Natalie Kuldell

Authentic teaching and learning through synthetic biology

Synthetic biology is an emerging engineering discipline that, if successful, will allow well-characterized biological components to be predictably and reliably built into robust organisms that achieve specific functions. Fledgling efforts to design and implement a synthetic biology curriculum for undergraduate students have shown that the co-development of this emerging discipline and its future practitioners does not undermine learning. Rather it can serve as the lynchpin of a synthetic biology curriculum. Here I describe educational goals uniquely served by synthetic biology teaching, detail ongoing curricula development efforts at MIT, and specify particular aspects of the emerging field that must develop rapidly in order to best train the next generation of synthetic biologists.

Site-Directed Mutagenesis to Improve Sensitivity of a Synthetic Two-Component Signaling System.

Two-component signaling (2CS) systems enable bacterial cells to respond to changes in their local environment, often using a membrane-bound sensor protein and a cytoplasmic responder protein to regulate gene expression. Previous work has shown that Escherichia coli’s natural EnvZ/OmpR 2CS could be modified to construct a light-sensing bacterial photography system. The resulting bacterial photographs, or “coliroids,” rely on a phosphotransfer reaction between Cph8, a synthetic version of EnvZ that senses red light, and OmpR. Gene expression changes can be visualized through upregulation of a LacZ reporter gene by phosphorylated OmpR. Unfortunately, basal LacZ expression leads to a detectable reporter signal even when cells are grown in the light, diminishing the contrast of the coliroids. We performed site-directed mutagenesis near the phosphotransfer site of Cph8 to isolate mutants with potentially improved image contrast. Five mutants were examined, but only one of the mutants, T541S, increased the ratio of dark/light gene expression, as measured by β-galactosidase activity. The ratio changed from 2.57 fold in the starting strain to 5.59 in the T541S mutant. The ratio decreased in the four other mutant strains we examined. The phenotype observed in the T541S mutant strain may arise because the serine sidechain is chemically similar but physically smaller than the threonine sidechain. This may minimally change the protein’s local structure, but may be less sterically constrained when compared to threonine, resulting in a higher probability of a phosphotransfer event. Our initial success pairing synthetic biology and site-directed mutagenesis to optimize the bacterial photography system’s performance encourages us to imagine further improvements to the performance of this and other synthetic systems, especially those based on 2CS signaling.

MIT’s Introduction to Biological Engineering: A Longitudinal Study of a Freshman Inquiry-Based Class

Abstract We describe an introductory class in biological engineering that uses project-based and mentored inquiry to create a supportive, exciting, and effective learning environment. Freshman students at MIT work in small teams and with senior MIT students to design a biotechnology that addresses a real-world challenge of their choosing. Students gain familiarity with the tools and vocabulary for biodesign first through some hands-on experiences with synthetic biological systems and later by working in teams to define, present and then refine their ideas. A multiyear study of the class experience and impact included postsurveys and semistructured interviews of two freshman cohorts and a retrospective survey of three freshman cohorts. Data support the claim that students perceive academic gains through their project-based classroom experience. Freshmen reported they are better able to understand content in some of their other MIT courses, are better able to read scientific articles, and now think differently about biology. Moreover, they indicated the class was valuable in learning technical content and synthetic biology. We find this project-based class helps students make meaningful connections to scientific ideas, to personal goals and to a vision of their future selves.

The Multiple Cellular Functions of TFIIIA

Transcription factor IIIA (TFIIIA) is a single polypeptide with several distinct functions in the cell. In this chapter I will review the role of TFIIIA in transcription initiation of the 5S rRNA gene. I will also describe the model by which TFIIIA associates with the 5S rRNA itself to regulate ribosome biosynthesis and assembly. Finally, I will compare these functions of TFIIIA in various eukaryotic cells, from yeast to vertebrate. In all cases, the part played by the protein’s zinc fingers will be emphasized.