An undergraduate research experience in CRISPR-Cas9 mediated eukaryotic genome editing to teach fundamental biochemistry techniques.

CRISPR-Cas9 technology is an established, powerful tool for genome editing through the ability to target specific DNA sequences of interest for introduction of desired genetic modifications. CRISPR-Cas9 is utilized for a variety of purposes, ranging from a research molecular biology tool to treatment for human diseases. Due to its prominence across a variety of applications, it is critical that undergraduates in the life sciences are educated on CRISPR-Cas9 technology. To this end, we created an intensive eight-week long course-based undergraduate research experience (CURE) designed for students to understand CRISPR-Cas9 genome editing and perform it in Saccharomyces cerevisiae. Students enrolled in the CURE participate in 2, 3-h sessions a week and are engaged in the entire process of CRISPR-Cas9 genome editing, from preparation of genome editing reagents to characterization of mutant yeast strains. During the process, students master fundamental techniques in the life sciences, including sterile technique, Polymerase Chain Reaction (PCR), primer design, sequencing requirements, and data analysis. The course is developed with flexibility in the schedule for repetition of techniques in the event of a failed experiment, providing an authentic research experience for the students. Additionally, we have developed the course to be easily modified for the editing of any yeast gene, offering the potential to expand the course in research-driven classroom or laboratory settings.

E!Canasta: A card game to teach ATP synthesis and metabolic regulation in biochemistry classes.

Understanding ATP formation is essential for learning metabolism and is central to grasping metabolic processes as a whole. However, due to the high level of abstraction, the number of intermediate substrates, the connections, and integrated regulation, its comprehension often poses a challenge. This and the fact that traditional teaching methods struggle when dealing with highly abstract concepts, game-based strategies present a more concrete and dynamic alternative, which led to the creation of E!Canasta (card game). Developed based on Canasta and adapted in order to improve the learning of concepts, including some of pathway's regulation and integration, E!Canasta motivates students and promotes engagement in a fun activity. Students assemble a sequence of cards representing the glycolysis, acetyl-CoA, Krebs cycle, and electron transport chain, which correspond to the card suits. Strategically, some of the cards hold special feats that simulate some aspects of metabolic regulation and integration (to give or take away points). At the end of the game, points are added up for sequences and cards with positive or negative effects. The game was played with two classes of students enrolled in biochemistry as part of their graduations (86 players). Student perception on gameplay, motivation and understanding was measured through an anonymous Likert scale questionnaire, with very positive results in all questions. Statistically significant correlations were observed regarding the perceived comprehension of pathways and their regulation, and in linking motivation with a positive gaming experience, showcasing that E!Canasta demonstrates considerable educational potential, along with an enjoyable experience for learning ATP synthesis.

A cost-effective enzyme kinetics and inhibition model for biochemistry education and research.

Enzyme kinetics and inhibition studies are crucial in biochemistry education and research. Conventional methods often require expensive equipment and reagents, potentially limiting their accessibility in limited resource settings. Our approach sought to develop a cost-effective experimental design for studying enzyme kinetics and inhibition. Lactase was chosen as a protein model and its activity was investigated by measuring glucose production from lactose hydrolysis. In the study, commercially available lactase pills were used as an enzyme source, while milk was used as a substrate. Instead of scientific equipment, glucometers were used to measure lactase activity. Enzyme kinetics were evaluated using Michaelis-Menten and Lineweaver-Burk plots. In the study, the effects of temperature, pH, and inhibitors were also investigated. The results of our study aligned with established enzyme kinetics theories and previous studies. Lactase showed temperature and pH-dependent activity, with decreased activity observed at both low and high extremes. Results also showed that galactose acts as a competitive inhibitor of lactase. The approach presented here offers a cost-effective procedure for studying enzyme kinetics and inhibition. It can act as a valuable tool for educational purposes and for preliminary research in settings with limited resources.

Problem-based learning (PBL) application in 'metabolic syndrome (MetS)' among common diseases of the modern age: A case study.

The present study was to teach metabolic syndrome (MetS) disease through a scenario developed according to the problem-based learning (PBL) approach in the biochemistry class. The study was designed as a single group pre-test and post-test research. The study group consisted of first-year students (N = 183) from the nursing department within the health sciences faculty of a state university in Turkey. The study findings indicated that PBL increased students' understanding and learning performances about MetS. It may be suggested that those learned by the scenario developed according to the PBL are effective in learning about the MetS.

Fidelity of Implementation as a Guiding Framework for Transitioning Research-Based Instructional Practices from On Site to Online.

In this Perspective, we contribute to the Journal of Microbiology & Biology Education special issue "Opportunities and Challenges of Online Instruction-Blurring the Lines Between Online and On-Site Teaching and Learning" by introducing a framework to guide instructors in transitioning from on-site to online instruction. The discipline-based education research community has produced a significant literature base demonstrating the effectiveness of various research-based instructional practices (RBIPs) that support student learning in face-to-face environments. However, little is known about how to transport these practices into the online environment. We introduce fidelity of implementation (FOI) as a framework for considering how to adapt RBIPs for online contexts while maintaining the integrity of the aspects of the practice that are thought to support student learning. We use our own experience responding to the global pandemic to provide rich examples of how FOI was used to anticipate challenges in transitioning online and describe how it was used to adapt an RBIP for online instruction.

The transition from the biochemistry laboratory to home discovery during COVID-19.

As a result of the COVID-19 pandemic, it is crucial for an introductory course in biochemistry to move from in-person instruction to total remote learning. There are four transferable skills in the course: problem-solving, laboratory psychomotor skills, data analysis and interpretation skills, and presentation skills. Since all lab buildings were closed for learning activities, we responded quickly to ensure the transferability of the skills. We modified the laboratory activity as a home discovery approach to achieve the desired skills. Students showed confidence and gratitude as they learned in a new way. In summary, modifying the laboratory activity helped students acquire laboratory-related skills but presented challenges in using laboratory equipment. This suggests that Home Discovery can be considered a hybrid approach to learning biochemistry.

"Involve Me and I Learn": Active Learning in a Hybrid Medical Biochemistry First Year Course on an American-Style MD Program in the UAE.

Perceived as a subject with abstract jargon, requiring extensive memorization of complex metabolic pathways, chemical structures, and names, students lose sight of the significance of biochemistry on their MD journey (Afshar M, Han Z. Teaching and learning medical biochemistry: Perspectives from a student and an educator. Med Sci Educ. 2014;24:339-41.). A disconnect between what is taught in the classroom and its application to clinical settings arises through over emphasis on the need to pass board exams, documented to be a poor measure of core competencies. Employing active learning strategies with meaningful activities with clinical applications, centered around the curriculum, cognitively engages students and is a deviation from the didactic way in which biochemistry is traditionally taught.

Perspective on pros and cons of microlearning in health education.

Recently, digital technology and digital materials have started to be widely used in education from primary school to college worldwide. Microlearning is one of the innovative teaching techniques that use digital technologies. In this review, benefits and disadvantages of microlearning is discussed. Many studies show that microlearning facilitated learning by dividing into smaller pieces encourages students to study. A wide range of activities might be used in this technique and it can be easily integrated into daily routine, it allows on-demand learning for the students. On the other hand, the success of microlearning techniques is closely related to the personal characteristics of learners, teachers' prone to use digital technology and the external factors such as access to learning materials. Its effectiveness on behavior and outcome which were defined in the third and fourth levels of Kirkpatrick's learning model is still obscure. In the light of the literature, it should be decided which microlearning method will be used for which educational subjects.

Mapping research on biochemistry education: A bibliometric analysis.

The purpose of this study was to map the research literature on Biochemistry education, covering the scientific production indexed on the Web of Science over the past 66 years. The open-source Bibliometrix R-package, an R-tool, was used to carry out the bibliometric analysis. Our results describe (1) how many articles were published per year and what is the annual average growth rate; (2) which are the core journals, authors, and publications in the field; (3) which countries and funding agencies contribute most to the development of research in the area; (4) the leading collaborative research and co-citation networks; (5) which articles were the most cited in the past 10 years; and (6) which are the trending topics in the field. Our main contribution is offering insights into the evolution of the field. Also, the use of a quantitative methodological design, which covers a large volume of publications, and could identify possible gaps in the area.

Made for students, by students: Integrating former-student voices into a de-densified biochemistry laboratory.

The COVID-19 pandemic emphasized the importance of peer communication networks for student outcomes. Herein, we describe the use of supplemental instructional videos created by former students and integrated into electronic lab notebooks, to restore the lost community-learning component using student voices in a de-densified upper-division biochemistry laboratory.

Student design and characterization of visible DHFR fusions for biochemistry tools to improve learning during lab exercises.

Student feedback from an undergraduate biochemistry lab course suggested the use of visibly traceable proteins may assist learning. Based on this feedback, we used guided inquiry lab exercises where students developed and characterized a suite of fluorescent protein-dihydrofolate reductase (DHFR) fusions as tools for a biochemistry teaching lab. In contrast to the unfused versions, members of this suite are well-expressed, soluble, visible, highly stable, and easily characterized. The color of mCherry and EGFP fluorescent fusions with microbial DHFR allows students to visibly track their target protein from expression through purification under ambient light, while fusions with BFP are visible under UV-light. Fusions were made to both wild-type and kinetically enhanced DHFR variants. Importantly, we found that fluorescent protein fusions with DHFR did not kinetically interfere as the KM and kcat values were not remarkably altered from the unfused variant. With these fusions, students can easily measure kinetic parameters under steady-state conditions with readily available substrate and common laboratory spectrophotometers. Additionally, students also determined IC50 values of trimethoprim for DHFR. These exercises can be completed in a series of up to six lab periods and we have included the protocols for instructors who wish undertake a similar series of experiments in their biochemistry teaching labs. Using these visible fusion enzymes with subsequent students, we observed potential learning gains on a course assessment and received positive student feedback. We suggest that the often over-looked element of visual cues in a biochemistry lab may be an exploitable component of learning.

Using online simulations to teach biochemistry laboratory content during COVID-19.

At the University of South Australia (UniSA), Biochemistry is a second year undergraduate course. The student cohort is diverse, with students enrolled in courses with a laboratory focus, such as Laboratory Medicine, Medical Science, Nutrition and Food Science and Pharmaceutical Science. The course is taught in a traditional manner, with weekly lectures, fortnightly tutorials and three practical sessions. In response to the growing numbers of COVID-19 cases, in mid-March the University leadership moved to cease face-to-face teaching. By this time, 58 of 96 students had completed the first two (of three) face-to-face laboratory practicals. In response to this decision, teaching of all practical based content was moved online for all students. The first question was, how do we teach practical content online? And secondly, how do we teach hands-on skills? The first question was addressed using a suite of online simulations, progressively developed since 2013. Simulations are widely used and shown to be useful as teaching aids in STEM. A total of five simulations were introduced each covering key aspects of laboratory practice, including fundamental mathematical skills, reading, and setting a pipette, basic Biochemistry assays, protein quantification, and enzyme kinetics. The second issue of teaching hands on skills was addressed once restrictions were eased. Students were invited to attend the laboratory to learn the kinesthetic skills with instructor guidance. Both approaches used proved to be highly effective and can be readily adapted not only to teaching Biochemistry, but any aspect of science education.

Bibliometric analysis of the brazilian periodical journal of biochemistry education.

The bibliometric analysis of the Brazilian periodical Journal of Biochemistry Education (JBE) covered the 117 articles published in 15 volumes in the period 2001-2017. Our results showed a positive trend in JBE publications with a significant increase in the number of articles since 2014, which can be related to the increase in research groups working in this area. The Southeast region of Brazil was the most productive one mainly due to the contribution of papers from institutions located in the State of São Paulo. Only four articles aimed the undergraduate courses (87.0%) showing methodological approaches to teach biochemistry (51.3%) and laboratory exercises (18.8%) among others. Most of the 332 authors contributed to a single article (87.7%) and just 3% of them published more than twice in JBE. The majority of the JBE articles had at least one citation in Google Scholar. There is also a great variety in the references used by the authors. Our analysis showed that JBE is an important peer reviewed publication aimed to improve teaching and learning of Biochemistry in Brazil. © 2019 International Union of Biochemistry and Molecular Biology, 47(3):249-256, 2019.

Characterization of the recombinant (R)- and (S)-hydroxypropyl-coenzyme M dehydrogenases: A case study to augment the teaching of enzyme kinetics and stereoselectivity.

A homologous pair of stereospecific NAD-dependent enzymes, (R)- and (S)-hydroxypropyl-coenzyme M dehydrogenase, are part of a bacterial pathway of short-chain alkene and epoxide metabolism. Their discovery and study, which spans multiple publications over more than a decade, is a data rich story that combines both classical and contemporary experimental biochemistry. A subset of the data for characterization of the recombinant enzymes was used as a case study to augment the teaching of enzyme kinetics and stereoselectivity in an undergraduate biochemistry course at California State University-Chico. © 2018 International Union of Biochemistry and Molecular Biology, 47(2): 124-132, 2019.

Improving large class performance and engagement through student-generated question banks.

Disciplines such as Biochemistry and Molecular Biology, which involve concepts not included in the high-school curriculum, are very challenging for many first year university students. These subjects are particularly difficult for students accustomed to surface learning strategies involving memorization and recall of facts, as a deeper understanding of the relationship between concepts is needed for successful transfer to related areas and subsequent study. In this article, we explore an activity in a very large first year Molecular Biology course, in which students create multiple-choice questions related to targeted learning outcomes, and then answer and evaluate one another's questions. This activity encompasses elements of both self- and peer-assessment and the generative tasks of creating questions and producing written feedback may contribute to a deeper understanding of the material. We make use of a free online platform to facilitate all aspects of the process and analyze the effect of student engagement with the task on overall course performance. When compared to previous semester's cohorts, we observe a pronounced improvement in class performance on exam questions targeting similar concepts to the student-generated questions. In addition, those students that engage to a greater extent with the activity perform significantly better on the targeted exam questions than those who are less active, yet all students perform similarly on a set of isolated control questions appearing on the same exam. © 2018 by The International Union of Biochemistry and Molecular Biology, 46:306-317, 2018.

The Topology Prediction of Membrane Proteins: A Web-Based Tutorial.

There is a great need for development of educational materials on the transfer of current bioinformatics knowledge to undergraduate students in bioscience departments. In this study, it is aimed to prepare an example in silico laboratory tutorial on the topology prediction of membrane proteins by bioinformatics tools. This laboratory tutorial is prepared for biochemistry lessons at bioscience departments (biology, chemistry, biochemistry, molecular biology and genetics, and faculty of medicine). The tutorial is intended for students who have not taken a bioinformatics course yet or already have taken a course as an introduction to bioinformatics. The tutorial is based on step-by-step explanations with illustrations. It can be applied under supervision of an instructor in the lessons, or it can be used as a self-study guide by students. In the tutorial, membrane-spanning regions and α-helices of membrane proteins were predicted by internet-based bioinformatics tools. According to the results achieved from internet-based bioinformatics tools, the algorithms and parameters used were effective on the accuracy of prediction. The importance of this laboratory tutorial lies on the facts that it provides an introduction to the bioinformatics and that it also demonstrates an in silico laboratory application to the students at natural sciences. The presented example education material is applicable easily at all departments that have internet connection. This study presents an alternative education material to the students in biochemistry laboratories in addition to classical laboratory experiments.

Impact of Virtual Patients as Optional Learning Material in Veterinary Biochemistry Education.

Biochemistry and physiology teachers from veterinary faculties in Hannover, Budapest, and Lublin prepared innovative, computer-based, integrative clinical case scenarios as optional learning materials for teaching and learning in basic sciences. These learning materials were designed to enhance attention and increase interest and intrinsic motivation for learning, thus strengthening autonomous, active, and self-directed learning. We investigated learning progress and success by administering a pre-test before exposure to the virtual patients (vetVIP) cases, offered vetVIP cases alongside regular biochemistry courses, and then administered a complementary post-test. We analyzed improvement in cohort performance and level of confidence in rating questions. Results of the performance in biochemistry examinations in 2014, 2015, and 2016 were correlated with the use of and performance in vetVIP cases throughout biochemistry courses in Hannover. Surveys of students reflected that interactive cases helped them understand the relevance of basic sciences in veterinary education. Differences between identical pre- and post-tests revealed knowledge improvement (correct answers: +28% in Hannover, +9% in Lublin) and enhanced confidence in decision making ("I don't know" answers: -20% in Hannover, -7.5% in Lublin). High case usage and voluntary participation (use of vetVIP cases in Hannover and Lublin >70%, Budapest <1%; response rates in pre-test 72% and post-test 48%) indicated a good increase in motivation for the subject of biochemistry. Despite increased motivation, there was only a weak correlation between performance in final exams and performance in the vetVIP cases. Case-based e-learning could be extended and generated cases should be shared across veterinary faculties.

Why should biochemistry students be introduced to molecular dynamics simulations--and how can we introduce them?

Molecular dynamics (MD) simulations play an increasingly important role in many aspects of biochemical research but are often not part of the biochemistry curricula at the undergraduate level. This article discusses the pedagogical value of exposing students to MD simulations and provides information to help instructors consider what software and hardware resources are necessary to successfully introduce these simulations into their courses. In addition, a brief review of the MD-based activities in this issue and other sources are provided.

Commentary: PhDs in biochemistry education-5 years later.

In this commentary, the discussion of PhDs in biochemistry education research is expanded to explore a number of diverse pathways leading to a competitive research program in biochemistry education research.