Tuning DNA binding and gene expression using zinc finger proteins and engineered promoters

Synthetic biology provides an ideal approach to build functional biological devices by assembling biological parts. Using synthetic biology, efficient control of gene regulation may be achieved to a degree that is not possible using natural genetic structures.1 However, previous studies on promoter engineering have focused on natural transcription factors (TFs),2 including the lac repressor, which produces a switch-like “all-or-none” response.3 In this project, we worked to develop a new system for transcriptional control based on tunable synthetic TFs, which are designed to yield programmable linear responses in gene expression. To accomplish this, we used zinc finger proteins (ZFPs) as regulators of engineered promoters assayed by green fluorescent protein (GFP) as a fluorescent transcriptional reporter probe. In particular, we designed strong-binding three finger ZFPs as proof-of-principle regulatory elements, with the intention of moving to weaker binding two finger ZFPs and the addition of the accessory binding module PAR (part of the protein Adr1).4 To generate engineered promoters, we integrated ZFP binding sites into known promoters of varying strength. To analyze the engineered activity of each promoter, we cultured E. coli cells transformed with plasmids containing sequences for both ZFP production and our engineered promoters and measured the resulting fluorescence intensity. In this way, we constructed a novel method for tuning gene expression as well as testing the DNA binding affinity of synthetic TFs. We anticipate that this general approach could be used in the future for designing and characterizing synthetic TFs for gene therapy and gene regulation applications

Leaders Like Me

The Workshop Program at the University of Rochester infuses collaborative learning into a variety of introductory STEM and non-STEM courses through small, weekly, peer-led problem solving sessions called Workshops. Decades of data from these Workshops indicate that 1) African American, Black, Hispanic, and Latinx students are less likely to attend them than White and Asian students and 2) that every additional Workshop students attend improves their final course grades, even if they only miss a single Workshop out of the 13 or 14 that are offered each semester. To address this situation, the UR Workshop Program has partnered with the People Like Me project at Bucknell University. Before the start of the Fall 2018 semester, Workshop leaders were asked to respond to the People Like Me survey questions, and we crafted their responses into profiles. We then posted these profiles for students in the courses to view on a platform on which we could track those views at the individual student level. In this work-in-progress, we hope to answer the question: to what extent does viewing personal information about Workshop leaders affect students\u27 likelihood to attend Workshops

Engineering Education Research

This chapter describes several aspects of engineering education research with an emphasis on how they might relate to computing education research. We briefly summarize the history of engineering education as a scholarly field, and we describe the current structures that support engineering education research: academic departments, scholarly journals, annual conferences, and professional societies. We identify the theories that often inform engineering education research studies, including theories of cognition, motivation, and identity. We explain how quantitative, qualitative, and mixed methods have been used. We summarize the results of an illustrative selection of empirical studies across a broad range of topics, including instructional methods, student development, faculty teaching practices, diversity, and assessment. Finally, we outline some similarities and differences between computing education research and engineering education research. Engineering education research has a longer history of research in professional development and assessment but an arguably shorter history in pre-college education and less international integration than computing education research

Improving motivation and engagement in core engineering courses with student teams

Team-based projects are common in capstone engineering design courses and increasingly common in first-year engineering programs. Despite high enrollments and budget cutbacks affecting many programs, second- and third-year students can also benefit from team-based project experiences, which motivate them to succeed in engineering and prepare them for a globally competitive workforce. My dissertation research demonstrates that team design projects can be incorporated into the curricula of engineering departments, and these projects result in positive affective outcomes for students. Using ABET outcomes and Self Determination Theory (SDT) as the background for my studies, I investigated students' confidence, motivation, and sense of community after experiencing team design projects in two different engineering departments at a large public institution. In the first study, I used a sequential mixed methods approach with a primary quantitative phase followed by an explanatory qualitative phase to evaluate a chemical engineering program that integrated team design projects throughout the curriculum. The evaluation methods included a survey based on desired ABET outcomes for students and focus groups to expand on the quantitative results. Students reported increased confidence in their design, teamwork, and communication skills after completing the projects. In my second and third studies, I used qualitative interviews based on SDT to explore student motivation in an electrical and computer engineering course redesigned to support students' intrinsic motivation to learn. SDT states that intrinsic motivation to learn is supported by increasing students' sense of autonomy, competence, and relatedness in regard to their learning. Using both narrative inquiry and phenomenological methodologies, I analyzed data from interviews of students for mentions of autonomy, competence, and relatedness as well as course events that were critical in changing students' motivation. Analysis revealed that individual choice, constructive failures, and a strong sense of community in the classroom were critical to moving students toward intrinsic motivation. Further, community building through team experiences characterized the essence of the student experience in the course. My research highlights a need for better quantitative measures of students' affective outcomes, specifically motivation, in the context of a single course. Based on the results of my studies, SDT should be reevaluated in terms of possible interdependencies between autonomy, competence, and relatedness, and how the social context of large engineering courses may create a deeper need for supporting relatedness

Improving Motivation and Engagement in Core Engineering Courses with Student Teams

Team-based projects are common in capstone engineering design courses and increasingly common in first-year engineering programs. Despite high enrollments and budget cutbacks affecting many programs, second- and third-year students can also benefit from team-based project experiences, which motivate them to succeed in engineering and prepare them for a globally competitive workforce. My dissertation research demonstrates that team design projects can be incorporated into the curricula of engineering departments, and these projects result in positive affective outcomes for students. Using ABET outcomes and Self Determination Theory (SDT) as the background for my studies, I investigated students’ confidence, motivation, and sense of community after experiencing team design projects in two different engineering departments at a large public institution. In the first study, I used a sequential mixed methods approach with a primary quantitative phase followed by an explanatory qualitative phase to evaluate a chemical engineering program that integrated team design projects throughout the curriculum. The evaluation methods included a survey based on desired ABET outcomes for students and focus groups to expand on the quantitative results. Students reported increased confidence in their design, teamwork, and communication skills after completing the projects. In my second and third studies, I used qualitative interviews based on SDT to explore student motivation in an electrical and computer engineering course redesigned to support students’ intrinsic motivation to learn. SDT states that intrinsic motivation to learn is supported by increasing students’ sense of autonomy, competence, and relatedness in regard to their learning. Using both narrative inquiry and phenomenological methodologies, I analyzed data from interviews of students for mentions of autonomy, competence, and relatedness as well as course events that were critical in changing students’ motivation. Analysis revealed that individual choice, constructive failures, and a strong sense of community in the classroom were critical to moving students toward intrinsic motivation. Further, community building through team experiences characterized the essence of the student experience in the course. My research highlights a need for better quantitative measures of students’ affective outcomes, specifically motivation, in the context of a single course. Based on the results of my studies, SDT should be reevaluated in terms of possible interdependencies between autonomy, competence, and relatedness, and how the social context of large engineering courses may create a deeper need for supporting relatedness.National Science Foundation / DUE-1140554U of I Onlythesi