{"id":714,"date":"2024-12-16T10:33:00","date_gmt":"2024-12-16T15:33:00","guid":{"rendered":"https:\/\/www.golive.clarku.edu\/faculty\/profiles\/robert-drewell\/"},"modified":"2026-04-04T15:35:55","modified_gmt":"2026-04-04T19:35:55","slug":"robert-drewell","status":"publish","type":"cu_faculty","link":"https:\/\/www.clarku.edu\/faculty\/profiles\/robert-drewell\/","title":{"rendered":"Robert Drewell"},"content":{"rendered":"

The research in my lab applies experimental molecular genomic, mathematical and computational approaches to investigate the regulation of gene expression during development. The major focus is on analyzing the epigenetic and regulatory networks that control transcription in the embryo in model insect species, including Drosophila and social insects.<\/span><\/p>\n","protected":false},"author":0,"featured_media":1857,"parent":0,"template":"","meta":{"cu_faculty_f180_userid":"C70227051","cu_faculty_first_name":"Robert","cu_faculty_last_name":"Drewell","cu_faculty_employment_status":"Full Time","cu_faculty_rank":"Professor","cu_faculty_position":"Professor","cu_faculty_phone":"","cu_faculty_email":"RDrewell@clarku.edu","cu_faculty_location":"","cu_faculty_about":"

The research in my lab applies experimental molecular genomic, mathematical and computational approaches to investigate the regulation of gene expression during development. The major focus is on analyzing the epigenetic and regulatory networks that control transcription in the embryo in model insect species, including Drosophila and social insects.<\/span><\/p>","cu_faculty_degrees":"Ph.D. in Molecular & Developmental Biology,<\/span> King's College, University of Cambridge, 1999\nB.S. in Molecular Genetics,<\/span> King's College, University of London, 1996","cu_faculty_cv":"https:\/\/faculty180.interfolio.com\/public\/download.php?key=SDRwNCtxSUpsamxBQ213WS9ucHFuNnMwT0hzQU11b2RPQkJ2cWc3amxyUmNRdVVXTkF4MU1zT21qREtJZEdWZ3IxMWRUUlltZGpIZjJIeGgzZFhZOVFUa0Q3SVVuenlCaE4xaFNhcjlYY1FqWXh6OHRlamlydz09","cu_faculty_links":"[]","cu_faculty_scholarly_interests":"","cu_faculty_scholarly_works":"[{\"activityid\":13464,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"<p><strong>Two coacting shadow enhancers regulate twin of eyeless expression during early Drosophila development<\\\/strong><\\\/p>\",\"Journal Title\":\"Genetics\",\"Series Title\":\"\",\"Month \\\/ Season\":\"\",\"Year\":2025,\"Publisher\":\"\",\"Publisher City and State\":\"\",\"Publisher Country\":\"\",\"Volume\":\"229\",\"Issue Number \\\/ Edition\":\"1\",\"Page Number(s) or Number of Pages\":\"1-43\",\"ISSN\":\"\",\"DOI\":\"\",\"CoAuthor\":null,\"URL\":\"\",\"Description\":\"<p>The Drosophila PAX6 homolog twin of eyeless (toy) sits at the pinnacle of the genetic pathway controlling eye development, the retinal determination network. Expression of toy in the embryo is first detectable at cellular blastoderm stage 5 in an anterior-dorsal band in the presumptive procephalic neuroectoderm, which gives rise to the primordia of the visual system and brain. Although several maternal and gap transcription factors that generate positional information in the embryo have been implicated in controlling toy, the regulation of toy expression in the early embryo is currently not well characterized. In this study, we adopt an integrated experimental approach utilizing bioinformatics, molecular genetic testing of putative enhancers in transgenic reporter gene assays and quantitative analysis of expression patterns in the early embryo, to identify 2 novel coacting enhancers at the toy gene. In addition, we apply mathematical modeling to dissect the regulatory landscape for toy. We demonstrate that relatively simple thermodynamic-based models, incorporating only 5 TF binding sites, can accurately predict gene expression from the 2 coacting enhancers and that the HUNCHBACK TF plays a critical regulatory role through a dual-modality function as an activator and repressor. Our analysis also reveals that the molecular architecture of the 2 enhancers is very different, indicating that the underlying regulatory logic they employ is distinct.<\\\/p>\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":13464,\"status\":\"Completed\\\/Published\",\"term\":\"Spring\",\"year\":2025,\"termid\":\"2024\\\/03\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Jacqueline M Dresch\",\"Luke L Nourie\",\"Regan D Conrad\",\"Lindsay T Carlson\",\"Elizabeth I Tchantouridze\",\"Biruck Tesfaye\",\"Eleanor Verhagen\",\"Mahima Gupta\",\"Diego Borges-Rivera\",\"Robert A Drewell\"],\"sort_date\":\"2025-1-01\"},{\"activityid\":13469,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"<p><strong>Experimental approaches to investigate biophysical interactions between homeodomain transcription factors and DNA<\\\/strong><\\\/p>\",\"Journal Title\":\"Biochimica et biophysica acta. Gene regulatory mechanisms\",\"Series Title\":\"\",\"Month \\\/ Season\":\"\",\"Year\":2025,\"Publisher\":\"\",\"Publisher City and State\":\"\",\"Publisher Country\":\"\",\"Volume\":\"1868\",\"Issue Number \\\/ Edition\":\"1\",\"Page Number(s) or Number of Pages\":\"195074\",\"ISSN\":\"\",\"DOI\":\"\",\"CoAuthor\":null,\"URL\":\"\",\"Description\":\"<p>Homeodomain transcription factors (TFs) bind to specific DNA sequences to regulate the expression of target genes. Structural work has provided insight into molecular identities and aided in unraveling structural features of these TFs. However, the detailed affinity and specificity by which these TFs bind to DNA sequences is still largely unknown. Qualitative methods, such as DNA footprinting, Electrophoretic Mobility Shift Assays (EMSAs), Systematic Evolution of Ligands by Exponential Enrichment (SELEX), Bacterial One Hybrid (B1H) systems, Surface Plasmon Resonance (SPR), and Protein Binding Microarrays (PBMs) have been widely used to investigate the biochemical characteristics of TF-DNA binding events. In addition to these qualitative methods, bioinformatic approaches have also assisted in TF binding site discovery. Here we discuss the advantages and limitations of these different approaches, as well as the benefits of utilizing more quantitative approaches, such as Mechanically Induced Trapping of Molecular Interactions (MITOMI), Microscale Thermophoresis (MST) and Isothermal Titration Calorimetry (ITC), in determining the biophysical basis of binding specificity of TF-DNA complexes and improving upon existing computational approaches aimed at affinity predictions.<\\\/p>\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":13469,\"status\":\"Completed\\\/Published\",\"term\":\"Spring\",\"year\":2025,\"termid\":\"2024\\\/03\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Fadwa Mekkaoui\",\"Robert A Drewell\",\"Jacqueline M Dresch\",\"Donald E Spratt\"],\"sort_date\":\"2025-1-01\"},{\"activityid\":13463,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"<p><strong>Transcription factor expression landscape in Drosophila embryonic cell lines<\\\/strong><\\\/p>\",\"Journal Title\":\"BMC genomics\",\"Series Title\":\"\",\"Month \\\/ Season\":\"\",\"Year\":2024,\"Publisher\":\"\",\"Publisher City and State\":\"\",\"Publisher Country\":\"\",\"Volume\":\"25\",\"Issue Number \\\/ Edition\":\"1\",\"Page Number(s) or Number of Pages\":\"307\",\"ISSN\":\"\",\"DOI\":\"\",\"CoAuthor\":null,\"URL\":\"\",\"Description\":\"<p>Transcription factor (TF) proteins are a key component of the gene regulatory networks that control cellular fates and function. TFs bind DNA regulatory elements in a sequence-specific manner and modulate target gene expression through combinatorial interactions with each other, cofactors, and chromatin-modifying proteins. Large-scale studies over the last two decades have helped shed light on the complex network of TFs that regulate development in Drosophila melanogaster.<\\\/p>\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":13463,\"status\":\"Completed\\\/Published\",\"term\":\"Summer\",\"year\":2024,\"termid\":\"2023\\\/05\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Robert A Drewell\",\"Daniel Klonaros\",\"Jacqueline M Dresch\"],\"sort_date\":\"2024-1-01\"},{\"activityid\":13465,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Supporting the democratization of science during a pandemic: genomics Course-based Undergraduate Research Experiences (CUREs) as an effective remote learning strategy\",\"Journal Title\":\"Journal of microbiology & biology education\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2023,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"24\",\"Issue Number \\\/ Edition\":\"3\",\"Page Number(s) or Number of Pages\":\"\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"The initial phase of the COVID-19 pandemic changed the nature of course delivery from largely in-person to exclusively remote, thus disrupting the well-established pedagogy of the Genomics Education Partnership (GEP; https:\\\/\\\/www.thegep.org). However, our web-based research adapted well to the remote learning environment. As usual, students who engaged in the GEP's Course-based Undergraduate Research Experience (CURE) received digital projects based on genetic information within assembled genomes. Adaptations for remote implementation included moving new member faculty training and peer Teaching Assistant office hours from in-person to online. Surprisingly, our faculty membership significantly increased and, hence, the number of supported students. Furthermore, despite the mostly virtual instruction of the 2020-2021 academic year, there was no significant decline in student learning nor attitudes. Based on successfully expanding the GEP CURE within a virtual learning environment, we provide four strategic lessons we infer toward democratizing science education. First, it appears that increasing access to scientific research and professional development opportunities by supporting virtual, cost-free attendance at national conferences attracts more faculty members to educational initiatives. Second, we observed that transitioning new member training to an online platform removed geographical barriers, reducing time and travel demands, and increased access for diverse faculty to join. Third, developing a Virtual Teaching Assistant program increased the availability of peer support, thereby improving the opportunities for student success. Finally, increasing access to web-based technology is critical for providing equitable opportunities for marginalized students to fully participate in research courses. Online CUREs have great potential for democratizing science education.\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":13465,\"status\":\"Completed\\\/Published\",\"term\":\"Fall\",\"year\":2023,\"termid\":\"2023\\\/01\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"David Lopatto\",\"S Catherin C Silver Key\",\"Melanie Van Stry\",\"Jamie Siders\",\"Wilson Leung\",\"Katie M Sandlin\",\"Chinmay P Rele\",\"Genomics Education Partnership \",\"Laura K Reed\"],\"sort_date\":\"2023-9-01\"},{\"activityid\":13456,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"<strong>The\\u00a0<span style="font-style:italic;">Dictyostelium discoideum<\\\/span>\\u00a0genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing<\\\/strong>\",\"Journal Title\":\"NAR Genomics and Bioinformatics\",\"Series Title\":\"\",\"Month \\\/ Season\":\"June\",\"Year\":2023,\"Publisher\":\"\",\"Publisher City and State\":\"\",\"Publisher Country\":\"\",\"Volume\":\"\",\"Issue Number \\\/ Edition\":\"\",\"Page Number(s) or Number of Pages\":\"\",\"ISSN\":\"\",\"DOI\":\"\",\"CoAuthor\":null,\"URL\":\"\",\"Description\":\"\",\"Include description in output citation\":0,\"Origin\":\"Manual\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":13456,\"status\":\"Completed\\\/Published\",\"term\":\"Summer\",\"year\":2023,\"termid\":\"2022\\\/05\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Robert Drewell\",\"Tayla C Cormier\",\"Jacob L Steenwyk\",\"James St. Denis\",\"Javier F Tabima Restrepo\",\"Jacqueline M. Dresch\",\"Denis A Larochelle\"],\"sort_date\":\"2023-6-01\"},{\"activityid\":13452,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Investigating the sequence landscape in the\\u00a0Drosophila\\u00a0initiator core promoter element using an enhanced MARZ algorithm.\\u00a0\",\"Journal Title\":\"PeerJ \",\"Series Title\":\"\",\"Month \\\/ Season\":\"\",\"Year\":2023,\"Publisher\":\"\",\"Publisher City and State\":\"\",\"Publisher Country\":\"\",\"Volume\":\"\",\"Issue Number \\\/ Edition\":\"11\",\"Page Number(s) or Number of Pages\":\"e15597\",\"ISSN\":\"\",\"DOI\":\"\",\"CoAuthor\":null,\"URL\":\"https:\\\/\\\/peerj.com\\\/articles\\\/15597\\\/\",\"Description\":\"\",\"Include description in output citation\":0,\"Origin\":\"Manual\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":13452,\"status\":\"Completed\\\/Published\",\"term\":\"May\",\"year\":2023,\"termid\":\"2022\\\/04\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Jacqueline M. Dresch\",\"Regan D. Conrad\",\"Daniel Klonaros\",\"Robert Drewell\"],\"sort_date\":\"2023-5-01\"},{\"activityid\":13458,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"<a href="https:\\\/\\\/academic.oup.com\\\/g3journal\\\/advance-article-abstract\\\/doi\\\/10.1093\\\/g3journal\\\/jkad054\\\/7068459?utm_source=advanceaccess&utm_campaign=g3journal&utm_medium=email">Transcriptome profile in\\u00a0<span style="font-style:italic;">Drosophila<\\\/span>\\u00a0Kc and S2 embryonic cell lines<\\\/a><span style="font-size:16px;color:#333333;">.<\\\/span>\",\"Journal Title\":\"G3: Genes|Genomes|Genetics\",\"Series Title\":\"\",\"Month \\\/ Season\":\"May\",\"Year\":2023,\"Publisher\":\"\",\"Publisher City and State\":\"\",\"Publisher Country\":\"\",\"Volume\":\"\",\"Issue Number \\\/ Edition\":\"\",\"Page Number(s) or Number of Pages\":\"\",\"ISSN\":\"\",\"DOI\":\"\",\"CoAuthor\":null,\"URL\":\"\",\"Description\":\"\",\"Include description in output citation\":0,\"Origin\":\"Manual\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":13458,\"status\":\"Completed\\\/Published\",\"term\":\"May\",\"year\":2023,\"termid\":\"2022\\\/04\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Daniel Klonaros\",\"Jacqueline M. Dresch\",\"Robert Drewell\"],\"sort_date\":\"2023-5-01\"},{\"activityid\":13457,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"<a href="https:\\\/\\\/www.sciencedirect.com\\\/science\\\/article\\\/abs\\\/pii\\\/S0025556421001292">Fitting thermodynamic-based models: Incorporating parameter sensitivity improves the performance of an evolutionary algorithm<\\\/a><span style="font-size:16px;color:#333333;">.<\\\/span>\",\"Journal Title\":\"Mathematical Biosciences\",\"Series Title\":\"\",\"Month \\\/ Season\":\"\",\"Year\":2021,\"Publisher\":\"\",\"Publisher City and State\":\"\",\"Publisher Country\":\"\",\"Volume\":\"\",\"Issue Number \\\/ Edition\":\"\",\"Page Number(s) or Number of Pages\":\"\",\"ISSN\":\"\",\"DOI\":\"\",\"CoAuthor\":null,\"URL\":\"\",\"Description\":\"\",\"Include description in output citation\":0,\"Origin\":\"Manual\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":13457,\"status\":\"Completed\\\/Published\",\"term\":\"Fall\",\"year\":2021,\"termid\":\"2021\\\/01\",\"listingorder\":6,\"completionorder\":6},{\"id\":13457,\"status\":\"Revise & Resubmit\",\"term\":\"Spring\",\"year\":2020,\"termid\":\"2019\\\/03\",\"listingorder\":3,\"completionorder\":3},{\"id\":13457,\"status\":\"Revise & Resubmit\",\"term\":\"Summer\",\"year\":2019,\"termid\":\"2018\\\/05\",\"listingorder\":3,\"completionorder\":3}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Michael Gaiewski\",\"Robert Drewell\",\"Jacqueline M. Dresch\"],\"sort_date\":\"2021-9-01\"},{\"activityid\":1039,\"fields\":{\"Type\":\"Papers Published - Conference Proceedings\",\"Title of Paper\":\"Biophysical and structural analysis of Drosophila transcription factors\",\"Title of Published Proceedings\":\"Protein Science\",\"Title of Conference\":\"\",\"Conference Location\":\"\",\"Month \\\/ Season\":\"\",\"Year\":2019,\"Publisher\":\"\",\"Publisher City and State\":\"\",\"Volume\":\"28\",\"Issue Number \\\/ Edition\":\"\",\"Page Numbers\":\"\",\"DOI\":\"\",\"CoAuthor\":null,\"URL\":\"\",\"Description\":\"\",\"Include description in output citation\":0,\"Origin\":\"Manual\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1039,\"status\":\"Completed\\\/Published\",\"term\":\"Fall\",\"year\":2019,\"termid\":\"2019\\\/01\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Aaron Bogle\",\"Rachel Orlomoski\",\"Jacqueline M. Dresch\",\"Robert Drewell\",\"Donald E. Spratt\"],\"sort_date\":\"2019-9-01\"},{\"activityid\":1040,\"fields\":{\"Type\":\"Papers Published - Conference Proceedings\",\"Title of Paper\":\"Biophysical and structural analysis of Antennapedia and Ultrabithorax homeodomain transcription factor-DNA binding affinities\",\"Title of Published Proceedings\":\"Protein Science\",\"Title of Conference\":\"\",\"Conference Location\":\"\",\"Month \\\/ Season\":\"\",\"Year\":2019,\"Publisher\":\"\",\"Publisher City and State\":\"\",\"Volume\":\"28\",\"Issue Number \\\/ Edition\":\"\",\"Page Numbers\":\"\",\"DOI\":\"\",\"CoAuthor\":null,\"URL\":\"\",\"Description\":\"\",\"Include description in output citation\":0,\"Origin\":\"Manual\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1040,\"status\":\"Completed\\\/Published\",\"term\":\"Fall\",\"year\":2019,\"termid\":\"2019\\\/01\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Jeanmarie Loss\",\"Jacqueline M. Dresch\",\"Robert Drewell\",\"Donald E. Spratt\"],\"sort_date\":\"2019-9-01\"},{\"activityid\":1041,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Analyzing the stability of gene expression using a simple reaction-diffusion model in an early Drosophila embryo\",\"Journal Title\":\"Mathematical biosciences\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2019,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"316\",\"Issue Number \\\/ Edition\":\"\",\"Page Number(s) or Number of Pages\":\"108239\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"In all complex organisms, the precise levels and timing of gene expression controls vital biological processes. In higher eukaryotes, including the fruit fly Drosophila melanogaster, the complex molecular control of transcription (the synthesis of RNA from DNA) and translation (the synthesis of proteins from RNA) events driving this gene expression are not fully understood. In particular, for Drosophila melanogaster, there is a plethora of experimental data, including quantitative measurements of both RNA and protein concentrations, but the precise mechanisms that control the dynamics of gene expression during early development and the processes which lead to steady-state levels of certain proteins remain elusive. This study analyzes a current mathematical modeling approach in an attempt to better understand the long-term behavior of gene regulation. The model is a modified reaction-diffusion equation which has been previously employed in predicting gene expression levels and studying the relative contributions of transcription and translation events to protein abundance [10,11,24]. Here, we use Matrix Algebra and Analysis techniques to study the stability of the gene expression system and analyze equilibria, using very general assumptions regarding the parameter values incorporated into the model. We prove that, given realistic biological parameter values, the system will result in a unique, stable equilibrium solution. Additionally, we give an example of this long-term behavior using the model alongside actual experimental data obtained from Drosophila embryos.\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1041,\"status\":\"Completed\\\/Published\",\"term\":\"Fall\",\"year\":2019,\"termid\":\"2019\\\/01\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Gregory D McCarthy\",\"Robert A Drewell\",\"Jacqueline M Dresch\"],\"sort_date\":\"2019-9-01\"},{\"activityid\":1042,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Rapid and efficient purification of Drosophila homeodomain transcription factors for biophysical characterization\",\"Journal Title\":\"Protein expression and purification\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2019,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"158\",\"Issue Number \\\/ Edition\":\"\",\"Page Number(s) or Number of Pages\":\"9-14\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"Homeodomain transcription factors (HD TFs) are a large class of evolutionarily conserved DNA binding proteins that contain a basic 60-amino acid region required for binding to specific DNA sites. In Drosophila melanogaster, many of these HD TFs are expressed in the early embryo and control transcription of target genes in development through their interaction with cis-regulatory modules. Previous studies where some of the Drosophila HD TFs were purified required the use of strong denaturants (i.e. 6\\u202fM urea) and multiple chromatography columns, making the downstream biochemical examination of the isolated protein difficult. To circumvent these obstacles, we have developed a streamlined expression and purification protocol to produce large yields of Drosophila HD TFs. Using the HD TFs FUSHI-TARAZU (FTZ), ANTENNAPEDIA (ANTP), ABDOMINAL-A (ABD-A), ABDOMINAL-B (ABD-B), and ULTRABITHORAX (UBX) as examples, we demonstrate that our 3-day protocol involving the overexpression of His-SUMO fusion constructs in E. coli followed by a Ni-IMAC, SUMO-tag cleavage with the SUMO protease Ulp1, and a heparin column purification produces pure, soluble protein in biological buffers around pH 7 in the absence of denaturants. Electrophoretic mobility shift assays (EMSA) confirm that the purified HD proteins are functional and nuclear magnetic resonance (NMR) spectra confirm that the purified HDs are well-folded. These purified HD TFs can be used in future biophysical experiments to structurally and biochemically characterize how and why these HD TFs bind to different DNA sequences and further probe how nucleotide differences contribute to TF-DNA specificity in the HD family.\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1042,\"status\":\"Completed\\\/Published\",\"term\":\"Spring\",\"year\":2019,\"termid\":\"2018\\\/03\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Rachel Orlomoski\",\"Aaron Bogle\",\"Jeanmarie Loss\",\"Rylee Simons\",\"Jacqueline M Dresch\",\"Robert A Drewell\",\"Donald E Spratt\"],\"sort_date\":\"2019-1-01\"},{\"activityid\":1038,\"fields\":{\"Type\":\"Presentations\",\"Title of Presentation\":\"Biophysical and structural analysis of Drosophila transcription factors\",\"Conference \\\/ Meeting Name\":\"Next-in-BIO 2018\",\"Location of Conference \\\/ Meeting\":\"Worcester MA\",\"Month \\\/ Season\":\"November\",\"Year\":2018,\"Sponsoring Organization\":\"\",\"CoAuthor\":null,\"URL\":\"\",\"Description\":\"\",\"Include description in output citation\":0,\"Origin\":\"Manual\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1038,\"status\":\"Completed\\\/Published\",\"term\":\"Fall\",\"year\":2018,\"termid\":\"2018\\\/01\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Aaron Bogle\",\"Jacqueline M. Dresch\",\"Robert Drewell\",\"Donald E. Spratt\"],\"sort_date\":\"2018-11-01\"},{\"activityid\":13462,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Whole genome bisulfite sequencing reveals a sparse, but robust pattern of DNA methylation in the Dictyostelium discoideum genome\",\"Journal Title\":\"BIORXIV\",\"Series Title\":\"\",\"Month \\\/ Season\":\"\",\"Year\":2017,\"Publisher\":\"\",\"Publisher City and State\":\"\",\"Publisher Country\":\"\",\"Volume\":\"\",\"Issue Number \\\/ Edition\":\"\",\"Page Number(s) or Number of Pages\":\"\",\"ISSN\":\"\",\"DOI\":\"\",\"CoAuthor\":null,\"URL\":\"\",\"Description\":\"\",\"Include description in output citation\":0,\"Origin\":\"Manual\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":13462,\"status\":\"Completed\\\/Published\",\"term\":\"Spring\",\"year\":2017,\"termid\":\"2016\\\/03\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Jacob Steenwyk\",\"James St. Denis\",\"Jacqueline M. Dresch\",\"Denis A Larochelle\",\"Robert Drewell\"],\"sort_date\":\"2017-1-01\"},{\"activityid\":1049,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Spatial distribution of predicted transcription factor binding sites in Drosophila ChIP peaks\",\"Journal Title\":\"Mechanisms of development\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2016,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"141\",\"Issue Number \\\/ Edition\":\"\",\"Page Number(s) or Number of Pages\":\"51-61\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"In the development of the Drosophila embryo, gene expression is directed by the sequence-specific interactions of a large network of protein transcription factors (TFs) and DNA cis-regulatory binding sites. Once the identity of the typically 8-10bp binding sites for any given TF has been determined by one of several experimental procedures, the sequences can be represented in a position weight matrix (PWM) and used to predict the location of additional TF binding sites elsewhere in the genome. Often, alignments of large (>200bp) genomic fragments that have been experimentally determined to bind the TF of interest in Chromatin Immunoprecipitation (ChIP) studies are trimmed under the assumption that the majority of the binding sites are located near the center of all the aligned fragments. In this study, ChIP\\\/chip datasets are analyzed using the corresponding PWMs for the well-studied TFs; CAUDAL, HUNCHBACK, KNIRPS and KRUPPEL, to determine the distribution of predicted binding sites. All four TFs are critical regulators of gene expression along the anterio-posterior axis in early Drosophila development. For all four TFs, the ChIP peaks contain multiple binding sites that are broadly distributed across the genomic region represented by the peak, regardless of the prediction stringency criteria used. This result suggests that ChIP peak trimming may exclude functional binding sites from subsequent analyses.\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1049,\"status\":\"Completed\\\/Published\",\"term\":\"Fall\",\"year\":2016,\"termid\":\"2016\\\/01\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Kade P Pettie\",\"Jacqueline M Dresch\",\"Robert A Drewell\"],\"sort_date\":\"2016-9-01\"},{\"activityid\":1045,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Parent-of-origin effects on genome-wide DNA methylation in the Cape honey bee (Apis mellifera capensis) may be confounded by allele-specific methylation\",\"Journal Title\":\"BMC genomics\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2016,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"17\",\"Issue Number \\\/ Edition\":\"\",\"Page Number(s) or Number of Pages\":\"226\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"Intersexual genomic conflict sometimes leads to unequal expression of paternal and maternal alleles in offspring, resulting in parent-of-origin effects. In honey bees reciprocal crosses can show strong parent-of-origin effects, supporting theoretical predictions that genomic imprinting occurs in this species. Mechanisms behind imprinting in honey bees are unclear but differential DNA methylation in eggs and sperm suggests that DNA methylation could be involved. Nonetheless, because DNA methylation is multifunctional, it is difficult to separate imprinting from other roles of methylation. Here we use a novel approach to investigate parent-of-origin DNA methylation in honey bees. In the subspecies Apis mellifera capensis, reproduction of females occurs either sexually by fertilization of eggs with sperm, or via thelytokous parthenogenesis, producing female embryos derived from two maternal genomes.\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1045,\"status\":\"Completed\\\/Published\",\"term\":\"Spring\",\"year\":2016,\"termid\":\"2015\\\/03\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Emily J Remnant\",\"Alyson Ashe\",\"Paul E Young\",\"Gabriele Buchmann\",\"Madeleine Beekman\",\"Mic H Allsopp\",\"Catherine M Suter\",\"Robert A Drewell\",\"Benjamin P Oldroyd\"],\"sort_date\":\"2016-1-01\"},{\"activityid\":1047,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Nucleotide Interdependency in Transcription Factor Binding Sites in the Drosophila Genome\",\"Journal Title\":\"Gene regulation and systems biology\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2016,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"10\",\"Issue Number \\\/ Edition\":\"\",\"Page Number(s) or Number of Pages\":\"21-33\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"A long-standing objective in modern biology is to characterize the molecular components that drive the development of an organism. At the heart of eukaryotic development lies gene regulation. On the molecular level, much of the research in this field has focused on the binding of transcription factors (TFs) to regulatory regions in the genome known as cis-regulatory modules (CRMs). However, relatively little is known about the sequence-specific binding preferences of many TFs, especially with respect to the possible interdependencies between the nucleotides that make up binding sites. A particular limitation of many existing algorithms that aim to predict binding site sequences is that they do not allow for dependencies between nonadjacent nucleotides. In this study, we use a recently developed computational algorithm, MARZ, to compare binding site sequences using 32 distinct models in a systematic and unbiased approach to explore nucleotide dependencies within binding sites for 15 distinct TFs known to be critical to Drosophila development. Our results indicate that many of these proteins have varying levels of nucleotide interdependencies within their DNA recognition sequences, and that, in some cases, models that account for these dependencies greatly outperform traditional models that are used to predict binding sites. We also directly compare the ability of different models to identify the known KRUPPEL TF binding sites in CRMs and demonstrate that a more complex model that accounts for nucleotide interdependencies performs better when compared with simple models. This ability to identify TFs with critical nucleotide interdependencies in their binding sites will lead to a deeper understanding of how these molecular characteristics contribute to the architecture of CRMs and the precise regulation of transcription during organismal development. \",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1047,\"status\":\"Completed\\\/Published\",\"term\":\"Spring\",\"year\":2016,\"termid\":\"2015\\\/03\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Jacqueline M Dresch\",\"Rowan G Zellers\",\"Daniel K Bork\",\"Robert A Drewell\"],\"sort_date\":\"2016-1-01\"},{\"activityid\":1046,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Global sensitivity analysis of a dynamic model for gene expression in Drosophila embryos\",\"Journal Title\":\"PeerJ\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2015,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"3\",\"Issue Number \\\/ Edition\":\"\",\"Page Number(s) or Number of Pages\":\"e1022\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"It is well known that gene regulation is a tightly controlled process in early organismal development. However, the roles of key processes involved in this regulation, such as transcription and translation, are less well understood, and mathematical modeling approaches in this field are still in their infancy. In recent studies, biologists have taken precise measurements of protein and mRNA abundance to determine the relative contributions of key factors involved in regulating protein levels in mammalian cells. We now approach this question from a mathematical modeling perspective. In this study, we use a simple dynamic mathematical model that incorporates terms representing transcription, translation, mRNA and protein decay, and diffusion in an early Drosophila embryo. We perform global sensitivity analyses on this model using various different initial conditions and spatial and temporal outputs. Our results indicate that transcription and translation are often the key parameters to determine protein abundance. This observation is in close agreement with the experimental results from mammalian cells for various initial conditions at particular time points, suggesting that a simple dynamic model can capture the qualitative behavior of a gene. Additionally, we find that parameter sensitivites are temporally dynamic, illustrating the importance of conducting a thorough global sensitivity analysis across multiple time points when analyzing mathematical models of gene regulation. \",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1046,\"status\":\"Completed\\\/Published\",\"term\":\"Spring\",\"year\":2015,\"termid\":\"2014\\\/03\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Gregory D McCarthy\",\"Robert A Drewell\",\"Jacqueline M Dresch\"],\"sort_date\":\"2015-1-01\"},{\"activityid\":1058,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"MARZ: an algorithm to combinatorially analyze gapped n-mer models of transcription factor binding\",\"Journal Title\":\"BMC bioinformatics\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2015,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"16\",\"Issue Number \\\/ Edition\":\"\",\"Page Number(s) or Number of Pages\":\"30\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"A key challenge in understanding the molecular mechanisms that control gene regulation is the characterization of the specificity with which transcription factor proteins bind to specific DNA sequences. A number of computational approaches have been developed to examine these interactions, including simple mononucleotide and dinucleotide position weight matrix models.\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1058,\"status\":\"Completed\\\/Published\",\"term\":\"Intersession\",\"year\":2015,\"termid\":\"2014\\\/02\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Rowan G Zellers\",\"Robert A Drewell\",\"Jacqueline M Dresch\"],\"sort_date\":\"2015-1-01\"},{\"activityid\":1043,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"A parent-of-origin effect on honeybee worker ovary size\",\"Journal Title\":\"Proceedings. Biological sciences\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2014,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"281\",\"Issue Number \\\/ Edition\":\"1775\",\"Page Number(s) or Number of Pages\":\"20132388\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"Apis mellifera capensis is unique among honeybees in that unmated workers can produce pseudo-clonal female offspring via thelytokous parthenogenesis. Workers use this ability to compete among themselves and with their queen to be the mother of new queens. Males could therefore enhance their reproductive success by imprinting genes that enhance fertility in their daughter workers. This possibility sets the scene for intragenomic conflict between queens and drones over worker reproductive traits. Here, we show a strong parent-of-origin effect for ovary size (number of ovarioles) in reciprocal crosses between two honeybee subspecies, A. m. capensis and Apis mellifera scutellata. In this cross, workers with an A. m. capensis father had 30% more ovarioles than genotypically matched workers with an A. m. scutellata father. Other traits we measured (worker weight at emergence and the presence\\\/absence of a spermatheca) are influenced more by rearing conditions than by parent-of-origin effects. Our study is the first to show a strong epigenetic (or, less likely, cytoplasmic maternal) effect for a reproductive trait in the honeybee and suggests that a search for parent-of-origin effects in other social insects may be fruitful. \",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1043,\"status\":\"Completed\\\/Published\",\"term\":\"Intersession\",\"year\":2014,\"termid\":\"2013\\\/02\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Benjamin P Oldroyd\",\"Mic H Allsopp\",\"Katherine M Roth\",\"Emily J Remnant\",\"Robert A Drewell\",\"Madeleine Beekman\"],\"sort_date\":\"2014-1-01\"},{\"activityid\":1055,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"The dynamic DNA methylation cycle from egg to sperm in the honey bee Apis mellifera\",\"Journal Title\":\"Development (Cambridge, England)\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2014,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"141\",\"Issue Number \\\/ Edition\":\"13\",\"Page Number(s) or Number of Pages\":\"2702-11\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"In honey bees (Apis mellifera), the epigenetic mark of DNA methylation is central to the developmental regulation of caste differentiation, but may also be involved in additional biological functions. In this study, we examine the whole genome methylation profiles of three stages of the haploid honey bee genome: unfertilised eggs, the adult drones that develop from these eggs and the sperm produced by these drones. These methylomes reveal distinct patterns of methylation. Eggs and sperm show 381 genes with significantly different CpG methylation patterns, with the vast majority being more methylated in eggs. Adult drones show greatly reduced levels of methylation across the genome when compared with both gamete samples. This suggests a dynamic cycle of methylation loss and gain through the development of the drone and during spermatogenesis. Although fluxes in methylation during embryogenesis may account for some of the differentially methylated sites, the distinct methylation patterns at some genes suggest parent-specific epigenetic marking in the gametes. Extensive germ line methylation of some genes possibly explains the lower-than-expected frequency of CpG sites in these genes. We discuss the potential developmental and evolutionary implications of methylation in eggs and sperm in this eusocial insect species. \",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1055,\"status\":\"Completed\\\/Published\",\"term\":\"Summer\",\"year\":2014,\"termid\":\"2013\\\/05\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Robert A Drewell\",\"Eliot C Bush\",\"Emily J Remnant\",\"Garre T Wong\",\"Suzannah M Beeler\",\"Jessica L Stringham\",\"Julianne Lim\",\"Benjamin P Oldroyd\"],\"sort_date\":\"2014-1-01\"},{\"activityid\":1056,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Deciphering the combinatorial architecture of a Drosophila homeotic gene enhancer\",\"Journal Title\":\"Mechanisms of development\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2014,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"131\",\"Issue Number \\\/ Edition\":\"\",\"Page Number(s) or Number of Pages\":\"68-77\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"In Drosophila, the 330 kb bithorax complex regulates cellular differentiation along the anterior\\u2013posterior axis during development in the thorax and abdomen and is comprised of three homeotic genes: Ultrabithorax, abdominal-A, and Abdominal-B. The expression of each of these genes is in turn controlled through interactions between transcription factors and a number of cis-regulatory modules in the neighboring intergenic regions. In this study, we examine how the sequence architecture of transcription factor binding sites mediates the functional activity of one of these cis-regulatory modules. Using computational, mathematical modeling and experimental molecular genetic approaches we investigate the IAB7b enhancer, which regulates Abdominal-B expression specifically in the presumptive seventh and ninth abdominal segments of the early embryo. A cross-species comparison of the IAB7b enhancer reveals an evolutionarily conserved signature motif containing two FUSHI-TARAZU activator transcription factor binding sites. We find that the transcriptional repressors KNIRPS, KRUPPEL and GIANT are able to restrict reporter gene expression to the posterior abdominal segments, using different molecular mechanisms including short-range repression and competitive binding. Additionally, we show the functional importance of the spacing between the two FUSHI-TARAZU binding sites and discuss the potential importance of cooperativity for transcriptional activation. Our results demonstrate that the transcriptional output of the IAB7b cis-regulatory module relies on a complex set of combinatorial inputs mediated by specific transcription factor binding and that the sequence architecture at this enhancer is critical to maintain robust regulatory function.\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1056,\"status\":\"Completed\\\/Published\",\"term\":\"Spring\",\"year\":2014,\"termid\":\"2013\\\/03\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Robert A Drewell\",\"Michael J Nevarez\",\"Je S Kurata\",\"Laure N Winkler\",\"Lily Li\",\"Jacqueline M Dresch\"],\"sort_date\":\"2014-1-01\"},{\"activityid\":1059,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Whole-genome DNA methylation profile of the jewel wasp (Nasonia vitripennis)\",\"Journal Title\":\"G3 (Bethesda, Md.)\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2014,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"4\",\"Issue Number \\\/ Edition\":\"3\",\"Page Number(s) or Number of Pages\":\"383-8\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"The epigenetic mark of DNA methylation, the addition of a methyl (CH3) group to a cytosine residue, has been extensively studied in many mammalian genomes and, although it is commonly found at the promoter regions of genes, it is also involved in a number of different biological functions. In other complex animals, such as social insects, DNA methylation has been determined to be involved in caste differentiation and to occur primarily in gene bodies. The role of methylation in nonsocial insects, however, has not yet been explored thoroughly. Here, we present the whole-genome DNA methylation profile of the nonsocial hymenopteran, the jewel wasp (Nasonia vitripennis). From high-throughput sequencing of bisulfite-converted gDNA extracted from male Nasonia thoraces, we were able to determine which cytosine residues are methylated in the entire genome. We found that an overwhelming majority of methylated sites (99.7%) occur at cytosines followed by a guanine in the 3' direction (CpG sites). Additionally, we found that a majority of methylation in Nasonia occurs within exonic regions of the genome (more than 62%). Overall, methylation is sparse in Nasonia, occurring only at 0.18% of all sites and at 0.63% of CpGs. Our analysis of the Nasonia methylome revealed that in contrast to the methylation profile typically seen in mammals, methylation is sparse and is constrained primarily to exons. This methylation profile is more similar to that of the social hymenopteran species, the honey bee (Apis mellifera). In presenting the Nasonia methylome, we hope to promote future investigation of the regulatory function of DNA methylation in both social and nonsocial hymenoptera. \",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1059,\"status\":\"Completed\\\/Published\",\"term\":\"Spring\",\"year\":2014,\"termid\":\"2013\\\/03\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Suzannah M Beeler\",\"Garre T Wong\",\"Jennifer M Zheng\",\"Eliot C Bush\",\"Emily J Remnant\",\"Benjamin P Oldroyd\",\"Robert A Drewell\"],\"sort_date\":\"2014-1-01\"},{\"activityid\":1048,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Flanking sequence context-dependent transcription factor binding in early Drosophila development\",\"Journal Title\":\"BMC bioinformatics\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2013,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"14\",\"Issue Number \\\/ Edition\":\"\",\"Page Number(s) or Number of Pages\":\"298\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"Gene expression in the Drosophila embryo is controlled by functional interactions between a large network of protein transcription factors (TFs) and specific sequences in DNA cis-regulatory modules (CRMs). The binding site sequences for any TF can be experimentally determined and represented in a position weight matrix (PWM). PWMs can then be used to predict the location of TF binding sites in other regions of the genome, although there are limitations to this approach as currently implemented.\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1048,\"status\":\"Completed\\\/Published\",\"term\":\"Fall\",\"year\":2013,\"termid\":\"2013\\\/01\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Jessica L Stringham\",\"Adam S Brown\",\"Robert A Drewell\",\"Jacqueline M Dresch\"],\"sort_date\":\"2013-9-01\"},{\"activityid\":1057,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Kin conflict in insect societies: a new epigenetic perspective\",\"Journal Title\":\"Trends in ecology & evolution\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2012,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"27\",\"Issue Number \\\/ Edition\":\"7\",\"Page Number(s) or Number of Pages\":\"367-73\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"The social hymenopterans (ants, wasps and bees) have all the enzymatic and genetic mechanisms necessary for the functional modification of DNA by methylation. Methylation appears to play a central role in shaping the developmental processes that give rise to the different castes. However, could DNA methylation have other roles in social insects? Theoretical arguments predict that male and female hymenopterans can be in conflict over the reproductive potential of their female offspring. An exciting prospect for future research is to examine the possibility that queens and males imprint the genomes of their gametes using DNA methylation to manipulate the reproductive potential of their progeny in ways that favour the inclusive fitness of the parent.\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1057,\"status\":\"Completed\\\/Published\",\"term\":\"Summer\",\"year\":2012,\"termid\":\"2011\\\/05\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Robert A Drewell\",\"Nathan Lo\",\"Pete R Oxley\",\"Benjamin P Oldroyd\"],\"sort_date\":\"2012-1-01\"},{\"activityid\":1053,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Molecular dissection of cis-regulatory modules at the Drosophila bithorax complex reveals critical transcription factor signature motifs\",\"Journal Title\":\"Developmental biology\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2011,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"359\",\"Issue Number \\\/ Edition\":\"2\",\"Page Number(s) or Number of Pages\":\"290-302\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"At the Drosophila melanogaster bithorax complex (BX-C) over 330kb of intergenic DNA is responsible for directing the transcription of just three homeotic (Hox) genes during embryonic development. A number of distinct enhancer cis-regulatory modules (CRMs) are responsible for controlling the specific expression patterns of the Hox genes in the BX-C. While it has proven possible to identify orthologs of known BX-C CRMs in different Drosophila species using overall sequence conservation, this approach has not proven sufficiently effective for identifying novel CRMs or defining the key functional sequences within enhancer CRMs. Here we demonstrate that the specific spatial clustering of transcription factor (TF) binding sites is important for BX-C enhancer activity. A bioinformatic search for combinations of putative TF binding sites in the BX-C suggests that simple clustering of binding sites is frequently not indicative of enhancer activity. However, through molecular dissection and evolutionary comparison across the Drosophila genus we discovered that specific TF binding site clustering patterns are an important feature of three known BX-C enhancers. Sub-regions of the defined IAB5 and IAB7b enhancers were both found to contain an evolutionarily conserved signature motif of clustered TF binding sites which is critical for the functional activity of the enhancers. Together, these results indicate that the spatial organization of specific activator and repressor binding sites within BX-C enhancers is of greater importance than overall sequence conservation and is indicative of enhancer functional activity.\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1053,\"status\":\"Completed\\\/Published\",\"term\":\"Fall\",\"year\":2011,\"termid\":\"2011\\\/01\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Michael O Starr\",\"Margaret C Ho\",\"Eric J Gunther\",\"Yen- K Tu\",\"Andrey S Shur\",\"Sara E Goetz\",\"Matthew J Borok\",\"Victoria Kang\",\"Robert A Drewell\"],\"sort_date\":\"2011-9-01\"},{\"activityid\":1054,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Transcription factor binding site redundancy in embryonic enhancers of the Drosophila bithorax complex\",\"Journal Title\":\"G3 (Bethesda, Md.)\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2011,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"1\",\"Issue Number \\\/ Edition\":\"7\",\"Page Number(s) or Number of Pages\":\"603-6\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"The molecular control of gene expression in development is mediated through the activity of embryonic enhancer cis-regulatory modules. This activity is determined by the combination of repressor and activator transcription factors that bind at specific DNA sequences in the enhancer. A proposed mechanism to ensure a high fidelity of transcriptional output is functional redundancy between closely spaced binding sites within an enhancer. Here I show that at the bithorax complex in Drosophila there is selective redundancy for both repressor and activator factor binding sites in vivo. The absence of compensatory binding sites is responsible for two rare gain-of-function mutations in the complex.\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1054,\"status\":\"Completed\\\/Published\",\"term\":\"Fall\",\"year\":2011,\"termid\":\"2011\\\/01\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Robert A Drewell\"],\"sort_date\":\"2011-9-01\"},{\"activityid\":1060,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Transcriptional repression by the proximal exonic region at the human TERT gene\",\"Journal Title\":\"Gene\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2011,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"486\",\"Issue Number \\\/ Edition\":\"1-2\",\"Page Number(s) or Number of Pages\":\"65-73\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"In humans, the enzyme telomerase (hTERT) is responsible for the synthesis of new repeat sequences at the telomeres of chromosomes. Although active in early embryogenesis, the hTERT gene is transcriptionally silenced in almost all somatic cells in the adult, but is aberrantly re-activated in over 90% of human cancers. The molecular mechanisms responsible for repression of this gene are thought to involve the transcription factor CTCF. In this study, we bioinformatically identify putative CTCF binding sites in the hTERT proximal exonic region (PER) and determine their functional relevance in mediating transcriptional silencing at this gene. Tests using a reporter gene assay in HeLa cancer cells demonstrate that a sub-region of the PER exhibits strong transcriptional repressive activity. This repression is independent of the previously identified CTCF binding site near the transcriptional start site of the hTERT gene. In addition, site directed mutagenesis of three predicted CTCF binding sites, including a previously characterized in vivo site in exon 2, does not result in a loss of the repression mediated by the PER. The results from this study indicate that expression of the hTERT gene in HeLa cells is regulated by sequences in the PER. This transcriptional control is mediated through additional regulatory molecular mechanisms, independent of CTCF binding.\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1060,\"status\":\"Completed\\\/Published\",\"term\":\"Fall\",\"year\":2011,\"termid\":\"2011\\\/01\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Teren C Wong\",\"Ethan S Sokol\",\"Alicia N Schep\",\"Meera Punjiya\",\"Di A Tran\",\"Divina Allan\",\"Robert A Drewell\"],\"sort_date\":\"2011-9-01\"},{\"activityid\":1050,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Disruption of the abdominal-B promoter tethering element results in a loss of long-range enhancer-directed Hox gene expression in Drosophila\",\"Journal Title\":\"PloS one\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2011,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"6\",\"Issue Number \\\/ Edition\":\"1\",\"Page Number(s) or Number of Pages\":\"e16283\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"There are many examples within gene complexes of transcriptional enhancers interacting with only a subset of target promoters. A number of molecular mechanisms including promoter competition, insulators and chromatin looping are thought to play a role in regulating these interactions. At the Drosophila bithorax complex (BX-C), the IAB5 enhancer specifically drives gene expression only from the Abdominal-B (Abd-B) promoter, even though the enhancer and promoter are 55 kb apart and are separated by at least three insulators. In previous studies, we discovered that a 255 bp cis-regulatory module, the promoter tethering element (PTE), located 5' of the Abd-B transcriptional start site is able to tether IAB5 to the Abd-B promoter in transgenic embryo assays. In this study we examine the functional role of the PTE at the endogenous BX-C using transposon-mediated mutagenesis. Disruption of the PTE by P element insertion results in a loss of enhancer-directed Abd-B expression during embryonic development and a homeotic transformation of abdominal segments. A partial deletion of the PTE and neighboring upstream genomic sequences by imprecise excision of the P element also results in a similar loss of Abd-B expression in embryos. These results demonstrate that the PTE is an essential component of the regulatory network at the BX-C and is required in vivo to mediate specific long-range enhancer-promoter interactions.\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1050,\"status\":\"Completed\\\/Published\",\"term\":\"Intersession\",\"year\":2011,\"termid\":\"2010\\\/02\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Margaret C Ho\",\"Ben J Schiller\",\"Omar S Akbari\",\"Esther Bae\",\"Robert A Drewell\"],\"sort_date\":\"2011-1-01\"},{\"activityid\":1044,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Characterization of an ultra-conserved putative cis-regulatory module at the mammalian telomerase reverse transcriptase gene\",\"Journal Title\":\"DNA and cell biology\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2010,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"29\",\"Issue Number \\\/ Edition\":\"9\",\"Page Number(s) or Number of Pages\":\"499-508\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"Telomeres are regions of repeated DNA sequence that cap the ends of eukaryotic chromosomes. They act as disposable safeguards to prevent the loss of important genetic information during DNA replication due to the inability of DNA polymerase to replicate DNA to the ends of linear chromosomes. The synthesis of new telomeric repeats using an RNA molecule as a template is catalyzed by the enzyme telomerase. In embryonic stem cells, the gene encoding the catalytic protein subunit of the telomerase complex (telomere reverse transcriptase [TERT]) is transcriptionally active and critical for telomere elongation, allowing for continued cellular differentiation during development. The TERT gene is down-regulated as embryogenesis progresses to limit the proliferative capacity of cells. As a result, in normal human adult somatic cells the TERT gene is silenced. However, in over 90% of cancers, the TERT gene is reactivated, allowing cells to bypass senescence and become immortalized. In this study, we explore the molecular mechanisms that regulate transcriptional expression of the TERT gene. Bioinformatic analysis of the noncoding genomic regions around the human TERT gene identified a TERT ultra-conserved (TUC) module located 5 kb upstream of the transcription start site. This 308 bp region is over 75% conserved between distantly related mammalian species and over 91% conserved among primate species. The cis-regulatory potential of the TUC region was tested in cell-based reporter gene assays. Transient transfections into HeLa and lung fibroblast cells demonstrated that the TUC module has transcriptional enhancer activity. Further bioinformatic analysis revealed that the TUC region is highly enriched in putative transcription factor binding sites for proteins involved during hematopoiesis, indicating that the TUC module may be an enhancer for the TERT gene in specific cell lineages.\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1044,\"status\":\"Completed\\\/Published\",\"term\":\"Fall\",\"year\":2010,\"termid\":\"2010\\\/01\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Di A Tran\",\"Teren C Wong\",\"Alicia N Schep\",\"Robert A Drewell\"],\"sort_date\":\"2010-9-01\"},{\"activityid\":1052,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Dissecting the regulatory switches of development: lessons from enhancer evolution in Drosophila\",\"Journal Title\":\"Development (Cambridge, England)\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2010,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"137\",\"Issue Number \\\/ Edition\":\"1\",\"Page Number(s) or Number of Pages\":\"5-13\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"Cis-regulatory modules are non-protein-coding regions of DNA essential for the control of gene expression. One class of regulatory modules is embryonic enhancers, which drive gene expression during development as a result of transcription factor protein binding at the enhancer sequences. Recent comparative studies have begun to investigate the evolution of the sequence architecture within enhancers. These analyses are illuminating the way that developmental biologists think about enhancers by revealing their molecular mechanism of function.\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1052,\"status\":\"Completed\\\/Published\",\"term\":\"Intersession\",\"year\":2010,\"termid\":\"2009\\\/02\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Matthew J Borok\",\"Di A Tran\",\"Margaret C Ho\",\"Robert A Drewell\"],\"sort_date\":\"2010-1-01\"},{\"activityid\":1051,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"Functional evolution of cis-regulatory modules at a homeotic gene in Drosophila\",\"Journal Title\":\"PLoS genetics\",\"Series Title\":null,\"Month \\\/ Season\":null,\"Year\":2009,\"Publisher\":null,\"Publisher City and State\":null,\"Publisher Country\":null,\"Volume\":\"5\",\"Issue Number \\\/ Edition\":\"11\",\"Page Number(s) or Number of Pages\":\"e1000709\",\"ISSN\":null,\"DOI\":null,\"CoAuthor\":null,\"URL\":null,\"Description\":\"It is a long-held belief in evolutionary biology that the rate of molecular evolution for a given DNA sequence is inversely related to the level of functional constraint. This belief holds true for the protein-coding homeotic (Hox) genes originally discovered in Drosophila melanogaster. Expression of the Hox genes in Drosophila embryos is essential for body patterning and is controlled by an extensive array of cis-regulatory modules (CRMs). How the regulatory modules functionally evolve in different species is not clear. A comparison of the CRMs for the Abdominal-B gene from different Drosophila species reveals relatively low levels of overall sequence conservation. However, embryonic enhancer CRMs from other Drosophila species direct transgenic reporter gene expression in the same spatial and temporal patterns during development as their D. melanogaster orthologs. Bioinformatic analysis reveals the presence of short conserved sequences within defined CRMs, representing gap and pair-rule transcription factor binding sites. One predicted binding site for the gap transcription factor KRUPPEL in the IAB5 CRM was found to be altered in Superabdominal (Sab) mutations. In Sab mutant flies, the third abdominal segment is transformed into a copy of the fifth abdominal segment. A model for KRUPPEL-mediated repression at this binding site is presented. These findings challenge our current understanding of the relationship between sequence evolution at the molecular level and functional activity of a CRM. While the overall sequence conservation at Drosophila CRMs is not distinctive from neighboring genomic regions, functionally critical transcription factor binding sites within embryonic enhancer CRMs are highly conserved. These results have implications for understanding mechanisms of gene expression during embryonic development, enhancer function, and the molecular evolution of eukaryotic regulatory modules.\",\"Include description in output citation\":0,\"Origin\":\"PubMed\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":1051,\"status\":\"Completed\\\/Published\",\"term\":\"Fall\",\"year\":2009,\"termid\":\"2009\\\/01\",\"listingorder\":6,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Margaret C Ho\",\"Holly Johnsen\",\"Sara E Goetz\",\"Ben J Schiller\",\"Esther Bae\",\"Di A Tran\",\"Andrey S Shur\",\"John M Allen\",\"Christoph Rau\",\"Welcome Bender\",\"William W W Fisher\",\"Susan E Celniker\",\"Robert A Drewell\"],\"sort_date\":\"2009-9-01\"},{\"activityid\":13466,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"<p><b><span>Identification of novel components of the retinal determination gene network in Drosophila cell lines<\\\/span><\\\/b><span><\\\/span><\\\/p>\",\"Journal Title\":\"Open Biology\",\"Series Title\":\"\",\"Month \\\/ Season\":\"\",\"Year\":null,\"Publisher\":\"\",\"Publisher City and State\":\"\",\"Publisher Country\":\"\",\"Volume\":\"\",\"Issue Number \\\/ Edition\":\"\",\"Page Number(s) or Number of Pages\":\"\",\"ISSN\":\"\",\"DOI\":\"\",\"CoAuthor\":null,\"URL\":\"\",\"Description\":\"\",\"Include description in output citation\":0,\"Origin\":\"Manual\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":13466,\"status\":\"Revise & Resubmit\",\"term\":\"Spring\",\"year\":2025,\"termid\":\"2024\\\/03\",\"listingorder\":3,\"completionorder\":3},{\"id\":13466,\"status\":\"Revise & Resubmit\",\"term\":\"Summer\",\"year\":2024,\"termid\":\"2023\\\/05\",\"listingorder\":3,\"completionorder\":3}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Robert Drewell\",\"Jacqueline M. Dresch\"],\"sort_date\":\"2000-01-01\"},{\"activityid\":13467,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"<p><b><span>Dissecting the function of the DNMT2-homolog (DNMA) in Dictyostelium discoideum<\\\/span><\\\/b><span><\\\/span><\\\/p>\",\"Journal Title\":\"Genetics\",\"Series Title\":\"\",\"Month \\\/ Season\":\"\",\"Year\":null,\"Publisher\":\"\",\"Publisher City and State\":\"\",\"Publisher Country\":\"\",\"Volume\":\"\",\"Issue Number \\\/ Edition\":\"\",\"Page Number(s) or Number of Pages\":\"\",\"ISSN\":\"\",\"DOI\":\"\",\"CoAuthor\":null,\"URL\":\"\",\"Description\":\"\",\"Include description in output citation\":0,\"Origin\":\"Manual\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":13467,\"status\":\"Submitted\",\"term\":\"Spring\",\"year\":2025,\"termid\":\"2024\\\/03\",\"listingorder\":2,\"completionorder\":2},{\"id\":13467,\"status\":\"Submitted\",\"term\":\"Summer\",\"year\":2024,\"termid\":\"2023\\\/05\",\"listingorder\":2,\"completionorder\":2}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Zaza Gelasvili\",\"Denis A Larochelle\",\"Jacqueline M. Dresch\",\"Maddie Hincher\",\"Javier F Tabima Restrepo\",\"Robert Drewell\"],\"sort_date\":\"2000-01-01\"},{\"activityid\":13468,\"fields\":{\"Type\":\"Articles in Refereed Journals\",\"Title\":\"<p><b><span>Biophysical DNA binding activities of the EVEN-SKIPPED and FUSHI-TARAZU homeodomain transcription factors<\\\/span><\\\/b><span><\\\/span><\\\/p>\",\"Journal Title\":\"Plos Genetics\",\"Series Title\":\"\",\"Month \\\/ Season\":\"\",\"Year\":null,\"Publisher\":\"\",\"Publisher City and State\":\"\",\"Publisher Country\":\"\",\"Volume\":\"\",\"Issue Number \\\/ Edition\":\"\",\"Page Number(s) or Number of Pages\":\"\",\"ISSN\":\"\",\"DOI\":\"\",\"CoAuthor\":null,\"URL\":\"\",\"Description\":\"\",\"Include description in output citation\":0,\"Origin\":\"Manual\"},\"facultyid\":\"C70227051\",\"status\":[{\"id\":13468,\"status\":\"In Progress\",\"term\":\"Spring\",\"year\":2025,\"termid\":\"2024\\\/03\",\"listingorder\":1,\"completionorder\":1},{\"id\":13468,\"status\":\"In Progress\",\"term\":\"Summer\",\"year\":2024,\"termid\":\"2023\\\/05\",\"listingorder\":1,\"completionorder\":1}],\"userid\":\"C70227051\",\"attachments\":[],\"coauthors_list\":[\"Jacqueline M. Dresch\",\"Fadwa Mekkaoui\",\"Don E. Spratt\",\"Robert Drewell\"],\"sort_date\":\"2000-01-01\"}]","cu_faculty_awards_and_grants":"[{\"activityid\":4952,\"fields\":{\"Title\":\"Regulation of\\u202ftwin of eyeless\\u202fin the retinal determination gene network in\\u202fDrosophila\",\"Sponsor\":\"NSF\",\"Grant ID \\\/ Contract ID\":\"\",\"Award Date\":null,\"Start Date\":\"2026-01-01\",\"End Date\":null,\"Period Length\":1,\"Period Unit\":\"Year\",\"Indirect Funding\":1,\"Indirect Cost Rate\":\"50.3\",\"Total Funding\":\"698895\",\"Total Direct Funding\":\"465000\",\"Currency Type\":\"USD\",\"Description\":\"\",\"Abstract\":\"\",\"Number of 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Periods\":4,\"URL\":\"\"},\"facultyid\":\"C70227051\",\"funding\":{\"8452\":{\"id\":8452,\"grantid\":367,\"fundedamount\":\"150300\",\"yearfunded\":1,\"fundedtype\":\"Total\",\"currencytype\":\"USD\",\"startdate\":\"2020-05-01\",\"enddate\":\"2021-05-01\"},\"8453\":{\"id\":8453,\"grantid\":367,\"fundedamount\":\"150300\",\"yearfunded\":2,\"fundedtype\":\"Total\",\"currencytype\":\"USD\",\"startdate\":\"2021-05-01\",\"enddate\":\"2022-05-01\"},\"8454\":{\"id\":8454,\"grantid\":367,\"fundedamount\":\"150300\",\"yearfunded\":3,\"fundedtype\":\"Total\",\"currencytype\":\"USD\",\"startdate\":\"2022-05-01\",\"enddate\":\"2023-05-01\"},\"8455\":{\"id\":8455,\"grantid\":367,\"fundedamount\":\"0\",\"yearfunded\":4,\"fundedtype\":\"Total\",\"currencytype\":\"USD\",\"startdate\":\"2023-05-01\",\"enddate\":\"2024-05-01\"},\"8456\":{\"id\":8456,\"grantid\":367,\"fundedamount\":\"100000\",\"yearfunded\":1,\"fundedtype\":\"Direct\",\"currencytype\":\"USD\",\"startdate\":\"2020-05-01\",\"enddate\":\"2021-05-01\"},\"8457\":{\"id\":8457,\"grantid\":367,\"fundedamount\":\"100000\",\"yearfunded\":2,\"fundedtype\":\"Direct\",\"currencytype\":\"USD\",\"startdate\":\"2021-05-01\",\"enddate\":\"2022-05-01\"},\"8458\":{\"id\":8458,\"grantid\":367,\"fundedamount\":\"100000\",\"yearfunded\":3,\"fundedtype\":\"Direct\",\"currencytype\":\"USD\",\"startdate\":\"2022-05-01\",\"enddate\":\"2023-05-01\"},\"8459\":{\"id\":8459,\"grantid\":367,\"fundedamount\":\"0\",\"yearfunded\":4,\"fundedtype\":\"Direct\",\"currencytype\":\"USD\",\"startdate\":\"2023-05-01\",\"enddate\":\"2024-05-01\"}},\"coauthors\":{\"7860\":{\"authorid\":7860,\"grantid\":367,\"firstname\":\"Robert\",\"middleinitial\":\"\",\"lastname\":\"Drewell\",\"authortype\":\"CoPI\",\"percenteffort\":null,\"sameschoolflag\":1,\"facultyid\":\"C70227051\",\"primaryunitid\":7},\"7861\":{\"authorid\":7861,\"grantid\":367,\"firstname\":\"Jacqueline\",\"middleinitial\":\"M.\",\"lastname\":\"Dresch\",\"authortype\":\"PI\",\"percenteffort\":null,\"sameschoolflag\":1,\"facultyid\":\"C70231168\",\"primaryunitid\":7}},\"status\":[{\"grantid\":367,\"status\":\"Completed\",\"statuslabel\":\"Completed\",\"term\":\"Summer\",\"year\":2024,\"termid\":\"2023\\\/05\",\"listingorder\":4,\"completionorder\":6}],\"userid\":\"C70227051\",\"attachments\":[],\"sort_date\":\"2024-04-30\"},{\"activityid\":366,\"fields\":{\"Title\":\"Decoding cis-regulatory grammar at Hox genes\",\"Sponsor\":\"National Institutes of Health\",\"Grant ID \\\/ Contract ID\":\"1R15GM110571\",\"Award Date\":\"2016-03-14\",\"Start Date\":\"2016-04-01\",\"End Date\":\"2020-03-31\",\"Period Length\":1,\"Period Unit\":\"Year\",\"Indirect Funding\":1,\"Indirect Cost Rate\":\"50.3\",\"Total Funding\":\"450900\",\"Total Direct Funding\":\"300000\",\"Currency Type\":\"USD\",\"Description\":\"\",\"Abstract\":\"\",\"Number of 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