Site-Directed Mutagenesis Study of an Antibiotic-Sensing Noncoding RNA Integrated into a One-Semester Project-Based Biochemistry Lab Course

Abstract

A laboratory sequence is described that is suitable for upper-level biochemistry or molecular biology laboratories that combines project-based and traditional laboratory experiments. In the project-based sequence, the individual laboratory experiments are thematically linked and aim to show how a bacterial antibiotic sensing noncoding RNA (the ykkCD riboswitch) recognizes its target antibiotic, tetracycline. The novelty of the curriculum lies in its extensive coverage of bioinformatics as well as its focus on synthesis, purification, and functional studies of a biologically active RNA. Further advantage of the curriculum is that the model system, the ykkCD riboswitch, regulates expression of a gene that is involved in bacterial antibiotic resistance. Hence, the project makes this important issue part of the undergraduate biochemistry curriculum. The curriculum is available in Open Access format as part of a biochemistry laboratory manual by Gerczei and Pattison. This manuscript summarizes the curriculum and provides suggestions to the instructor regarding its implementation.

An Interdisciplinary, Project-Based Inquiry into the Chemistry and Geology of Alkaline Surface Lake Waters in the General Chemistry Laboratory

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Combining Inquiry-Based and Team-Teaching Models to Design a Research-Driven, Cross-Disciplinary Laboratory Course

“…This technique has been employed by a diverse variety of disciplines, from the sciences to business and marketing courses, with instructors in many fields observing similar positive educational outcomes. , While the specific types of experiences and practices vary from discipline to discipline, the benefits to the students taking those courses are ultimately the same. The new course described in this article is certainly not the first report of inquiry- or research-based pedagogies, nor the first report of a cross-disciplinary, team-teaching approach. − However, it is the combination of these powerful educational techniques described here that is a novel and attractive option for programs looking for additional ways to deepen the engagement of their students.…”

Activation of Split RNA Aptamers: Experiments Demonstrating the Enzymatic Synthesis of Short RNAs and Their Assembly As Observed by Fluorescent Response

“…In recent years, there has been a shift in the aims of scientific education toward developing critical thinking skills as well as a deeper understanding for better conceptual applications . A combination of project-based and expository laboratory experiments in biochemistry has since been used to introduce a comprehensive array of techniques representative of what is currently being done in both academia and industry . Although many such approaches feature one biomoecule for cohesiveness of the teaching lab, only a few focus solely on RNA and its unique functionalities. , With the study of noncoding RNAs as part of the human genome project, it has become apparent that RNA has a multitude of different functions not previously anticipated.…”

“…2 Although many such approaches feature one biomoecule for cohesiveness of the teaching lab, only a few focus solely on RNA and its unique functionalities. 2,3 With the study of noncoding RNAs as part of the human genome project, it has become apparent that RNA has a multitude of different functions not previously anticipated. This has been the impetus for continued RNA research worldwide.…”