Biochemistry Teaching Research Articles

A Semester-Long Learning Path Teaching Computational Skills via Molecular Graphics in PyMOL

ABSTRACT Structural biology describes biological processes at the molecular level and is an integral part of undergraduate study programs in molecular biosciences. Students are often fascinated by the visualizations created by molecular graphics software, which allow them to see the molecular world for the first time. Today, molecular visualization and structural analysis do not require expensive high-end computers but can be performed on the students' own laptops and are therefore highly suited for active learning approaches. We have designed a semester-long learning path that integrates molecular graphics and structural analysis using PyMOL into an undergraduate course in biomolecular structure and function. Compared to stand-alone PyMOL introductions, the semester-long learning path allows for an improved pedagogical design. The path progressively introduces more advanced functions in relevant scientific contexts and allows for spaced repetition. Advanced analysis functions in PyMOL are available only via the command line, so the learning path also teaches basic scripting and serves as an accessible introduction to computational thinking because a few lines of code can produce stunning results. Student surveys carried out at the end of the course suggest that the learning path supported the ability to perform structural analysis to a high degree. Moreover, a simulated exam showed that almost all students were able to carry out basic visualization tasks using PyMOL scripts, while three-quarters could undertake advanced structural analysis after following the course. In summary, integration of molecular graphics software with teaching of structural biochemistry allows a hands-on approach to analyzing molecular mechanisms and introduces biologically oriented students to computational thinking.

Reflections on the 50-year history of the Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB).

The Federation of Asian and Oceanian Biochemists and Molecular Biologists, Inc. (FAOBMB) celebrates its Golden Jubilee in 2022. Established in August 1972 as a regional grouping of three national societies of biochemists in Australia, India and Japan, it took the name Federation of Asian and Oceanian Biochemists (FAOB). The Federation rapidly grew to encompass another 12 national societies (or groups) of biochemists within 6 years, eventually increasing the number of Constituent Members to 21 by 2014. FAOB soon established regular scientific meetings, including triennial Congresses and annual Symposia; from 1980 FAOB Travel Fellowships enabled regional young scientists to participate in them. In 1992, FAOB was constituted as an Incorporated Association in Victoria, Australia, changing its name 1 year later (yielding the acronym FAOBMB). A printed Newsletter/Bulletin was distributed through each Constituent Society or Group from 1972 to 1999. With the advent of the internet and email in the late 1990s, communication rapidly improved, such that the first webpage of FAOBMB was set up in 1995. From the inception of the Federation, an international journal sponsored by FAOB was foreshadowed but only commenced in 1997, sadly lasting only 6 years. Education in biochemistry and molecular biology became prominent in FAOBMB from the 1990s. In the 21st century, awards to high-achieving scientists and educationists were introduced, the first being the Young Scientist Awards in 2006. The Fellowships program was extended to young educationists in 2018. FAOB(MB) has been supported by the International Union of Biochemistry (and Molecular Biology) almost its entire history, mostly for support of Congresses, Conferences and Symposia, but also for Young Scientist Programs. The most recent challenge to FAOBMB came with the COVID-19 pandemic. Executive Committee and the Constituent Members rapidly adapted to virtual communications for their administrative meetings and Education Symposia, and a memorable Congress was held totally on-line in 2021.

Application of problem-based learning combined with a virtual simulation training platform in clinical biochemistry teaching during the COVID-19 pandemic.

The coronavirus disease 2019 (COVID-19) pandemic has had a great impact on the traditional teaching mode (Lecture-based Learning, LBL) and laboratory teaching. To address this challenge, the researchers conducted online Problem-based learning (PBL) teaching and virtual simulation laboratory teaching through DingTalk, and evaluated the effectiveness of this method in teaching clinical biochemistry. With the method of cluster sampling, the researchers randomly selected 60 students from two classes of the Class 2019 as the experimental group for this prospective experimental study. The theory class was taught online PBL through DingTalk, and experimental lectures were given by virtual simulation. After the experimental teaching, students were assessed for theory and operation. Self-administered questionnaires were administered through DingTalk. 65 students from our 2018 medical laboratory class were randomly selected as the control group, and offline LBL and traditional experimental teaching methods were used. Examination results were obtained through teaching portfolios. The experimental group had significantly better examination scores in theoretical knowledge and experimental operational skills than the control group (87.45 ± 5.91 vs. 83.52 ± 9.94, P = 0.0095; 87.08 ± 12.42 vs. 80.18 ± 14.04, P = 0.0044). The results of the questionnaire survey revealed that the experimental group was more receptive to the DingTalk-PBL teaching method and virtual simulation laboratory teaching. Moreover, this hybrid teaching method was more effective in promoting basic knowledge understanding (95.0%, 57/60), facilitating the mastery of operational skills (93.3, 56/60), cultivating interest in learning (96.7%, 58/60), training clinical thinking (95.0%, 57/60), improving communication skills (95.0%, 57/60), and enhancing self-learning ability (91.7%, 55/60) and was more satisfying than traditional teaching method (all P < 0.05). The DingTalk-based PBL method combined with virtual simulation experiments was an effective and acceptable teaching strategy during the pandemic compared with the traditional teaching method.

Comparison of academic performance of medical undergraduate students between routine class room teaching and online assisted teaching in biochemistry during COVID pandemic.

The new curriculum of competency based medical education (CBME) implemented for phase1 medical undergraduates could not go on to completion due to the sudden outbreak of the COVID-19 pandemic. The educational institutions therefore resorted to online teaching modalities over conventional class room teachings. Hence this study aimed to compare the academic performance of students between routine classroom teaching and online assisted teaching with assignments.94 phase 1 MBBS students admitted in the year 2019-2020 was divided into low (<50%), medium (51%-70%) and high performers (71%-100%) based on the average marks in the initial formative assessments. Academic performance of students in three types of teaching modalities namely classroom teaching (CRT), classroom teaching with assignment (CRA), and online assisted teaching (OAT) were compared using ANOVA. Wilcoxon signed ranks test was used to find the difference in marks between CRT and CRA which was calculated as gain 1 and that between OAT and CRT is gain 2. Out of 94 students, 19 were low performers, 53 were medium performers and 22 were high performers when grouped at baseline. All these groups performed significantly well with OAT compared to CRT and CRA. The overall performance of girls was found to be significantly higher. There was no significant difference between Gain 1 and Gain 2. All group of students scored high in assessments following online teaching compared to conventional classroom teaching. The gain of online teaching did not outweigh the conventional teaching methods implying that face to face lectures is still an effective teaching modality.

Exploration and Application of Western Blotting in Comprehensive Experiment Teaching of Biochemistry

Exploration and Application of Western Blotting in Comprehensive Experiment Teaching of Biochemistry

Exploratory application of an integrated topic-based curriculum in biochemistry experimental teaching.

Biochemistry, a complicated basic course in health sciences, plays a fundamental role in describing pathogenic mechanism of illness in molecular terms, and is required to be learned for all medical students. Due to various obstacles to biochemistry learning and teaching, there is a pressing issue of curriculum reform to arouse the student's enthusiasm in biochemistry learning. In this study, an integrated topic-based biochemistry training program (TBBTP) combining the traditional lectures, question-based learning and experimental practices, was introduced in biochemistry teaching. Its effectiveness was evaluated through examination and questionnaire analyses. Consequently, we found that TBBTP promoted the dissemination of biochemical knowledge via traditional lecture, designated learning issues and experimental practices, and acquisition of various skills through practical operation, presentation, and independent learning. It motivated students to study biochemistry with intense interest and enthusiasm. This study explored the feasibility of the topic-based biochemistry teaching as a supplement to biochemistry curriculum in medical education and as a mainstream pedagogy in biochemistry lab.

Comparative Analysis of Student’s Academic Performance in Online and Face to Face Teaching of Biochemistry at HITEC-IMS Taxila

Background: During Covid pandemic the teaching/learning shifted from face to face to online. All institutions around the world developed learning environment for the students to facilitate distant learning. Subsequently assessments also followed online. After opening of the institutions on campus learning and assessments were carried out as usual. Objective: To see the effectiveness of teaching methods (online versus on campus) and to suggest improvement in both methods of teaching. Study Design: Retrospective comparative study Place and Duration of Study: Hitec-IMS, Taxila Pakistan from 1st September 2021 to 29th February 2022. Methodology: One hundred and ninety six academic performances of students in both the methods of learning were enrolled. Using purposive sampling technique, the EOB results of online and on campus were analyzed. Results: The better performance of student in term of summative assessments during online learning. Conclusion: Students found online environment better for learning and performing during examinations. Keywords: HITEC-IMS (Hitec Institute of Medical Sciences), NUMS (National University of Medical Sciences), EOB (end of block)

IMPLEMENTASI E-MODUL METABOLISME PROTEIN DALAM PEMBELAJARAN BIOKIMIA UNTUK MENINGKATKAN KEMAMPUAN BERPIKIR KRITIS

Appropriate media and learning resources can optimize learning innovations in the 21st century. The use of technology has become an efficient alternative in the implementation of learning. This research aims to implement the protein metabolism electronic modules (e-modules) as biochemistry teaching materials to improve students’ critical thinking (CT) skills. This research refers to comparative quantitative nonparametric methods by comparing measurements of CT skills before applying e-modules during the lesson with the height of CT skills after using the e-module. The e-modules include videos, images, animations, links to various primary sources, and formative tests that follow the learning outcomes. As the result, the advancement of CT skills from the final measurements illustrated a reduction in the number of students categorized as bad and poor and an increasing number of students categorized as good and excellent. Furthermore, the skill improvement can also be seen through the Two Tail T-Test, with a tcount of 4.7752, while the ttable value for the Two Tail T-Test of 2.0262. Since tcount &gt; ttable suggests a significant difference between the initial and final measurement scores test, H0 is rejected, and H1 is accepted. This research concludes that there is an increase in students' CT skills after participating in biochemistry learning using this protein metabolism e-module.

Bioluminescence Color-Tuning Firefly Luciferases: Engineering and Prospects for Real-Time Intracellular pH Imaging and Heavy Metal Biosensing.

Firefly luciferases catalyze the efficient production of yellow-green light under normal physiological conditions, having been extensively used for bioanalytical purposes for over 5 decades. Under acidic conditions, high temperatures and the presence of heavy metals, they produce red light, a property that is called pH-sensitivity or pH-dependency. Despite the demand for physiological intracellular biosensors for pH and heavy metals, firefly luciferase pH and metal sensitivities were considered drawbacks in analytical assays. We first demonstrated that firefly luciferases and their pH and metal sensitivities can be harnessed to estimate intracellular pH variations and toxic metal concentrations through ratiometric analysis. Using Macrolampis sp2 firefly luciferase, the intracellular pH could be ratiometrically estimated in bacteria and then in mammalian cells. The luciferases of Macrolampis sp2 and Cratomorphus distinctus fireflies were also harnessed to ratiometrically estimate zinc, mercury and other toxic metal concentrations in the micromolar range. The temperature was also ratiometrically estimated using firefly luciferases. The identification and engineering of metal-binding sites have allowed the development of novel luciferases that are more specific to certain metals. The luciferase of the Amydetes viviani firefly was selected for its special sensitivity to cadmium and mercury, and for its stability at higher temperatures. These color-tuning luciferases can potentially be used with smartphones for hands-on field analysis of water contamination and biochemistry teaching assays. Thus, firefly luciferases are novel color-tuning sensors for intracellular pH and toxic metals. Furthermore, a single luciferase gene is potentially useful as a dual bioluminescent reporter to simultaneously report intracellular ATP and/or luciferase concentrations luminometrically, and pH or metal concentrations ratiometrically, providing a useful tool for real-time imaging of intracellular dynamics and stress.

Championing the Involvement of Practitioners in the Biochemistry Educational Research Process: A Phenomenological View of the Early Stages of Collaborative Action Research

The disparity between post-secondary STEM instruction and the practices suggested in education and cognitive research is not a novel issue. Despite evidence-based practices being available to practitioners, traditional lecture-based instruction continues to dominate higher STEM education. In this study, we discussed practitioner involvement in biochemistry education research as a potential means to address the gap between research and practice. We used phenomenology as a lens through which to view faculty experiences of participating in a team-based curricular redesign. We administered a concept inventory to examine undergraduate students’ understanding of key concepts and to identify misconceptions. We captured faculty perspectives and reflections on student data through semi-structured interviews, finding that faculty dissatisfaction with traditional practices were rooted in experiences from early on in their teaching careers. Their students demonstrated a lack of conceptual understanding, similar to findings of other studies in undergraduate biochemistry, and key misconceptions the student population held were identified. When examining students’ conceptual understanding data, the faculty gained new insights into where students struggle in the course that they would not have gained without participation in this project. This reinforced their desire to implement curricular change. These findings add to the available data on students’ conceptual understanding in biochemistry and suggest that shared assessments like concept inventories can unify instructors as they engage in team-based curricular reform.

Exploration on the Mode of "Online Teaching + Course Ideological and Political" in Biochemistry

For the integrated development of online and offline education, teachers tap the ideological and political elements in biochemistry based on the software such as rain classroom, questionnaire star, blue ink cloud class and Tencent classroom and the actual situation of undergraduates, so as to organically integrate online teaching, curriculum ideological and political education and biochemistry. This paper introduces the exploration and practice of biochemistry and curriculum ideological politics from four aspects: the necessity of curriculum ideological politics, the mining of Ideological and political teaching elements of Biochemistry, the practical ways of online teaching and curriculum ideological politics, and the online evaluation of curriculum ideological politics. Combined with the author's practical experience, it provides reference for the interspersed of biochemical education and curriculum ideological politics in Colleges and universities.

Gesticulating Biochemistry: Exploring the Impact of using Augmented Reality Models on Students’ Usage of Gestures when Talking about Biochemistry

There are multiple examples in the literature highlighting the connection between gestures and meaning‐making by students learning chemical concepts in chemistry; however, there is little known about whether this connection extends to student learning in biochemistry. Moreover, learning biochemistry often involves the use and coordination of multiple external representations (ranging from 2D illustrations and physical models to 3D virtual models) of macromolecules. How does use of these external representations impact student gesture production and meaning‐making when learning new biochemical content? In this study, we used a newly developed augmented reality (AR) model of the KscA channel to investigate the influence of external representations on student produced gestures during a discussion on KscA function. We focused on several research questions: what are the different biochemistry content knowledge that students express through gestures? What are the different types of gestures and patterns of gesture production used by students to express content knowledge? What are the differences, if any, in student produced gestures before and after the introduction of an AR model? What are the relationships between student produced gestures and the AR model? Semi‐structured clinical interviews were conducted and recorded through Zoom. Seven undergraduate students who enrolled in an upper‐division biochemistry course participated in the interview. During the interview, participants were presented with an AR model of KcsA channel after proposing a theory of how potassium ions move through the channel. Participants were then asked to modify their theory. In the first stage of analysis, interview participants’ utterances were transcribed and their gestures were described in terms of hand shape and movement. The identification of unique gestures as part of the coding process highlighted the importance of hand shape vs movement vs a combination of both as ways to delineate different gestures. In the second stage of analysis, qualitative and quantitative differences in student gesture production were identified through a comparative analysis of student gestures before and after their exposure to the AR model. Exposure to the AR model resulted in a shift from gestures that were more general (for example, holding two hands parallel to represent the channel) to more specific to the channel representation they say (for example, holding two hands to form a funnel shape or curling one hand into a tube shape). Our findings add to existing literature on the use of external representation in biochemistry education by highlighting the relationships between AR mediated external representations and gesture mediated external representations. Implications for both the development of new external representations and instructor’s choice of external representations are discussed.

Randomised controlled monocentric trial to compare the impact of using professional actors or peers for communication training in a competency-based inverted biochemistry classroom in preclinical medical education

ObjectiveIn medical education, biochemistry topics are usually knowledge based, and students often are unaware of their clinical relevance. To improve students’ awareness of the relevance, we integrated communication skills training...

Moving biochemistry and molecular biology courses online in times of disruption

When the COVID‐19 pandemic necessitated a rapid pivot to online instruction, a team of faculty teaching biochemistry and molecular biology courses created a resource to help other educators approach online education. The group, comprised of educators with experience teaching hybrid and fully online courses, described their strategies in areas like course design, promoting engagement, and assessing student performance. Each topic has a dedicated webpage with brief recommendations, along with a curated list of links to relevant reading, videos, and resources. The American Society for Biochemistry and Molecular Biology (ASBMB) supported the project by hosting the resource on their website (https://www.asbmb.org/education/online‐teaching). At this time, I was transitioning into a position focused on curriculum redesign; one key goal was to introduce discussion sections into a biochemistry course for majors. Drawing from the team’s ideas to promote online engagement, I designed many of these activities using a collaborative whiteboard tool. These activities have now been successfully implemented both online and in‐person, and offer flexibility to instructors and students as we continue to develop engaging activities for hybrid and blended courses.

Pengembangan Suplemen Bahan Ajar Biokimia Dasar Materi Hormon Berbasis Kearifan Lokal Masyarakat Desa Pasti Jaya

The purpose of this study was to produce a supplement of basic biochemical teaching materials based on local wisdom of medicinal plants of the Pasti Jaya village community on appropriate hormone materials. The type of research used is Research and Development (R&amp;D) which refers to research procedures according to Borg &amp; Gall which have been simplified by the Center for Policy Research and Educational Innovation (Puslitjaknov) team, namely analyzing developed products, developing initial products, validating and revising, conducting small-scale field trials and revisions, as well as large-scale field trials and final products. Due to time constraints, the stages in this study were limited to the third stage, so that these stages were adjusted to the needs of the research. The resulting product was validated by 9 experts for each aspect of language, material, and graphics. The data collection technique used a feasibility validation questionnaire measurement technique which showed the validation results of all aspects with a very feasible category, respectively 96.3%, 95%, and 93.7% so that it was concluded that the supplement of basic biochemistry teaching materials based on local wisdom of the Pasti village community Jaya on the hormone material developed deserves to be tested in further research.

How useful is post-graduate education in biochemistry for entry into the South African labour market?

Biochemistry encompasses a broad range of life science disciplines. Unlike more vocational disciplines such as pharmacy or medicine, the career path associated with biochemistry is less clearly defined. An important question is whether the skills set provided by post-graduate biochemistry education, defined as BSc (Hons.), MSc, or PhD degrees, is aligned with the requirements of a career in academia or industry. This article reports on former post-graduate biochemistry students and their careers and aims to establish whether former post-graduate students perceive a post-graduate qualification in biochemistry as useful for entry into the job market. This article is based on responses of 64 former post-graduate biochemistry students from South African universities who have graduated between 2010 and 2019. Findings show that most post-graduate biochemistry graduates continue a career in academia after graduating. Some pursue a career in the industry, while a very small number of biochemistry post-graduates are currently unemployed. These findings suggest that a post-graduate degree in biochemistry provides the necessary scientific and research skills sought after by the employment sector in South Africa.

Using e-learning tools in biochemistry teaching for undergraduate medical students in multicultural environment in Ukraine during COVID-19 crisis.

Through the special situation like the COVID‐2019 lockdown, interactive techniques play a prime role in the study process. The strategy of lockdown ways of higher education was provided in Ukraine as well as in other countries since March 2020. Our investigation was performed at the Department of Biochemistry and Medical Chemistry of Dnipro State Medical University during the first lockdown of COVID‐19 from March to June 2020. The main aim of the research was the evaluation of the students' attitudes to studying Biochemistry using Google classrooms and Moodle. Four hundred and sixty‐three students studying in English, French, and Ukrainian took part in the survey. Our results reveal that majority of the students found Google classrooms and Moodle as useful e‐learning tools. However, questions dealing with the technical issues of using the Google classrooms on laptops and mobile phones and submitting the replies to the Google classrooms cause difficulties among the students.

COMPARATIVE STUDY OF CASE BASED LEARNING WITH TRADITIONAL TEACHING METHODS IN BIOCHEMISTRY FOR FIRST YEAR MEDICAL STUDENTS

Background: Case based learning (CBL), is a learning method aids learner to reorganize, elaborate their information and provide connection between current and new information. Moreover CBL is student centered, taken in small groups where teacher acts as facilitator or guide. This study was planned to perceive the need for initiating CBL, this study aimed to compare the biochemistry teaching among rst year medical students with that of traditional teaching. Methods This is an observational study conducted from August 2021 to December 2021. This research study was conducted on 99 students of First year MBBS students. Ten ideal case scenarios on the topic of protein energy malnutrition(PEM) in children and acid base balance were prepared, and pre validated by the faculty of Biochemistry, Paediatrics and Surgery medical education department in our institution. CBL was introduced and total three sessions were conducted and compared with traditional teaching. Results The mean (±SD) value of the score of gain in knowledge was 3.90±1.86 (n=99) for the batch of students who attended case based learning while the mean (±SD) gain in knowledge for the batch who underwent, traditional learning ( TL) was 2.60±2.29 (n=99). A paired t-test comparing didactic lectures with self-directed learning showed that the scores following didactic lectures were more compared to SDL and the results were statistically signicant. An unpaired t-test comparing case based learning to SDL also showed statistically signicant gain in knowledge following didactic lectures. Conclusion This study clearly showed that CBL is more effective over traditional teaching for our rst year MBBS students and for covering a wider area.

Benefits and challenges in the implementation of virtual laboratory simulations (vLABs) for medical biochemistry in Indonesia.

The pandemic caused major shifts in the delivery of education worldwide. In the teaching of medical biochemistry, the greatest impact was towards the delivery of traditional laboratory simulations. In this study, we highlight the benefits and barriers encountered in the use of virtual laboratories (vLABs) to substitute traditional laboratory practicals. The subjects were a class of 271 medical students at the Faculty of Medicine, Hasanuddin University, all freshman undergoing the Biomedicine Block. The study assessed the use of a commercial vLAB on antibodies and blood typing procedures, which were implemented using our four-step model of vLAB implementation. Collected data include the lecturer-assigned pre- and post-test result, built-in vLAB assessment result of the student first and best attempts, a student perception questionnaire based on a 5-point Likert scale, and an open ended questionnaire regarding student perceptions of the advantages and disadvantages of the vLAB. We observed a remarkable increase of lecturer assigned pre- and post-test scores and built-in first and best attempt scores (p < 0.0001, Wilcoxon signed rank test). A majority of students reported increased motivation when using the vLABs, and favored the ability of mastery through repetition. However, technical and language barriers were highlighted by students during the vLAB implementation. We demonstrate a successful implementation of commercial vLABs in a cohort of non-native English speakers using our four-step approach. Implementation requires strong support from faculty to address technical and language barriers that arise during use of vLABs.

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.