Exploring Undergraduate Biochemistry Students' Gesture Production Through an Embodied Framework.

Interpreting three-dimensional models of biological macromolecules is a key skill in biochemistry, closely tied to students' visuospatial abilities. As students interact with these models and explain biochemical concepts, they often use gesture to complement verbal descriptions. Here, we utilize an embodied cognition-based approach to characterize undergraduate students' gesture production as they described and interpreted an augmented reality (AR) model of potassium channel structure and function. Our analysis uncovered two emergent patterns of gesture production employed by students, as well as common sets of gestures linked across categories of biochemistry content. Additionally, we present three cases that highlight changes in gesture production following interaction with a 3D AR visualization. Together, these observations highlight the importance of attending to gesture in learner-centered pedagogies in undergraduate biochemistry education.

A simple method to resolve rate constants when the binding mechanism obeys induced fit or conformational selection.

Many interactions involving a ligand and its molecular target are studied by rapid kinetics using a stopped-flow apparatus. Information obtained from these studies is often limited to a single, saturable relaxation that is insufficient to resolve all independent rate constants even for a two-step mechanism of binding obeying induced fit (IF) or conformational selection (CS). We introduce a simple method of general applicability where this limitation is overcome. The method accurately reproduces the rate constants for ligand binding to the serine protease thrombin determined independently from the analysis of multiple relaxations. Application to the inactive zymogen precursor of thrombin, prethrombin-2, resolves all rate constants for a binding mechanism of IF or CS from a single, saturable relaxation. Comparison with thrombin shows that the prethrombin-2 to thrombin conversion enhances ligand binding to the active site not by improving accessibility through the value of kon but by reducing the rate of dissociation koff. The conclusion holds regardless of whether binding is interpreted in terms of IF or CS and has general relevance for the mechanism of zymogen activation of serine proteases. The method also provides a simple test of the validity of IF and CS and indicates when more complex mechanisms of binding should be considered.

When Paul Berg meets Donald Crothers: an achiral connection through protein biosynthesis.

Outliers in scientific observations are often ignored and mostly remain unreported. However, presenting them is always beneficial since they could reflect the actual anomalies that might open new avenues. Here, we describe two examples of the above that came out of the laboratories of two of the pioneers of nucleic acid research in the area of protein biosynthesis, Paul Berg and Donald Crothers. Their work on the identification of D-aminoacyl-tRNA deacylase (DTD) and 'Discriminator hypothesis', respectively, were hugely ahead of their time and were partly against the general paradigm at that time. In both of the above works, the smallest and the only achiral amino acid turned out to be an outlier as DTD can act weakly on glycine charged tRNAs with a unique discriminator base of 'Uracil'. This peculiar nature of glycine remained an enigma for nearly half a century. With a load of available information on the subject by the turn of the century, our work on 'chiral proofreading' mechanisms during protein biosynthesis serendipitously led us to revisit these findings. Here, we describe how we uncovered an unexpected connection between them that has implications for evolution of different eukaryotic life forms.

An idea to explore: Introduction of "biochemical tales" in medical education-Learning made fun.

Innovations in medical education, including the integration of narrative-based tales, are transforming the way complex biochemical concepts are taught and understood. In this "Idea to Explore", the essence of integrating tales that personify molecules and depict biochemical processes as engaging stories to enhance student engagement, promote active learning, and improve knowledge retention is discussed. It also explores the effectiveness of scientific discovery games and traditional scientific stories in deepening students' interest in biochemistry. Highlighting the potential of narrative methods to make biochemistry more accessible and engaging, educators are encouraged to adopt creative teaching tools that promote critical thinking, problem-solving, and communication skills, thereby inspiring active participation, and lifelong learning in biochemistry.

Volodymyr Oleksiyovych SHLYAKHOVENKO.

With deep sadness, we announce that on December 10, 2023, at the age of 86 passed away an outstanding Ukrainian scientist in the field of oncology, analytical enzymology, and pharmacology, a Laureate of the State Prize of Ukraine for Science and Technology, a member of the Federation of European Biochemical Societies, a member of the State Expert Center of the Ministry of Health of Ukraine, Doctor of Medical Sciences, Professor Volodymyr Oleksiyovych SHLYAKHOVENKO.

Special Issue with Research Topics on "Recent Analysis and Applications of Mass Spectra on Biochemistry".

Analytical mass spectrometry applies irreplaceable mass spectrometric (MS) methods to analytical chemistry and chemical analysis, among other areas of analytical science [...].

Blended learning in biochemistry: The development of pre-class and post-class learning aids for electron transport chain and oxidative phosphorylation.

Electron transport chain and oxidative phosphorylation are always a challenging topic for students studying metabolism. We had adopted blended learning in metabolism teaching and evaluated the learning experiences of students. In this project, a pre-class learning aid the Story Mode and a post-class learning aid the Revision Mode in the Powerland was developed that facilitated students learning electron transport chain and oxidative phosphorylation. In the Story Mode, pathways were presented by short animations and simplified diagram that allowed students to understand basic concepts and recall simple facts of the topic. Students were asked to watch the animations before class to acquire lower level of cognitive learning first, and this facilitated students in understanding more complicated concepts later on during class. Another challenge that students faced was that they were especially weak at integrating metabolic pathways and understand the relationships between these pathways. A metro map was designed in the Revision Mode that aided students in knowledge integration, and the functions of biomolecules were summarized in flashcards that helped students in revising the concepts. This interactive self-learning tool was packaged as a courseware using the Articulate Storyline.

Ninety-eight semesters of cytochrome P450 enzymes and related topics-What have I taught and learned?

This Reflection article begins with my family background and traces my career through elementary and high school, followed by time at the University of Illinois, Vanderbilt University, the University of Michigan, and then for 98 semesters as a Vanderbilt University faculty member. My research career has dealt with aspects of cytochrome P450 enzymes, and the basic biochemistry has had applications in fields as diverse as drug metabolism, toxicology, medicinal chemistry, pharmacogenetics, biological engineering, and bioremediation. I am grateful for the opportunity to work with the Journal of Biological Chemistry not only as an author but also for 34 years as an Editorial Board Member, Associate Editor, Deputy Editor, and interim Editor-in-Chief. Thanks are extended to my family and my mentors, particularly Profs. Harry Broquist and Minor J. Coon, and the more than 170 people who have trained with me. I have never lost the enthusiasm for research that I learned in the summer of 1968 with Harry Broquist, and I have tried to instill this in the many trainees I have worked with. A sentence I use on closing slides is "It's not just a laboratory-it's a fraternity."

Stereocontrolled access to thioisosteres of nucleoside di- and triphosphates.

Nucleoside diphosphates and triphosphates impact nearly every aspect of biochemistry; however, the use of such compounds as tools or medicinal leads for nucleotide-dependent enzymes and receptors is hampered by their rapid in vivo metabolism. Although a successful strategy to address the instability of the monophosphate moiety in oligonucleotide therapeutics has been accomplished by their isosteric replacement with phosphorothioates, no practical methods exist to rapidly and controllably access stereopure di- and triphosphate thioisosteres of both natural and unnatural nucleosides. Here we show how a modular, reagent-based platform can enable the stereocontrolled and scalable synthesis of a library of such molecules. This operationally simple approach provides access to pure stereoisomers of nucleoside α-thiodiphosphates and α-thiotriphosphates, as well as symmetrical or unsymmetrical dinucleoside thiodiphosphates and thiotriphosphates (including RNA cap reagents). We demonstrate that ligand-receptor interactions can be dramatically influenced by P-stereochemistry, showing that such thioisosteric replacements can have profound effects on the potency and stability of lead candidates.

Evolution of a self-renewing, participant-centered workshop series in BMB assessment.

We present as a case study the evolution of a series of participant-centered workshops designed to meet a need in the life sciences education community-the incorporation of best practices in the assessment of student learning. Initially, the ICABL (Inclusive Community for the Assessment of Biochemistry and Molecular Biology/BMB Learning) project arose from a grass-roots effort to develop material for a national exam in biochemistry and molecular biology. ICABL has since evolved into a community of practice in which participants themselves-through extensive peer review and reflection-become integral stakeholders in the workshops. To examine this evolution, this case study begins with a pilot workshop supported by seed funding and thoughtful programmatic assessment, the results of which informed evidence-based changes that, in turn, led to an improved experience for the community. Using participant response data, the case study also reveals critical features for successful workshops, including participant-centered activities and the value of frequent peer review of participants' products. Furthermore, we outline a train-the-trainer model for creating a self-renewing community by bringing new perspectives and voices into an existing core leadership team. This case study, then, offers a blueprint for building a thriving, evolving community of practice that not only serves the needs of individual scientist-educators as they seek to enhance student learning, but also provides a pathway for elevating members to positions of leadership.

CUR(E)ating a new approach to study fungal effectors and enhance undergraduate education through authentic research.

Course-based Undergraduate Research Experiences (CUREs) integrate active, discovery-based learning into undergraduate curricula, adding tremendous value to Biochemistry and Molecular Biology (BMB) education. There are multiple challenges in transforming a research project into a CURE, such as the readiness of students, the time commitment of the instructor, and the productivity of the research. In this article, we report a CURE course developed and offered in the University of Massachusetts Amherst BMB Department since 2018 that addresses these challenges. Our CURE focuses on fungal effectors which are proteins secreted by a destructive pathogenic fungus Fusarium oxysporum, one of the top five most devastating plant pathogens. By studying this group of proteins, students are connected to real-world problems and participate in the search for potential solutions. A 3-week "standard Boot Camp" is implemented to help students familiarize themselves with all basic techniques and boost their confidence. Next, molecular cloning, a versatile technique with modularity and repeatability, is used as the bedrock of the course. Our past 5 years of experience have confirmed that we have developed a novel and feasible CURE protocol. Measurable progress documented by students who took this course includes stimulated active learning and increased career trajectory to pursue hypothesis-based research to address societal needs. In addition, data generated through the course advance ongoing lab research. Collectively, we encourage the implementation of CURE among research-intensive faculty to provide a more inclusive research experience to undergraduate students, an important element in predicting career success.

A cord of four strands: Perspective of pre-medical and medical students on combined teaching modalities in undergraduate biochemistry.

Despite being a traditional coursework for pre-medical and medical students around the globe, biochemistry education suffers from a lack of positive appreciation due to the nature of the subject combined with deficiency of teaching modalities. A first semester biochemistry course was designed to include four different teaching modalities: lectures, recitations, case studies, and student presentations. A multi-item, anonymous, and voluntary questionnaire was distributed to students who had just completed the course and to those who had taken it the previous year. The questionnaire asked students to evaluate the course and how the different modalities affected their learning. These questionnaires took place in a two-year period between 2020 and 2021. Eighty-six (46%) of 186 total students responded. The vast majority of respondents agreed with the use of multimodal teaching techniques with respect to its impact on overall preparedness for future coursework, understanding, and enjoyability. Lectures and recitations were found to be the most useful in information retention and learning, although the same were found to be less enjoyable than other modalities. Although case studies and presentations were found to be enjoyable, most students ranked them low in terms of information retention and were the most voted to be removed from the course. There was general agreement between premedical and medical students' perception on the usefulness of the multimodal teaching techniques with respect to medical biochemistry modules and standardized exams. The agreement between cohorts suggests the premedical students accurately evaluated the usefulness of the course for the following year and validates the usefulness of the premedical student surveys. Use of multiple modalities in biochemistry education can be of substantial benefit in engaging and preparing students for further education.

An integrated laboratory work to improve students' practical skills and attitudes toward biochemistry in the biochemistry course.

This research reports on implementing the integrated laboratory work to achieve effective learning in the biochemistry course. The integrated laboratory work includes three stages: pre-laboratory, lab work, and post-laboratory. In other words, the three stages include planning, implementing, and evaluating investigation activities in the laboratory. The research design used was a posttest control group design consisting of a control and an experimental group. There were 67 students as respondents, who were divided into control (N = 33) and experimental (N = 34) groups. Practical skills were measured using an assessment rubric with the involvement of the observer. The categories of practical skills measured were procedural skills, observation skills, interpretation skills, and reporting skills. Attitude toward biochemistry was measured using a questionnaire with five Likert scales. The indicators of attitudes toward biochemistry used were liking for a biochemistry theory lesson, liking for biochemistry laboratory work, evaluative beliefs about biochemistry, and behavioral tendencies to learn biochemistry. The influence of the implementation of the integrated laboratory work on the students' practical skills and attitudes toward biochemistry was analyzed using MANOVA. The research result shows that implementing the integrated laboratory work improves students' average scores in practical skills and attitudes toward biochemistry. All the practical skills and attitudes categories in the experimental group have a higher score than those in the control group. The reason is that the work of the integrated laboratory can prepare students to conduct better investigations in biochemistry laboratory work.

Quantification of all 12 canonical ribonucleotides by real-time fluorogenic in vitro transcription.

Enzymatic methods to quantify deoxyribonucleoside triphosphates have existed for decades. In contrast, no general enzymatic method to quantify ribonucleoside triphosphates (rNTPs), which drive almost all cellular processes and serve as precursors of RNA, exists to date. ATP can be measured with an enzymatic luminometric method employing firefly luciferase, but the quantification of other ribonucleoside mono-, di-, and triphosphates is still a challenge for a non-specialized laboratory and practically impossible without chromatography equipment. To allow feasible quantification of ribonucleoside phosphates in any laboratory with typical molecular biology and biochemistry tools, we developed a robust microplate assay based on real-time detection of the Broccoli RNA aptamer during in vitro transcription. The assay employs the bacteriophage T7 and SP6 RNA polymerases, two oligonucleotide templates encoding the 49-nucleotide Broccoli aptamer, and a high-affinity fluorogenic aptamer-binding dye to quantify each of the four canonical rNTPs. The inclusion of nucleoside mono- and diphosphate kinases in the assay reactions enabled the quantification of the mono- and diphosphate counterparts. The assay is inherently specific and tolerates concentrated tissue and cell extracts. In summary, we describe the first chromatography-free method to quantify ATP, ADP, AMP, GTP, GDP, GMP, UTP, UDP, UMP, CTP, CDP and CMP in biological samples.

Embedding retrieval practice in undergraduate biochemistry teaching using PeerWise.

Retrieval practice is an evidence-based approach to teaching; here, we evaluate the use of PeerWise for embedding retrieval practice into summative assessment. PeerWise allows anonymous authoring, sharing, answering, rating, and feedback on peer-authored multiple choice questions. PeerWise was embedded as a summative assessment in a large first-year introductory biochemistry module. Engagement with five aspects of the tool was evaluated against student performance in coursework, exam, and overall module outcome. Results indicated a weak-to-moderate positive but significant correlation between engagement with PeerWise and assessment performance. Student feedback showed PeerWise had a polarizing effect; the majority recognized the benefits as a learning and revision tool, but a minority strongly disliked it, complaining of a lack of academic moderation and irrelevant questions unrelated to the module. PeerWise can be considered a helpful learning tool for some students and a means of embedding retrieval practice into summative assessment.

Demystifying dimensionality reduction techniques in the 'omics' era: A practical approach for biological science students.

Dimensionality reduction techniques are essential in analyzing large 'omics' datasets in biochemistry and molecular biology. Principal component analysis, t-distributed stochastic neighbor embedding, and uniform manifold approximation and projection are commonly used for data visualization. However, these methods can be challenging for students without a strong mathematical background. In this study, intuitive examples were created using COVID-19 data to help students understand the core concepts behind these techniques. In a 4-h practical session, we used these examples to demonstrate dimensionality reduction techniques to 15 postgraduate students from biomedical backgrounds. Using Python and Jupyter notebooks, our goal was to demystify these methods, typically treated as "black boxes", and empower students to generate and interpret their own results. To assess the impact of our approach, we conducted an anonymous survey. The majority of the students agreed that using computers enriched their learning experience (67%) and that Jupyter notebooks were a valuable part of the class (66%). Additionally, 60% of the students reported increased interest in Python, and 40% gained both interest and a better understanding of dimensionality reduction methods. Despite the short duration of the course, 40% of the students reported acquiring research skills necessary in the field. While further analysis of the learning impacts of this approach is needed, we believe that sharing the examples we generated can provide valuable resources for others to use in interactive teaching environments. These examples highlight advantages and limitations of the major dimensionality reduction methods used in modern bioinformatics analysis in an easy-to-understand way.

Tools for investigating O-GlcNAc in signaling and other fundamental biological pathways.

Cells continuously fine-tune signaling pathway proteins to match nutrient and stress levels in their local environment by modifying intracellular proteins with O-linked N-acetylglucosamine (O-GlcNAc) sugars, an essential process for cell survival and growth. The small size of these monosaccharide modifications poses a challenge for functional determination, but the chemistry and biology communities have together created a collection of precision tools to study these dynamic sugars. This review presents the major themes by which O-GlcNAc influences signaling pathway proteins, including G-protein coupled receptors, growth factor signaling, mitogen-activated protein kinase (MAPK) pathways, lipid sensing, and cytokine signaling pathways. Along the way, we describe in detail key chemical biology tools that have been developed and applied to determine specific O-GlcNAc roles in these pathways. These tools include metabolic labeling, O-GlcNAc-enhancing RNA aptamers, fluorescent biosensors, proximity labeling tools, nanobody targeting tools, O-GlcNAc cycling inhibitors, light-activated systems, chemoenzymatic labeling, and nutrient reporter assays. An emergent feature of this signaling pathway meta-analysis is the intricate interplay between O-GlcNAc modifications across different signaling systems, underscoring the importance of O-GlcNAc in regulating cellular processes. We highlight the significance of O-GlcNAc in signaling and the role of chemical and biochemical tools in unraveling distinct glycobiological regulatory mechanisms. Collectively, our field has determined effective strategies to probe O-GlcNAc roles in biology. At the same time, this survey of what we do not yet know presents a clear roadmap for the field to use these powerful chemical tools to explore cross-pathway O-GlcNAc interactions in signaling and other major biological pathways.