el_before_av_one_full  flex_column_div  '     ><div  class='avia-video av-m2ti3vb2-d3e253a91eee3948ba460de602413acc avia-video-16-9 av-no-preview-image avia-video-load-always avia-video-html5'  itemprop=\"video\" itemtype=\"https:\/\/schema.org\/VideoObject\"  data-original_url='https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/WT_trimmed2_croppedv3.mp4'><video class='avia_video'    preload=\"auto\"  controls id='player_70_188789306_1196533316'><source src='https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/WT_trimmed2_croppedv3.mp4' type='video\/mp4' \/><\/video><\/div><\/div><\/p>\n<div  class='flex_column av-yr7m-e34874dfbbf3ff9c2adc902529fd56d1 av_one_full  avia-builder-el-5  el_after_av_two_fifth  el_before_av_hr  first flex_column_div  '     ><section  class='av_textblock_section av-m2urn9em-4f3c3fb0edae3d07307320f8939b78e8 '   itemscope=\"itemscope\" itemtype=\"https:\/\/schema.org\/CreativeWork\" ><div class='avia_textblock'  itemprop=\"text\" ><p><span style=\"font-family: arial, helvetica, sans-serif\"><span style=\"font-size: 14pt\"><span style=\"font-weight: 400\"><strong>Our lab<\/strong> harnesses root developmental plasticity to study how post-embryonic tissues and organs are initiated in different developmental and environmental contexts. <\/span><span style=\"font-weight: 400\">Our long-term goal is to <\/span><\/span><span style=\"font-weight: 400\"><span style=\"font-size: 14pt\">define fundamental principles underlying the specification and function of regenerative cells. Taking advantage of the simplifying properties of Arabidopsis, a genetically tractable model plant, we apply cutting edge omics and imaging techniques to investigate cell fate decisions and link them to cell behavior.<\/span><\/span><\/span><\/p>\n<\/div><\/section><\/div><div  class='hr av-1j6xq-58099d4d4a23c7d7ecd25da1e15d5b78 hr-default  avia-builder-el-7  el_after_av_one_full  el_before_av_textblock '><span class='hr-inner '><span class=\"hr-inner-style\"><\/span><\/span><\/div><\/p>\n<section  class='av_textblock_section av-xjb2-1b54a99be65b815fccb68ed4c233870e '   itemscope=\"itemscope\" itemtype=\"https:\/\/schema.org\/CreativeWork\" ><div class='avia_textblock'  itemprop=\"text\" ><h5><span style=\"font-size: 18pt\"><strong>Research Directions<\/strong><\/span><\/h5>\n<\/div><\/section>\n<div  class='flex_column av-zdqq-26aa9968e28d2e4513f75c03b4ed848b av_one_half  avia-builder-el-9  el_after_av_textblock  el_before_av_one_half  first flex_column_div  column-top-margin'     ><section  class='av_textblock_section av-m2ur57ot-beb902b6df5dd2cb24bc1b5cccdee488 '   itemscope=\"itemscope\" itemtype=\"https:\/\/schema.org\/CreativeWork\" ><div class='avia_textblock'  itemprop=\"text\" ><p><span style=\"font-size: 14pt\"><strong>Elaboration of the plant body plan. <\/strong>As shown in the video above, <span style=\"font-weight: 400\">the Arabidopsis root system is elaborated by the periodic formation of lateral roots which emerge horizontally from the vertical primary root. The spatiotemporal patterning indicates that only some cells in the primary root will initiate a lateral root. A key question is what determines this subset of cells.<\/span><\/span><\/p>\n<p><span style=\"font-size: 14pt\"><span style=\"font-weight: 400\"><strong><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/20829477\/\">Previous work<\/a><\/strong> found that a luciferase reporter driven by a synthetic promoter, DR5, is rhythmically expressed and marks the primary root cells that will eventually form a lateral root.<\/span> <span style=\"font-weight: 400\">Microarray experiments of finely dissected primary root sections identified genes that oscillate in phase and anti-phase with the DR5:Luciferase reporter.<\/span>\u00a0<span style=\"font-weight: 400\">This observation led to the hypothesis that a biological oscillator specifies the primary root cells that will become \u2018founder cells\u2019 and later divide to form the new stem cell niche from which a lateral root will emerge.<\/span> <span style=\"font-weight: 400\">It is unknown what transcriptional mechanism regulates the oscillations and how one or multiple cell types remember and respond to this transient event. <\/span><\/span><\/p>\n<p><span style=\"font-size: 14pt\"><span style=\"font-weight: 400\">Using lateral root development as a model, <strong>our lab applies single cell omics approaches to investigate how gene regulatory programs in distinct primary root cell types orchestrate organ neogenesis.<\/strong><\/span><strong>\u00a0<\/strong><\/span><\/p>\n<\/div><\/section><\/div>\n<div  class='flex_column av-1c1re-fae1809cf54d4da711458a0be5702792 av_one_half  avia-builder-el-11  el_after_av_one_half  el_before_av_textblock  flex_column_div  column-top-margin'     ><style type=\"text\/css\" data-created_by=\"avia_inline_auto\" id=\"style-css-av-m2urax90-4d87629db3faaf4c33fc059527064552\">\n.avia-image-container.av-m2urax90-4d87629db3faaf4c33fc059527064552 img.avia_image{\nbox-shadow:none;\n}\n.avia-image-container.av-m2urax90-4d87629db3faaf4c33fc059527064552 .av-image-caption-overlay-center{\ncolor:#ffffff;\n}\n<\/style>\n<div  class='avia-image-container av-m2urax90-4d87629db3faaf4c33fc059527064552 av-styling- avia-align-center  avia-builder-el-12  avia-builder-el-no-sibling '   itemprop=\"image\" itemscope=\"itemscope\" itemtype=\"https:\/\/schema.org\/ImageObject\" ><div class=\"avia-image-container-inner\"><div class=\"avia-image-overlay-wrap\"><img decoding=\"async\" fetchpriority=\"high\" class='wp-image-546 avia-img-lazy-loading-not-546 avia_image ' src=\"https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/Root_atlas-705x382.jpg\" alt='' title='Root_atlas'  height=\"382\" width=\"705\"  itemprop=\"thumbnailUrl\" srcset=\"https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/Root_atlas-705x382.jpg 705w, https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/Root_atlas-300x163.jpg 300w, https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/Root_atlas-1030x558.jpg 1030w, https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/Root_atlas-768x416.jpg 768w, https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/Root_atlas-1536x832.jpg 1536w, https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/Root_atlas-2048x1110.jpg 2048w, https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/Root_atlas-1500x813.jpg 1500w\" sizes=\"(max-width: 705px) 100vw, 705px\" \/><\/div><\/div><\/div><\/div>\n<section  class='av_textblock_section av-zfo6-abe74cbb3de70ab776b3c9434f585507 '   itemscope=\"itemscope\" itemtype=\"https:\/\/schema.org\/CreativeWork\" ><div class='avia_textblock'  itemprop=\"text\" ><\/div><\/section>\n<div  class='hr av-39jgi-cf61746d1d56fc6142b24b62b4a21330 hr-default  avia-builder-el-14  el_after_av_textblock  el_before_av_three_fifth '><span class='hr-inner '><span class=\"hr-inner-style\"><\/span><\/span><\/div>\n<div  class='flex_column av-8vkq-2833443c5771057afe86bc6615629679 av_three_fifth  avia-builder-el-15  el_after_av_hr  el_before_av_one_third  first flex_column_div  '     ><section  class='av_textblock_section av-27ksi-403dc8bcdf14fe7c6f5a4fea3e45a73a '   itemscope=\"itemscope\" itemtype=\"https:\/\/schema.org\/CreativeWork\" ><div class='avia_textblock'  itemprop=\"text\" ><p><span style=\"font-weight: 400;font-size: 14pt\"><strong>Age-related developmental changes. <\/strong>Development happens in four dimensions where the fourth dimension is time. The Arabidopsis root, with its radial symmetry and immobile cells, simplifies a 4D problem to 2D. Thus, the root enables us to study cell maturation, a continuous developmental process, with information collected from a snapshot in time.\u00a0<\/span><\/p>\n<p><span style=\"font-size: 14pt\"><span style=\"font-weight: 400\">Using single cell RNA-seq data from a single snapshot, we ask questions such as i) how does gene expression change over developmental time; ii) what transcription factors drive cell fate decisions; and iii) how do genetic perturbations affect cell identity specification and maturation? <strong>We are now<\/strong> <strong>poised to ask <\/strong><\/span><b>how gene expression changes over actual time as a seedling ages.<\/b><\/span><\/p>\n<p><span style=\"font-weight: 400;font-size: 14pt\">We generated time series single cell RNA-seq data from root tissue collected at 24 hour intervals. We are asking how age-related molecular changes in specific cell types relate to changes in root tissue patterning and root system architecture. We are specifically interested in understanding:<\/span><\/p>\n<p><span style=\"font-size: 14pt\">i) If there are age-dependent transcription factors and gene regulatory networks controlling cell fate specification<\/span><\/p>\n<p><span style=\"font-size: 14pt\">ii) If there are age-related differences in the connections between cell fate and cell division decisions<\/span><\/p>\n<\/div><\/section><\/div>\n<div  class='flex_column av-1cgni-9abbd1704f7f74c58b066fb9c8e42369 av_one_third  avia-builder-el-17  el_after_av_three_fifth  avia-builder-el-last  flex_column_div  '     ><style type=\"text\/css\" data-created_by=\"avia_inline_auto\" id=\"style-css-av-m2v0dlji-017bb28efdcc9bb66909573dc4f87c4c\">\n.avia-image-container.av-m2v0dlji-017bb28efdcc9bb66909573dc4f87c4c img.avia_image{\nbox-shadow:none;\n}\n.avia-image-container.av-m2v0dlji-017bb28efdcc9bb66909573dc4f87c4c .av-image-caption-overlay-center{\ncolor:#ffffff;\n}\n<\/style>\n<div  class='avia-image-container av-m2v0dlji-017bb28efdcc9bb66909573dc4f87c4c av-styling- avia-align-center  avia-builder-el-18  avia-builder-el-no-sibling '   itemprop=\"image\" itemscope=\"itemscope\" itemtype=\"https:\/\/schema.org\/ImageObject\" ><div class=\"avia-image-container-inner\"><div class=\"avia-image-overlay-wrap\"><img decoding=\"async\" fetchpriority=\"high\" class='wp-image-617 avia-img-lazy-loading-not-617 avia_image ' src=\"https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/rootcartoon2.jpg\" alt='' title='rootcartoon2'  height=\"1746\" width=\"1287\"  itemprop=\"thumbnailUrl\" srcset=\"https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/rootcartoon2.jpg 1287w, https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/rootcartoon2-221x300.jpg 221w, https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/rootcartoon2-759x1030.jpg 759w, https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/rootcartoon2-768x1042.jpg 768w, https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/rootcartoon2-1132x1536.jpg 1132w, https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/rootcartoon2-1106x1500.jpg 1106w, https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-content\/uploads\/sites\/325\/2024\/10\/rootcartoon2-520x705.jpg 520w\" sizes=\"(max-width: 1287px) 100vw, 1287px\" \/><\/div><\/div><\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1570,"featured_media":0,"parent":0,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-70","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-json\/wp\/v2\/pages\/70","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-json\/wp\/v2\/users\/1570"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-json\/wp\/v2\/comments?post=70"}],"version-history":[{"count":80,"href":"https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-json\/wp\/v2\/pages\/70\/revisions"}],"predecessor-version":[{"id":655,"href":"https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-json\/wp\/v2\/pages\/70\/revisions\/655"}],"wp:attachment":[{"href":"https:\/\/sites.lifesci.ucla.edu\/mcdb-shahan\/wp-json\/wp\/v2\/media?parent=70"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}