A laboratory-intensive course on RNA interference and model organisms

A "Choose-Your-Own" Classroom-Based Activity That Promotes Scientific Inquiry about RNA Interference

RNA interference (RNAi), the process that results in the degradation of a target gene's mRNA, is a fundamental part of eukaryotic gene regulation and is also an important molecular technique that allows for experimental manipulation of gene expression without altering DNA sequences. Despite the importance of RNAi, there have been relatively few lecture-based activities designed to teach about the consequences of this process and counter common misconceptions. I present here an inquiry-based activity that is centered around a "choose your own experiment" design where students generate hypotheses and critically evaluate their ideas by choosing several simulated experiments. The activity presents students with one of the original puzzling observations, the discovery that triggering overexpression of a given gene in a flower resulted in an opposite change in phenotype than expected, and the subsequent discovery that there was a dramatic decrease of that gene's mRNA, that sparked the discovery of RNAi. Students then propose a molecular mechanism for these results before using a limited budget of funding to simulate their choice of experiments. Simulated results are provided for these experiments, and students must work together to interpret and discuss these results before deciding on the next experiment. I provide a guide for instructors on how to implement this activity, with suggestions on how to vary the activity to fit different class sizes as well as an abbreviated version for instructors who are short on time. Finally, I include an aligned assessment so that instructors may check student learning about the impacts of RNAi.

An investigative graduate laboratory course for teaching modern DNA techniques

This graduate-level DNA methods laboratory course is designed to model a discovery-based research project and engages students in both traditional DNA analysis methods and modern recombinant DNA cloning techniques. In the first part of the course, students clone the Drosophila ortholog of a human disease gene of their choosing using Gateway^® cloning. In the second part of the course, students examine the expression of their gene of interest in human cell lines by reverse transcription PCR and learn how to analyze data from quantitative reverse transcription PCR (qRT-PCR) experiments. The adaptability of the Gateway^® cloning system is ideally suited for students to design and create different types of expression constructs to achieve a particular experimental goal (e.g., protein purification, expression in cell culture, and/or subcellular localization), and the genes chosen can be aligned to the research interests of the instructor and/or ongoing research in a department. Student evaluations indicate that the course fostered a genuine excitement for research and in depth knowledge of both the techniques performed and the theory behind them. Our long-term goal is to incorporate this DNA methods laboratory as the foundation for an integrated laboratory sequence for the Master of Science degree program in Molecular and Cellular Biology at Quinnipiac University, where students use the reagents and concepts they developed in this course in subsequent laboratory courses, including a protein methods and cell culture laboratory. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):351-359, 2017.

Epigenetics and allergy: from basic mechanisms to clinical applications

Allergic diseases are on the rise in the Western world and well-known allergy-protecting and -driving factors such as microbial and dietary exposure, pollution and smoking mediate their influence through alterations of the epigenetic landscape. Here, we review key facts on the involvement of epigenetic modifications in allergic diseases and summarize and critically evaluate the lessons learned from epigenome-wide association studies. We show the potential of epigenetic changes for various clinical applications: as diagnostic tools, to assess tolerance following immunotherapy or possibly predict the success of therapy at an early time point. Furthermore, new technological advances such as epigenome editing and DNAzymes will allow targeted alterations of the epigenome in the future and provide novel therapeutic tools.

Using Tinbergen's Four Questions as the Framework for a Neuroscience Capstone Course

Capstone courses for upper-division students are a common feature of the undergraduate neuroscience curriculum. Here is described a method for adapting Nikolaas Tinbergen's four questions to use as a framework for a neuroscience capstone course, in this case with a particular emphasis on neurotoxins. This course is intended to be a challenging opportunity for students to integrate and apply knowledge and skills gained from their major study, a B.S. in Biological Sciences with a Concentration in Integrative Physiology and Neurobiology. In particular, a broad, integrative approach is favored, with emphasis placed on primary literature, scientific process and effective, professional communication. To achieve this, Tinbergen's four questions were adapted and implemented as the overarching framework of the course. Tinbergen's questions range from the proximate to ultimate/evolutionary view, providing an excellent base upon which to teach students an integrative approach to understanding neuroscientific phenomena. For example, a particular neurotoxin can be examined from the proximate level (i.e., mechanism: how does this toxin specifically impact neural physiology) to the ultimate/evolutionary level (i.e., adaptation: why and to what extent did this toxin evolve naturally or the reason that it was initially invented by humans). The mechanics, goals, and objectives of the course are presented as we believe that it will serve as a flexible and useful model for neuroscience capstone courses concerning a wide variety of topics across multiple types of institutions.

Immunological tools: engaging students in the use and analysis of flow cytometry and enzyme-linked immunosorbent assay (ELISA)

Flow cytometry and enzyme-linked immunosorbent assay (ELISA) are commonly used techniques associated with clinical and research applications within the immunology and medical fields. The use of these techniques is becoming increasingly valuable in many life science and engineering disciplines as well. Herein, we report the development and evaluation of a novel half-semester course that focused on introducing undergraduate and graduate students to advance conceptual and technical skills associated with flow cytometry and ELISA, with emphasis on applications, experimental design, and data analysis. This course was offered in the North Carolina State University Biotechnology Program over three semesters and consisted of weekly lectures and laboratories. Students performed and/or analyzed flow cytometry and ELISA in three separate laboratory exercises: (1) identification of transgenic zebrafish hematopoietic cells, (2) analysis of transfection efficiency, and (3) analysis of cytokine production upon lipopolysaccharide stimulation. Student learning outcomes were achieved as demonstrated by multiple means of assessment, including three laboratory reports, a data analysis laboratory practicum, and a cumulative final exam. Further, anonymous student self-assessment revealed increased student confidence in the knowledge and skill sets defined in the learning outcomes.

A contemporary, laboratory-intensive course on messenger RNA transcription and processing

Messenger ribonucleic acid (mRNA) plays a pivotal role in the central dogma of molecular biology. Importantly, molecular events occurring during and after mRNA synthesis have the potential to create multiple proteins from one gene, leading to some of the remarkable protein diversity that genomes hold. The North Carolina State University Biotechnology Program developed and implemented a new, laboratory-intensive course to provide students with a contemporary view of mRNA entitled "mRNA: Transcription and Processing." This course, offered at both the undergraduate and graduate levels, aimed to introduce students to the many functions of RNA, with an emphasis on mRNA. In addition to fundamental aspects of these processes, students were exposed to cutting-edge techniques used to analyze mRNA in both lecture and laboratory components. We evaluated this course over two semesters and found that learning outcomes were met by both undergraduate and graduate students, based on assessments such as laboratory reports, pre-lab assignments, a final exam, and successful results in the laboratory. We also examined student perceptions through anonymous surveys, where students reported gains in confidence in both conceptual knowledge and technical skill after completing this course.

Student learning outcomes and attitudes when biotechnology lab partners are of different academic levels

The North Carolina State University Biotechnology Program offers laboratory-intensive courses to both undergraduate and graduate students. In "Manipulation and Expression of Recombinant DNA," students are separated into undergraduate and graduate sections for the laboratory, but not the lecture, component. Evidence has shown that students prefer pairing with someone of the same academic level. However, retention of main ideas in peer learning environments has been shown to be greater when partners have dissimilar abilities. Therefore, we tested the hypothesis that there will be enhanced student learning when lab partners are of different academic levels. We found that learning outcomes were met by both levels of student, regardless of pairing. Average undergraduate grades on every assessment method increased when undergraduates were paired with graduate students. Many of the average graduate student grades also increased modestly when graduate students were paired with undergraduates. Attitudes toward working with partners dramatically shifted toward favoring working with students of different academic levels. This work suggests that offering dual-level courses in which different-level partnerships are created does not inhibit learning by students of different academic levels. This format is useful for institutions that wish to offer "boutique" courses in which student enrollment may be low, but specialized equipment and faculty expertise are needed.

Studying human disease genes in Caenorhabditis elegans: a molecular genetics laboratory project

Scientists routinely integrate information from various channels to explore topics under study. We designed a 4-wk undergraduate laboratory module that used a multifaceted approach to study a question in molecular genetics. Specifically, students investigated whether Caenorhabditis elegans can be a useful model system for studying genes associated with human disease. In a large-enrollment, sophomore-level laboratory course, groups of three to four students were assigned a gene associated with either breast cancer (brc-1), Wilson disease (cua-1), ovarian dysgenesis (fshr-1), or colon cancer (mlh-1). Students compared observable phenotypes of wild-type C. elegans and C. elegans with a homozygous deletion in the assigned gene. They confirmed the genetic deletion with nested polymerase chain reaction and performed a bioinformatics analysis to predict how the deletion would affect the encoded mRNA and protein. Students also performed RNA interference (RNAi) against their assigned gene and evaluated whether RNAi caused a phenotype similar to that of the genetic deletion. As a capstone activity, students prepared scientific posters in which they presented their data, evaluated whether C. elegans was a useful model system for studying their assigned genes, and proposed future directions. Assessment showed gains in understanding genotype versus phenotype, RNAi, common bioinformatics tools, and the utility of model organisms.

A laboratory-intensive course on the experimental study of protein-protein interactions

The study of protein-protein interactions is important to scientists in a wide range of disciplines. We present here the assessment of a lab-intensive course that teaches students techniques used to identify and further study protein-protein interactions. One of the unique elements of the course is that students perform a yeast two-hybrid screen and identify novel protein-protein interactions in what is essentially the beginning of an independent research project in the context of a class. While students benefit from the research-like experience, data is actively generated that can be further studied in independent research projects. Student learning outcomes were assessed using a questionnaire that was given to students before and after the course. The results indicate that students' conceptual and technical understanding of the methodologies taught in the class increased, and that hands-on experience in the lab was perceived to be the most important component of the course.