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Mechanistic studies of the RNA chaperone activities of the DEAD-box RNA helicase CYT-19
textStructured RNAs are pervasive in biology, spanning a functional repertoire that includes messengers, regulators of gene expression and catalysts of translation and splicing. From the relatively simple tRNAs and riboswitches to the highly structured ribosomal RNAs, the ability of RNAs to function is dependent on well-defined secondary and tertiary structures. However, studies of RNA folding in vitro have revealed an extreme propensity to form alternative structures, which can be long-lived and interfere with function. In the cell, a diverse array of RNA binding proteins and RNA chaperones guide RNAs towards the correct structure and disrupt misfolded intermediates. Among these proteins, DEAD-box protein family stands out as one of the largest groups, with its members ubiquitously involved in RNA metabolism across all domains of life. DEAD-box proteins can function as both specific and general RNA chaperones by disrupting RNA structures in an ATP-dependent manner. Here I describe my work studying the general RNA chaperone mechanism of the Neurospora crassa protein CYT-19, a model DEAD-box protein and a biological RNA chaperone that is required for efficient folding of self-splicing group I intron RNAs in vivo. After an introduction to DEAD-box proteins and their mechanisms as RNA remodelers (Chapter 1), I will first describe studies of group I intron unfolding by CYT-19, focusing on the effects of RNA tertiary structure stability on CYT-19 activity and targeting to RNA substrates (Chapter 2). I will then describe the characterization of ATP-dependent mechanisms during CYT-19-mediated refolding of the misfolded group I intron (Chapter 3). In Chapter 4, I will present small-angle X-ray scattering (SAXS) studies of structural features of DEAD-box proteins that allow them to efficiently interact with large structured RNA substrates. Finally, I will turn to studies of DEAD-box protein involvement during early steps of RNA compaction and folding, using SAXS and activity-based approaches (Chapter 5). I will conclude with a general discussion of superfamily 2 RNA helicases, which include DEAD-box and related proteins, and their functions and mechanisms as remodelers of structured RNAs and RNPs.Biochemistr
Science Educational Outreach Programs That Benefit Students and Scientists
<div><p>Both scientists and the public would benefit from improved communication of basic scientific research and from integrating scientists into education outreach, but opportunities to support these efforts are limited. We have developed two low-cost programs—"Present Your PhD Thesis to a 12-Year-Old" and "Shadow a Scientist”—that combine training in science communication with outreach to area middle schools. We assessed the outcomes of these programs and found a 2-fold benefit: scientists improve their communication skills by explaining basic science research to a general audience, and students' enthusiasm for science and their scientific knowledge are increased. Here we present details about both programs, along with our assessment of them, and discuss the feasibility of exporting these programs to other universities.</p></div
Survey responses of student participants.
<p>(A–D) The “Present Your PhD Thesis to a 12-Year-Old” program (<i>n</i> = 37) and (E–H) the “Shadow a Scientist” program (<i>n</i> = 31).</p
Survey responses of scientist participants.
<p>(A–E) The “Present Your PhD Thesis to a 12-Year-Old” program (<i>n</i> = 15) and (F–J) the “Shadow a Scientist” program (<i>n</i> = 18).</p