Project-oriented Laboratory Research Articles

Exploring protein structure and dynamics through a project-oriented biochemistry laboratory module.

Here, we present a 10-week project-oriented laboratory module designed to provide a course-based undergraduate research experience in biochemistry that emphasizes the importance of biomolecular structure and dynamics in enzyme function. This module explores the impact of mutagenesis on an important active site loop for a biomedically-relevant human enzyme, protein tyrosine phosphatase 1B (PTP1B). Over the course of the semester students guide their own mutant of PTP1B from conception to characterization in a cost-effective manner and gain exposure to fundamental techniques in biochemistry, including site-directed DNA mutagenesis, bacterial recombinant protein expression, affinity column purification, protein quantitation, SDS-PAGE, and enzyme kinetics. This project-based approach allows an instructor to simulate a research setting and prepare students for productive research beyond the classroom. Potential modifications to expand or contract this module are also provided. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(5):403-410, 2017.

Biomonitoring Laboratory Oriented to Software Applications Development

Abstract This paper presents a project-oriented laboratory. It is intended to provide an educational and research environment that stimulates innovative solutions in the growing field of Bioengineering. The authors took the advantages of the emerging technology and the increasing popularity of wearable biomonitoring devices, to teach students the key elements regarding the application of Information Technology in health monitoring. The students were involved in a complex project, along which they gain basic knowledge about the software development for biomonitoring, and apply it to effectively develop common structures and software applications. There are presented the stages of the laboratory work, with illustrations of the applications implementation at different levels of the hierarchy, starting from collecting data from the biomonitoring device, and finalizing with the data visualization by the end-user.

Heteronuclear Multidimensional Protein NMR in a Teaching Laboratory

Heteronuclear multidimensional NMR techniques are commonly used to study protein structure, function, and dynamics, yet they are rarely taught at the undergraduate level. Here, we describe a senior undergraduate laboratory where students collect, process, and analyze heteronuclear multidimensional NMR experiments using an unstudied Ig domain (Ig2 of human obscurin) in order to sequence-specifically assign this domain. In this way, this project-oriented laboratory tries to simulate an authentic biomolecular NMR research experience. Through the semester, students gain a more thorough understanding of both the specific technical aspects of multidimensional NMR analysis and the process by which raw data are converted into sequence-specific secondary structural information.

Synthesis of Two Local Anesthetics from Toluene: An Organic Multistep Synthesis in a Project-Oriented Laboratory Course

This article describes one of the projects in the advanced undergraduate organic chemistry laboratory course concerning the synthesis of two local anesthetic drugs, prilocaine and benzocaine, with a common three-step sequence starting from toluene. Students undertake, in a several-week independent project, the multistep synthesis of a pharmaceutical drug, comprising instructor-guided tasks such as literature search, planning, critical discussion, experimental design, observation, and results interpretation. In this project, in addition to searching and using information found in primary and secondary sources, students learn to design the methodology for several of the steps in the reaction sequence, bearing in mind safety and environmental concerns.

Integrating Computational Chemistry into a Project-Oriented Biochemistry Laboratory Experience: A New Twist on the Lysozyme Experiment

The biochemistry laboratory at many universities is becoming more focused on a project-oriented experience. For example, a single enzyme is chosen and studied throughout the entire semester. A project-oriented laboratory has been adapted and expanded to include computational and carbohydrate chemistry. Egg-white lysozyme was purified and characterized. To expand and update the experiment, a computational module was added in which a theoretical structure of tri-N-acetylchitotriose was produced through a conformational analysis. The theoretical conformation was compared to the lysozyme-bound conformation, which has been determined through X-ray methods. An aspect of molecular visualization was also used to help the students answer the question, How are carbohydrates recognized by proteins? Overall, students learned the basics of computational chemistry, the subtle aspects of carbohydrate structure, and protein purification and characterization, all within the context of a project-oriented laboratory.

A Project-Oriented Biochemistry Laboratory Course

A project-oriented laboratory course has been designed to introduce students to the study of biochemistry as it is practiced. The course is designed to be a capstone experience for students enrolled in a variety of majors at the Rochester Institute of Technology, including those who enter our new B.S. Biochemistry program. The experiments in this course enable the students to explore the protein chemistry, enzymology, and molecular biology of a single enzyme, threonine dehydrogenase, in a series of integrated experiments. The laboratory incorporates both traditional methods (centrifugation, UV-vis spectroscopy, gel electrophoresis, and chromatography) and more recent developments in the field (polymerase chain reaction). Students use a small computer network to prepare for experiments (using simulation software developed at RIT), to evaluate data, to access sequence homology databases over the Internet, and to visualize and model proteins and nucleic acids. The change in the biochemistry teaching lab from a sequence of unrelated experiments to an integrated series of experiments is a model that can be readily adapted by other educators, who can change their courses to focus on a single enzyme with which they are most familiar.

Isolation and characterization of bacterial DNA: A project-oriented laboratory in physical biochemistry

Isolation and characterization of bacterial DNA: A project-oriented laboratory in physical biochemistry

A Project-Oriented Laboratory Course in Electronics

A project-oriented laboratory course in electronics has been introduced at the University of Lagos. It concerns the penultimate year of the degree program and consists of traditional experiments which are punctuated by short projects. The scheme has produced significant improvement in the final year independent work. Furthermore, student reaction to the scheme is encouraging.