{"id":85,"date":"2017-11-17T16:38:41","date_gmt":"2017-11-17T16:38:41","guid":{"rendered":"https:\/\/bussemakerlab.org\/site\/?page_id=85"},"modified":"2018-03-02T03:50:09","modified_gmt":"2018-03-02T03:50:09","slug":"research","status":"publish","type":"page","link":"https:\/\/bussemakerlab.org\/site\/research\/","title":{"rendered":"RESEARCH"},"content":{"rendered":"<div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-1 nonhundred-percent-fullwidth non-hundred-percent-height-scrolling\" style=\"background-color: rgba(255,255,255,0);background-position: center center;background-repeat: no-repeat;padding-top:0px;padding-right:0px;padding-bottom:100px;padding-left:0px;margin-bottom: 0px;margin-top: 0px;border-width: 0px 0px 0px 0px;border-color:#eae9e9;border-style:solid;\" ><div class=\"fusion-builder-row fusion-row\"><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-0 fusion_builder_column_1_1 1_1 fusion-one-full fusion-column-first fusion-column-last fusion-column-no-min-height fusion-no-medium-visibility fusion-no-large-visibility\" style=\"margin-top:0px;margin-bottom:20px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;padding: 0px 0px 0px 0px;\"><style type=\"text\/css\"><\/style><div class=\"fusion-title title fusion-title-1 fusion-title-center fusion-title-text fusion-title-size-one\" style=\"margin-top:0px;margin-right:0px;margin-bottom:31px;margin-left:0px;\"><div class=\"title-sep-container title-sep-container-left\"><div class=\"title-sep sep-double sep-solid\" style=\"border-color:#c4c2c2;\"><\/div><\/div><span class=\"awb-title-spacer\"><\/span><h1 class=\"title-heading-center\" style=\"margin:0;\">Our Research<\/h1><span class=\"awb-title-spacer\"><\/span><div class=\"title-sep-container title-sep-container-right\"><div class=\"title-sep sep-double sep-solid\" style=\"border-color:#c4c2c2;\"><\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-1 fusion_builder_column_1_1 1_1 fusion-one-full fusion-column-first fusion-column-last\" style=\"margin-top:0px;margin-bottom:40px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;background-color:#ffffff;padding: 20px 20px 10px 20px;\"><style type=\"text\/css\"><\/style><div class=\"fusion-title title fusion-title-2 fusion-sep-none fusion-title-text fusion-title-size-two\" style=\"margin-top:0px;margin-right:0px;margin-bottom:31px;margin-left:0px;\"><h2 class=\"title-heading-left\" style=\"margin:0;\">New Method for Identifying Genetic Alterations that Modulate Gene Expression<\/h2><\/div><div class=\"fusion-builder-row fusion-builder-row-inner fusion-row\"><div class=\"fusion-layout-column fusion_builder_column_inner fusion-builder-nested-column-0 fusion_builder_column_inner_1_3 1_3 fusion-one-third fusion-column-first\" style=\"width:33.333333333333%;width:calc(33.333333333333% - ( ( 4% ) * 0.33333333333333 ) );margin-right: 4%;margin-top:0px;margin-bottom:20px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;padding: 0px 0px 0px 0px;\"><span class=\" fusion-imageframe imageframe-none imageframe-1 hover-type-none\"><img decoding=\"async\" width=\"300\" height=\"99\" title=\"Bussemaker_figure_edit\" src=\"https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2018\/03\/Bussemaker_figure_edit-300x99.jpg\" alt class=\"img-responsive wp-image-178\" srcset=\"https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2018\/03\/Bussemaker_figure_edit-200x66.jpg 200w, https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2018\/03\/Bussemaker_figure_edit-400x132.jpg 400w, https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2018\/03\/Bussemaker_figure_edit-600x198.jpg 600w, https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2018\/03\/Bussemaker_figure_edit.jpg 750w\" sizes=\"(max-width: 800px) 100vw, 400px\" \/><\/span><div class=\"fusion-clearfix\"><\/div><\/div><\/div><div class=\"fusion-layout-column fusion_builder_column_inner fusion-builder-nested-column-1 fusion_builder_column_inner_2_3 2_3 fusion-two-third fusion-column-last\" style=\"width:66.666666666667%;width:calc(66.666666666667% - ( ( 4% ) * 0.66666666666667 ) );margin-top:0px;margin-bottom:20px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;padding: 0px 0px 0px 0px;\"><div class=\"fusion-text fusion-text-1\"><p>Read about our various methodologies for mapping trans-acting genetic determinants of gene expression in a recent <a href=\"https:\/\/systemsbiology.columbia.edu\/news\/new-method-for-identifying-genetic-alterations-that-modulate-gene-expression\">news story<\/a> on the website of the Department of Systems Biology.<\/p>\n<\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-2 fusion_builder_column_1_1 1_1 fusion-one-full fusion-column-first fusion-column-last\" style=\"margin-top:0px;margin-bottom:40px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;background-color:#ffffff;padding: 20px 20px 10px 20px;\"><style type=\"text\/css\"><\/style><div class=\"fusion-title title fusion-title-3 fusion-sep-none fusion-title-text fusion-title-size-two\" style=\"margin-top:0px;margin-right:0px;margin-bottom:31px;margin-left:0px;\"><h2 class=\"title-heading-left\" style=\"margin:0;\">Discovery of PQM-1 as a key regulator of aging and longevity<\/h2><\/div><div class=\"fusion-builder-row fusion-builder-row-inner fusion-row\"><div class=\"fusion-layout-column fusion_builder_column_inner fusion-builder-nested-column-2 fusion_builder_column_inner_1_3 1_3 fusion-one-third fusion-column-first\" style=\"width:33.333333333333%;width:calc(33.333333333333% - ( ( 4% ) * 0.33333333333333 ) );margin-right: 4%;margin-top:0px;margin-bottom:20px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;padding: 0px 0px 0px 0px;\"><span class=\" fusion-imageframe imageframe-none imageframe-2 hover-type-none\"><img decoding=\"async\" width=\"400\" height=\"400\" title=\"Graphical_Abstract_v2\" src=\"https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/11\/Graphical_Abstract_v2.png\" alt class=\"img-responsive wp-image-86\" srcset=\"https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/11\/Graphical_Abstract_v2-200x200.png 200w, https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/11\/Graphical_Abstract_v2.png 400w\" sizes=\"(max-width: 800px) 100vw, 400px\" \/><\/span><div class=\"fusion-clearfix\"><\/div><\/div><\/div><div class=\"fusion-layout-column fusion_builder_column_inner fusion-builder-nested-column-3 fusion_builder_column_inner_2_3 2_3 fusion-two-third fusion-column-last\" style=\"width:66.666666666667%;width:calc(66.666666666667% - ( ( 4% ) * 0.66666666666667 ) );margin-top:0px;margin-bottom:20px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;padding: 0px 0px 0px 0px;\"><div class=\"fusion-text fusion-text-2\"><p>Aging is fundamental to the human life cycle and intimately connected with disease. Understanding the genetic and molecular determinants of animal longevity will provide new avenues for slowing the negative effects of aging. Using the nematode\u00a0C. elegans\u00a0as a model organism, and applying a combination of computational and experimental methodsin close collaboration with the lab of Dr. Coleen Murphy at Princeton University, Ronald Tepper in the Bussemaker lab has discovered (<a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/23911329\">Tepper\u00a0et al.,\u00a0Cell, 2013<\/a>) that the little-studied transcription factor PQM-1 is a key regulator of development and longevity, and the long-sought factor that binds the so-called DAF-16 associated element (DAE). As it turns out, PQM-1 complements the well-known aging transcription factor DAF-16\/FOXO in many respects. Both act as transcriptional activators, but they control distinct sets of target genes (stress response vs. growth). Whether DAF-16 or PQM-1 is nuclear or cytoplasmic depends on the status of the insulin\/IGF-1 signaling pathway, but in opposite ways. This causes only one of the factors to be active as a regulator at any given time, depending on the conditions (e.g. low nutrients) and genetic background (e.g., loss of\u00a0daf-2\u00a0or\u00a0daf-18\/PTEN). At the same time, as we have shown, the two factors interact with each other in an essential way: loss of\u00a0pqm-1\u00a0affects DAF-16 subcellular localization, and vice versa. The molecular mechanisms underlying these important processes, however, remain obscure.<\/p>\n<\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-3 fusion_builder_column_1_1 1_1 fusion-one-full fusion-column-first fusion-column-last\" style=\"margin-top:0px;margin-bottom:40px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;background-color:#ffffff;padding: 20px 20px 10px 20px;\"><style type=\"text\/css\"><\/style><div class=\"fusion-title title fusion-title-4 fusion-sep-none fusion-title-text fusion-title-size-two\" style=\"margin-top:0px;margin-right:0px;margin-bottom:31px;margin-left:0px;\"><h2 class=\"title-heading-left\" style=\"margin:0;\">DSSR: New software for dissecting the spatial structure of RNA<\/h2><\/div><div class=\"fusion-builder-row fusion-builder-row-inner fusion-row\"><div class=\"fusion-layout-column fusion_builder_column_inner fusion-builder-nested-column-4 fusion_builder_column_inner_1_3 1_3 fusion-one-third fusion-column-first\" style=\"width:33.333333333333%;width:calc(33.333333333333% - ( ( 4% ) * 0.33333333333333 ) );margin-right: 4%;margin-top:0px;margin-bottom:20px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;padding: 0px 0px 0px 0px;\"><span class=\" fusion-imageframe imageframe-none imageframe-3 hover-type-none\"><img decoding=\"async\" width=\"1024\" height=\"620\" title=\"DSSR-twister-updated\" src=\"https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/11\/DSSR-twister-updated-1024x620.png\" alt class=\"img-responsive wp-image-87\" srcset=\"https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/11\/DSSR-twister-updated-200x121.png 200w, https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/11\/DSSR-twister-updated-400x242.png 400w, https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/11\/DSSR-twister-updated-600x363.png 600w, https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/11\/DSSR-twister-updated-800x484.png 800w, https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/11\/DSSR-twister-updated-1200x726.png 1200w, https:\/\/bussemakerlab.org\/site\/wp-content\/uploads\/2017\/11\/DSSR-twister-updated.png 1800w\" sizes=\"(max-width: 800px) 100vw, 400px\" \/><\/span><div class=\"fusion-clearfix\"><\/div><\/div><\/div><div class=\"fusion-layout-column fusion_builder_column_inner fusion-builder-nested-column-5 fusion_builder_column_inner_2_3 2_3 fusion-two-third fusion-column-last\" style=\"width:66.666666666667%;width:calc(66.666666666667% - ( ( 4% ) * 0.66666666666667 ) );margin-top:0px;margin-bottom:20px;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\" style=\"background-position:left top;background-repeat:no-repeat;-webkit-background-size:cover;-moz-background-size:cover;-o-background-size:cover;background-size:cover;padding: 0px 0px 0px 0px;\"><div class=\"fusion-text fusion-text-3\"><p>Insight into the three-dimensional architecture of RNA is essential for understanding its numerous cellular functions. Recent discoveries of new RNA folds and functions have stimulated interest in the development of technologies that can make sense of the complex spatial arrangements of these molecules. To address this need,\u00a0<a href=\"https:\/\/systemsbiology.columbia.edu\/people\/xiang-jun-lu\">Dr. Xiang-Jun Lu<\/a>, an NIH-funded Associate Research Scientist affiliated with the\u00a0<a href=\"http:\/\/biology.columbia.edu\/people\/bussemaker\">Bussemaker Lab<\/a>\u00a0who previously developed the widely used\u00a0<a href=\"http:\/\/x3dna.org\/\">3DNA<\/a>software, has developed a new computational tool named DSSR (Dissecting the Spatial Structure of RNA). DSSR has already been integrated into\u00a0<a href=\"http:\/\/jmol.x3dna.org\/\">Jmol<\/a>\u00a0and\u00a0<a href=\"http:\/\/pymolwiki.org\/index.php\/Dssr_block\">PyMOL<\/a>, two widely used molecular graphics programs. It can serve as a cornerstone for RNA structural bioinformatics and will benefit a broad range of possible applications. [read the\u00a0<a href=\"http:\/\/nar.oxfordjournals.org\/content\/43\/21\/e142.long\">paper<\/a>][download the\u00a0<a href=\"http:\/\/x3dna.org\/\">software<\/a>]<\/p>\n<\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"nf_dc_page":"","footnotes":""},"class_list":["post-85","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/bussemakerlab.org\/site\/wp-json\/wp\/v2\/pages\/85","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/bussemakerlab.org\/site\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/bussemakerlab.org\/site\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/bussemakerlab.org\/site\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/bussemakerlab.org\/site\/wp-json\/wp\/v2\/comments?post=85"}],"version-history":[{"count":8,"href":"https:\/\/bussemakerlab.org\/site\/wp-json\/wp\/v2\/pages\/85\/revisions"}],"predecessor-version":[{"id":181,"href":"https:\/\/bussemakerlab.org\/site\/wp-json\/wp\/v2\/pages\/85\/revisions\/181"}],"wp:attachment":[{"href":"https:\/\/bussemakerlab.org\/site\/wp-json\/wp\/v2\/media?parent=85"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}