Publications

β-Lactamases in the biochemistry and molecular biology laboratory

This study compared an old, standard curriculum with a newer curriculum that uses the pGLO Bacterial Transformation kit in a biochemistry and molecular biology laboratory class. The kit was used as the basis for student mini–research projects to study antibiotic resistance.

In the paper's conclusion, the researchers note that "the overall results seem to be very consistent in the sense that students who were enrolled in the new curriculum seemed to be more enthusiastic when answering the questions. This enthusiasm may be explained by their participation in these classes. During the trimester they seem very interested to participate in the new tasks, but also referred that they had to work more in order not to forget important concepts from previous laboratory exercises. This increased (student) investment may also explain the differences observed between the grades of the two groups of students."

Reference Amador P et al. (2009). β-Lactamases in the biochemistry and molecular biology laboratory. Biochem Mol Biol Education 37, 301–306. (PDF)

Abstract β-lactamases are hydrolytic enzymes that inactivate the β-lactam ring of antibiotics such as penicillins and cephalosporins. The major diversity of studies carried out until now have mainly focused on the characterization of β-lactamase recovered among clinical isolates of Gram-positive staphylococci and Gram-negative enterobacteria, amongst others. However, only some studies refer to the detection and development of β-lactamase carriers in healthy humans, sick animals, or even in strains isolated from environmental stocks such as food, water, or soils. Considering this, we proposed a 10-week laboratory program for the Biochemistry and Molecular Biology laboratory for majors in the health, environmental, and agronomical sciences. During those weeks, students would be dealing with some basic techniques such as DNA extraction, bacterial transformation, polymerase chain reaction (PCR), gel electrophoresis, and the use of several bioinformatics tools. These laboratory exercises would be conducted as a mini–research project in which all the classes would be connected with the previous ones. This curriculum was compared in an experiment involving two groups of students from two different majors. The new curriculum, with classes linked together as a mini–research project, was taught to Pharmacy majors, and an old curriculum was taught to Environmental Health students. The results showed that students who were enrolled in the new curriculum obtained better results in the final exam than the students who were enrolled in the former curriculum. Likewise, these students were found to be more enthusiastic during the laboratory classes than those from the former curriculum.

Protein Expression and Purification Series — A Laboratory Course for Training Researchers

For an overview of how the Protein Expression and Purification Series provides hands-on laboratory experience with the full sequence of protein purification and analysis, read this article in BioRadiations to see some of the many topics that can be addressed with this series.

Teaching biochemistry and molecular biology using dihydrofolate reductase as an expression system

This poster explores the use of the Protein Expression and Purification Series to gain experience with a wide range of different techniques. In this series, students follow a sequence of standard research laboratory procedures to purify and analyze expression of the enzyme dihydrofolate reductase (DHFR). Techniques used include protein purification, enzyme activity measurement, protein electrophoresis, western blotting, PCR, transformation into competent cells, restriction digestion, and bioinformatics analysis. Students generate mutant DHFR by designing primers for site-directed mutagenesis and compare their mutant’s activity to that of the wild type.

DHFR is often used as a model system because it is found in both prokaryotes and eukaryotes and displays highly conserved sequences at the active sites. Additionally, DHFR is important in cell proliferation, and DHFR inhibitors such as methotrexate are used in cancer treatment, making this a topical subject.

The authors conclude that the Protein Expression and Purification Series provides hands-on experience in a wide array of techniques using a real-world model system.

Reference Lau JM and Gilbert M (2012). Teaching biochemistry and molecular biology using dihydrofolate reductase as an expression system. ASBMB Annual Meeting A383 620.5 (PDF)

Summary In this project, students not only gained hands-on experience with a multitude of standard laboratory techniques (e.g., protein purification, measurement of specific enzyme activity, western blot analysis, PCR amplification, transformation into competent cells, restriction digestion, and bioinformatics), but they also have the opportunity to design and implement cutting-edge research approaches to the study of a critical enzyme. All student groups successfully purified DHFR and detected His and GST tags by western blot analysis. A PCR product was obtained by three of the four groups by site-directed mutagenesis (results from week 9; data not shown). Mutant DHFR showed a 32–122% decrease in activity relative to the wild-type protein. However 18–155% increases were also obtained (data not shown). DNA sequencing and protein alignments confirmed that the mutations were successfully introduced into the DHFR gene.

Effectiveness of a cloning and sequencing exercise on student learning with subsequent publication in the National Center for Biotechnology Information GenBank

This manuscript describes an assessment of the Cloning and Sequencing Explorer Series in the classroom. There were several goals. Students were assessed to determine whether they gained competence in widely used laboratory techniques. The level of familiarity with bioinformatics and proficiency in specific uses of bioinformatics software (including contigs, translation, and intron/exon boundaries) were evaluated. Additionally, an objective was the identification of unique DNA sequences that could be published (with instructor and students as coauthors) in the National Center for Biotechnology Information (NCBI) GenBank.

The students used the modules in the series to clone a housekeeping gene, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), from a plant species or cultivar not yet in GenBank. Students were assessed before, during, and after completing the series. The assessment showed that student confidence with laboratory techniques and instrumentation was increased as was knowledge of bioinformatics tools. The authors state, "We feel that this exercise is a unique opportunity for students to be involved in a research process that eventually leads to a tangible end product, which is rather unusual for an educational exercise aimed at the undergraduate, or even high school, level."

Reference Lau JM and Robinson DL (2009). Effectiveness of a cloning and sequencing exercise on student learning with subsequent publication in the National Center for Biotechnology Information GenBank. CBE Life Sci Edu 8, 326-37. PMID: 19952101 (Free PMC article)

Abstract With rapid advances in biotechnology and molecular biology, instructors are challenged to not only provide undergraduate students with hands-on experiences in these disciplines but also to engage them in the “real-world” scientific process. Two common topics covered in biotechnology or molecular biology courses are gene cloning and bioinformatics, but to provide students with a continuous, laboratory-based research experience in these techniques is difficult. To meet these challenges, we have partnered with Bio-Rad Laboratories in the development of the “Cloning and Sequencing Explorer Series,” which combines wet-lab experiences (e.g., DNA extraction, polymerase chain reaction, ligation, transformation, and restriction digestion) with bioinformatics analysis (e.g., evaluation of DNA sequence quality, sequence editing, Basic Local Alignment Search Tool searches, contig construction, intron identification, and six-frame translation) to produce a sequence publishable in the National Center for Biotechnology Information GenBank. This 6–8-week project-based exercise focuses on a pivotal gene of glycolysis (glyceraldehyde-3-phosphate dehydrogenase), in which students isolate, sequence, and characterize the gene from a plant species or cultivar not yet published in GenBank. Student achievement was evaluated using pre-, mid-, and final-test assessments, as well as with a survey to assess student perceptions. Student confidence with basic laboratory techniques and knowledge of bioinformatics tools were significantly increased upon completion of this hands-on exercise.

Cloning and Sequencing the GAPC Gene of Delospermia cooperi

This poster was presented at the 2013 Idaho INBRE (IDeA Network of Biomedical Research Excellence, funded by NIH) meeting. The two student authors both won Scholars of the Year awards. Using the Cloning and Sequencing Series, DNA was isolated from a recently divergent succulent plant species, amplified by PCR, cloned, and sequenced. In their conclusions, the students stated that "we believe that we have gained knowledge of many of the procedures using in genomic cloning and sequencing along with an appreciation for the genetic theories behind these methods".

Reference Rhinehart B et al. (2013). Cloning and Sequencing the GAPC Gene of Delospermia Cooperi. Idaho INBRE Meeting. (PDF)

Conclusions on Poster Through multiple confirmation tests conducted during the cloning process, along with comparisons of the deciphered genomic sequence against previously published works in genomic libraries, it was concluded that the Delospermia cooperi GAPC gene had been successfully sequenced. Though it was confirmed that the target gene originated from the Delospermia cooperi GAPC gene, the protein sequence differed by four amino acids from a previous attempt to sequence the gene. This is a significant enough difference that further sequencing experiments need to be confirmed to verify the correct sequence. Through the many successes and failures we encountered during the project, we believe that we have gained knowledge of many of the procedures using in genomic cloning and sequencing along with an appreciation for the genetic theories behind these methods.

Assessment of an ELISA Laboratory Exercise

This study used the ELISA Immuno Explorer kit to evaluate learning and teaching principles. Alternate laboratory scenarios and supplementary exercises were used in three different courses (Forensic Sciences, Cell Biology, and Drugs and the Human Body) aimed at two populations of students: those in General Biology classes and those starting a Biological Sciences track.

The assessment demonstrated that after use of the kit there were significant levels of learning about basic immunology, ELISA, and interpretation of results. Additionally, student levels of confidence increased, partially due to the 100% success rate with the kit.

Reference Robinson DL and Lau JM (2012). Assessment of an ELISA Laboratory Exercise. The American Biology Teacher 74, 558–563. (PDF)

Abstract The enzyme-linked immunosorbent assay (ELISA) is a powerful immunological technique for quantifying small amounts of compounds and has been used in research and clinical settings for years. Although there are laboratory exercises developed to introduce the ELISA technique to students, their ability to promote student learning has not been thoroughly assessed. We found that a commercially available ELISA kit increased student performance on pre- and post-tests in three undergraduate college courses, especially in those taught to general-education students. Student confidence levels about ELISA methodology, as well as comfort level in performing the technique, increased significantly in both general- education and biology-major courses.

Engineering Technology Curricula

The expanding complexity of biotechnology is making it critical for students to have an understanding of the basics of the relevant science. This publication describes the implementation of a new biotechnology course based on the Bio-Rad Biotechnology Explorer modules. The aim was to increase the hands-on exposure to genomics, proteomics, and bioinformatics for students with diverse backgrounds.

Clase K (2008). Design and Implementation of an Interdepartmental Biotechnology Program Across Engineering Technology Curricula. J Technol Studies 34, 12–19. (PDF)

Abstract The health industry is an important and growing economic engine. Advances are being made in pharmaceutical and biotechnology discoveries and their applications (including manufacturing) as well as in health care services. As a result, there is an increasing sophistication of the products and services available and being developed, with an ever-widening scale of applications and marketing, producing an ever-expanding need for college graduates who have knowledge of life science–based products and processes. There have been numerous reports of current and projected shortages of human resources possessing the required knowledge in the growing industry. The objectives of this paper are to describe the implementation of a biotechnology program that crosses discipline boundaries, integrates science and technology, and attracts a diverse group of students. The curriculum addresses critical workforce needs and teaches students the content knowledge and skills of emerging biotechnology industries.