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The coronavirus disease 2019 (COVID-19) pandemic is a case that can be used as a biochemistry learning resource in relation to the topic of viruses. Learning to use cases will be effective if students are assigned to produce reports, articles, or other scientific papers. Self-assessment can be used to assess the competencies that have been learnt in the writing process. This study aims to analyze the scientific papers and self-assessment of students using the COVID-19 pandemic case. It includes qualitative research with scientific paper and self-assessment questionnaire analyses. The research sample was chemistry education study program students (N = 57) following biochemistry course, out of a population of 87 students. The results show that the students have a good understanding of explaining COVID-19. Self-assessment analysis shows that 80% of the students responded positively to eight statements; those who gave positive responses to each questionnaire statement were able to produce scientific papers. Good self-assessment is in line with the ability of students to compile good scientific papers., (© 2020 International Union of Biochemistry and Molecular Biology.)

Zacharias Dische's discovery of feedback inhibition in metabolism was one of the most important in the history of biochemistry. However, his paper was written and published under very difficult circumstances in wartime and passed almost completely unnoticed. It is almost never cited, and the discovery itself is usually attributed to later work of others. Here I provide a discussion of Dische's work, a translation of his paper into English, and a transcription of the original French version, which is almost unobtainable anywhere., (Copyright © 2020. Published by Elsevier B.V.)

Nobel laureate Aziz Sancar writes about his decades-long relationship with the Journal of Biological Chemistry. Since 1984, he has published 100 papers in JBC, including this "Reflections.", Competing Interests: Conflict of interest The author declares no conflict of interest with the contents of this article., (Copyright © 2020 The Author. Published by Elsevier Inc. All rights reserved.)

The scientific publication landscape is changing quickly, with an enormous increase in options and models. Articles can be published in a complex variety of journals that differ in their presentation format (online-only or in-print), editorial organizations that maintain them (commercial and/or society-based), editorial handling (academic or professional editors), editorial board composition (academic or professional), payment options to cover editorial costs (open access or pay-to-read), indexation, visibility, branding, and other aspects. Additionally, online submissions of non-revised versions of manuscripts prior to seeking publication in a peer-reviewed journal (a practice known as pre-printing) are a growing trend in biological sciences. In this changing landscape, researchers in biochemistry and molecular biology must re-think their priorities in terms of scientific output dissemination. The evaluation processes and institutional funding for scientific publications should also be revised accordingly. This article presents the results of discussions within the Department of Biochemistry, University of São Paulo, on this subject.

Identification of Cronobacter represent a major challenge for laboratories testing powdered infant formula (PIF). In the present study, two biochemical galleries and three molecular methods have been applied to confirm 276 Cronobacter spp. and non-Cronobacter isolates from different sources. Using the latest database of API 20 E and ID 32 E biochemical miniaturized kits, 53% and 78% of the isolates were identified respectively. From the available results, total accuracy for Cronobacter detection was in 97% (API 20 E) and 99% (ID 32 E). The three molecular methods were based on rRNA based lateral flow, Real Time PCR combined with either a hybridization or hydrolysis probe. For all three methods total accuracy was more than 99%. A pilot trial using Next Generation Sequencing (NGS) correctly identified 58 out of 66 isolates (88%) in DNA mixtures. The results indicate that the commercially available approaches such as ID 32 E, rRNA based lateral flow and Real Time PCR are all suitable for Cronobacter identification at the genus level. The NGS method may become a suitable alternative in the future, provided that the sequence database is improved., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

The modern definition of enzymology is synonymous with the Michaelis-Menten equation instituted by Leonor Michaelis and Maud Menten. Most textbooks, or chapters within, discussing enzymology start with the derivation of the equation under the assumption of rapid equilibrium (as done by Michaelis-Menten) or steady state (as modified by Briggs and Haldane) conditions to highlight the importance of this equation as the bedrock on which interpretation of enzyme kinetic results is dependent. However, few textbooks or monographs take the effort of placing the equation within its right historical context and discuss the assumptions that have gone into its institution. This guide will dwell on these in substantial detail. Further, this guide will attempt to instil a sense of appreciation for the mathematical curve rectangular hyperbola, its unique attributes and how ubiquitous the curve is in biological systems. To conclude, this guide will discuss the limitations of the equation, and the method it embodies, and trace the journey of how investigators are attempting to move beyond the steady-state approach and the Michaelis-Menten equation into full progress curve, pre-steady state and single-turnover kinetic analysis to obtain greater insights into enzyme kinetics and catalysis., (© 2021 Federation of European Biochemical Societies.)

Every branch of science needs visitors' attention during the poster presentation session at conferences, symposiums, seminars, etc. In particular, participants in the chemistry and biochemistry conference need more visual tools to explain their research work in detail. Presence of smartphones and the ability of 2D barcodes will allow chemical reactions or processes to be shown in the form of a movie, animation or augmented reality (AR). Therefore, the next generation of posters will be more interested in this view. Here, the ability of 2D barcodes or QR codes to help researchers to catch more attention in their research work was presented during a poster presentation session. In this way, the visitors showed positive attitudes to the applicability of such tools. Also, some information including the number of poster visitors and interesting topics in the conference can be collected easily which is useful for the scientific and organizing committee of conferences. As a result, biochemistry conference posters can be presented in new ways, based on animation images or video, to capture the attention of viewers and deepen their understanding of poster concepts., (© 2021 International Union of Biochemistry and Molecular Biology.)

Philosophers of science diverge on the question what drives the growth of scientific knowledge. Most of the twentieth century was dominated by the notion that theories propel that growth whereas experiments play secondary roles of operating within the theoretical framework or testing theoretical predictions. New experimentalism, a school of thought pioneered by Ian Hacking in the early 1980s, challenged this view by arguing that theory-free exploratory experimentation may in many cases effectively probe nature and potentially spawn higher evidence-based theories. Because theories are often powerless to envisage workings of complex biological systems, theory-independent experimentation is common in the life sciences. Some such experiments are triggered by compelling observation, others are prompted by innovative techniques or instruments, whereas different investigations query big data to identify regularities and underlying organizing principles. A distinct fourth type of experiments is motivated by a major question. Here I describe two question-guided experimental discoveries in biochemistry: the cyclic adenosine monophosphate mediator of hormone action and the ubiquitin-mediated system of protein degradation. Lacking underlying theories, antecedent data bases, or new techniques, the sole guides of the two discoveries were respective substantial questions. Both research projects were similarly instigated by theory-free exploratory experimentation and continued in alternating phases of results-based interim working hypotheses, their examination by experiment, provisional hypotheses again, and so on. These two cases designate theory-free, question-guided, stepwise biochemical investigations as a distinct subtype of the new experimentalism mode of scientific enquiry., (© 2022. Springer Nature Switzerland AG.)

Extracellular vesicles (EVs) are heterogeneous lipid containers with a complex molecular cargo comprising several populations with unique roles in biological processes. These vesicles are closely associated with specific physiological features, which makes them invaluable in the detection and monitoring of various diseases. EVs play a key role in pathophysiological processes by actively triggering genetic or metabolic responses. However, the heterogeneity of their structure and composition hinders their application in medical diagnosis and therapies. This diversity makes it difficult to establish their exact physiological roles, and the functions and composition of different EV (sub)populations. Ensemble averaging approaches currently employed for EV characterization, such as western blotting or 'omics' technologies, tend to obscure rather than reveal these heterogeneities. Recent developments in single-vesicle analysis have made it possible to overcome these limitations and have facilitated the development of practical clinical applications. In this review, we discuss the benefits and challenges inherent to the current methods for the analysis of single vesicles and review the contribution of these approaches to the understanding of EV biology. We describe the contributions of these recent technological advances to the characterization and phenotyping of EVs, examination of the role of EVs in cell-to-cell communication pathways and the identification and validation of EVs as disease biomarkers. Finally, we discuss the potential of innovative single-vesicle imaging and analysis methodologies using microfluidic devices, which promise to deliver rapid and effective basic and practical applications for minimally invasive prognosis systems.

Ionization of amino acids (AA) is very important concept in biochemistry. We integrate the mathematical concept of probability with biochemically relevant process of AA ionization. We visualize the ionization process with Mathematica software discussing intramolecular interactions between weakly acidic/basic functional groups and charge-pH variation of amino acids in water solution. The visualizations rely on the notion of probability of ionization of functional groups and demonstrate how the extent of ionization and charge varies with pH of the solution. The examples described include amino acids and weak diprotic acids and bases. The aim is to help students better appreciate the importance and consequences of AA ionization and correct some misconceptions., (© 2020 International Union of Biochemistry and Molecular Biology.)

The COVID-19 pandemic has forced a shift in thinking regarding the safe delivery of wet laboratory courses. While we were fortunate to have the capacity to continue delivering wet laboratory experiments with physical distancing and other measures in place, modifications to the mechanisms of delivery within courses were necessary to minimize risk to students and teaching staff. One such modification was introduced in BCH370H, an introductory biochemistry laboratory course, where a OneNote Class Notebook (ONCN) was used as an electronic laboratory notebook (ELN) in place of the traditional hardbound paper laboratory notebook (PLN) used prior to the pandemic. The initial reasoning for switching to an ELN was around safety-allowing course staff and students to maintain physical distancing whenever possible and eliminating the need for teaching assistants to handle student notebooks; however, the benefits of the ONCN proved to be significantly more. OneNote acted not only as a place for students to record notes but the Class Notebook's unique features allowed easy integration of other important aspects of the course, including delivery of laboratory manuals, posting of student results, notetaking feedback, sharing of instructional materials with teaching assistants, and more. Student and teacher experiences with the ONCN as used within a fully in person biochemistry laboratory course, as well as learned best practices, are reviewed., (© 2024 The Authors. Biochemistry and Molecular Biology Education published by Wiley Periodicals LLC on behalf of International Union of Biochemistry and Molecular Biology.)

An integrated and projected-based laboratory course was described, integrating interconnected knowledge points and biochemistry and molecular biology techniques on a research project-based system. The program, which served as an essential extension of theoretical courses to practice, was conducted with a sophomore of basic medical science who had completed the course in medical biochemistry and molecular biology. This course engaged students in learning "genetic manipulation" and "recombinant DNA technology" to understand the target gene's role in disease mechanics, thus altering evaluation and treatment for clinical disease. Students could master applied and advanced techniques, such as cell culture, transfection, inducing exogenous fusion protein expression, purifying protein and its concentration assay, quantitative polymerase chain reaction, and western bot analysis. This laboratory exercise links laboratory practices with the methods of current basic research. Students need to complete the experimental design report and laboratory report, which could be advantageous for improving their ability to write lab summaries and scientific papers in the future. The reliability and validity analyses were conducted on the questionnaire, and we examined students' satisfaction with the course and their gains from the course. The student feedback was generally positive, indicating that the exercise helped consolidate theoretical knowledge, increase scientific research enthusiasm, and provide a powerful tool to be a better person and make informed decisions., (© 2024 International Union of Biochemistry and Molecular Biology.)

"Didn't understand or not fully understand" is the most common situation that students experience when they learn medical biochemistry and molecular biology (MBMB). Therefore, the primary task of teaching MBMB is to help students overcome the difficulties in "conceptual understanding." The core of the solution to these problems lies in the acquisition and application of cognitive skills. The key to applying Ausubel cognitive assimilation theory (A's CAT) is to expand the knowledge capacity of students' cognitive structure through the purposeful "production" and employment of advanced organizers, with which students can replace "rote learning" with "meaningful learning" and ultimately develop an interest in MBMB courses. The results showed that the application of A's CAT did not only encourage the students to use cognitive skills to learn and understand MBMB knowledge and overcome the barrier to learning that results from the characteristics of the MBMB course, but also expanded and deepened the MBMB course contents. As a branch of learning theory, A's CAT provides practical methods for the several hypotheses of learning theory. Among these, the advanced organizer strategy realizes the organization and reorganization of new knowledge; the progressive differentiation strategy reduces the difficulty of complex and abstract knowledge; the implementation of the advanced organizer strategy and integrative reconciliation strategy forms the concept map. Taken together, the application of A's CAT includes cognitive strategy and metacognitive strategy when the cognitive process is conducted in a meaningful way. More importantly, application of A's CAT guides students to participate in active learning and builds "scaffolding" for the teaching/learning MBMB of student-centered goals., (© 2019 International Union of Biochemistry and Molecular Biology.)

The flipped classroom is a relatively new active learning pedagogical intervention, gaining popularity as a blended learning methodology. The flipped classroom comprises two distinct parts, directed learning carried out at the student's own pace away from the classroom and an interactive, class-based activity encouraging problem-solving and experiential learning. This research presents a 1-year study to measure student performance and perception toward a flipped classroom approach to teaching core biochemical calculations to first-year undergraduate biochemistry and genetics students. A post-task questionnaire showed an overall positive student perception with an associated significant improvement in the end of module summative assessment. These results suggest that this teaching approach offers some advantages over more traditional teaching pedagogies., (© 2019 International Union of Biochemistry and Molecular Biology.)

Biochemistry textbooks often provide a disconnected, highly mathematical, and decontextualized treatment of thermodynamic and kinetic principles, which renders topics like protein folding difficult to teach. This is concerning given that graduates entering careers, like the pharmaceutical industry, must be able to apply such knowledge and related research methods to solve biochemistry research problems. Thus, it is essential that instructors have strategies to incorporate research methods and representations to help students understand the source of such scientific knowledge. Therefore, the goal of our work is to examine expert practice and use the findings to identify instructional strategies to incorporate more cutting-edge research and authentic ways of knowing into science classrooms and textbooks. Toward this goal, we examined how four scientists explain protein folding and dynamics research, focusing on the interaction of spoken language and representations, including gesture. Our analysis indicates that experts employ multiple representations and research methods to communicate how evidence can be used to understand phenomena. In contrast, textbooks explain what is known but seldom use representations to explain how it is known. Based on our findings, we suggest implications for instruction, including the design of textbooks, as well as potential instructional strategies to incorporate discussion of experimental methods and interpretation of representations during classroom activities. © 2019 International Union of Biochemistry and Molecular Biology, 47(5):513-531, 2019., (© 2019 International Union of Biochemistry and Molecular Biology.)

Advances in the site-specific chemical modification of proteins, also referred to as protein bioconjugation, have proved instrumental in revolutionary approaches to designing new protein-based therapeutics. Of the sites available for protein modification, cysteine residues or the termini of proteins have proved especially popular owing to their favorable properties for site-specific modification. Strategies that, therefore, specifically target cysteine at the termini offer a combination of these favorable properties of cysteine and termini bioconjugation. In this review, we discuss these strategies with a particular focus on those reported recently and provide our opinion on the future direction of the field., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

In the recently published article by Koza et al. (SAGE Open, 2023, 13, doi: 10.1177/21582440231177974), the authors analyzed the academic promotion system in Poland between 2011 and 2020. They concluded that "the Polish system of academic promotions in the past decade can hardly be regarded as based on pure merit", suggesting the impropriety, based on the participance of the members of the Central Board for Degrees and Titles in panels of experts evaluating the applications. Biochemistry was provided as a research discipline in which such an "impropriety" was the most pronounced, though other disciplines were only slightly less "improperly affected". Although the calculations presented by Koza and others (Koza et al., 2023) were proper, their conclusions were affected by fundamental errors in assessing the roles of the panelists and misinterpretation of the data. The drawbacks of the interpretations of the facts and in drawing conclusions are presented and discussed in this paper, underlining the necessity of being very careful when assessing any phenomenon and concluding about any mechanism. Indeed, only very well substantiated conclusions, strongly supported by objective data, should be published. This rule is very well known in biochemistry and other exact and natural sciences, and should be mandatory in all other research disciplines.

Anaerobic digestion is another important anaerobic catabolism pathway besides lactic acid and ethanol fermentation, which is of great significance for recycling resources, maintaining the ecological balance, optimizing the energy structure, alleviating the energy crisis, and promoting the implementation of the "Carbon Peaking and Carbon Neutrality" strategy. However, such an important metabolic process has not been involved in the current textbooks and teaching of biochemistry courses, making the teaching system incomplete. The anaerobic digestion process involves many reactions and complex metabolic pathways. In order to improve the students' understanding to this process, we created a full chart of the whole anaerobic digestion process based on systemic literature review and integrated it into the classroom teaching through the BOPPPS teaching mode. It was found that the classroom teaching assisted by this metabolic chart could help students establish the structural framework of the anaerobic digestion process and enrich the knowledge system of metabolism, achieving a good teaching effect. This paper introduces the content of the metabolic pathways of anaerobic digestion and the design of the teaching process, which would facilitate the teaching reforms and perfection of textbooks for related courses, such as Biochemistry, Environmental Engineering Microbiology and New Energy Engineering.

As a representative catabolic reaction that widely exists in nature, anaerobic digestion (AD) exhibits great value regarding the global carbon cycle, renewable energy development, and environmental protection. Such an important biochemical reaction was ignored before and should be introduced into the teaching and textbooks of undergraduate biochemistry courses. However, students may face obstructions when learning AD theories since the metabolic pathways in AD are very complex. To solve these problems, an instructive metabolic minimap of the AD reaction was designed, including its reaction stages, reaction pathways, substrates, and enzymes. Furthermore, the interrelationships between aerobic catabolism (AEC) and anaerobic catabolism (ANC) were also summarized by combining the catabolic pathways of typical biological macromolecules. In this paper, AD theories were first replenished into undergraduate biochemistry courses by metabolic minimap, which not only provided valuable supports for the practical teaching of AD in undergraduate biochemistry courses, but also acted as an important reference for students in biology-related majors and biochemistry teachers., (© 2022 International Union of Biochemistry and Molecular Biology.)

Fifty-five years ago, Norman Good and colleagues authored a paper that fundamentally advanced wet biochemistry [Good, N. E., Winget, G. D., Winter, W., Connolly, T. N., Izawa, S., and Singh, R. M. M. (1966) Hydrogen ion buffers for biological research. Biochemistry 5 , 467-477] and in doing so has amassed more than 2500 citations. They laid out the properties required for useful, biochemically relevant hydrogen-ion buffers and then synthesized and tested 10 of them. Soon after, these buffers became commercially available. Since then, most of us never gave them a second thought. We just use them. Here, I discuss some of the background regarding the genesis of "Good's buffers", make a few (disparaging) observations about the non-Good's buffer, Tris, and suggest that we synthesize new buffers by combining the ideas of Good et al. with results from the past 60 years of protein chemistry.

Every reader knows that an enzyme accelerates a reaction by reducing the activation-energy barrier. However, understanding how this is achieved by the structure of the enzyme and its interactions with stable complexes and transition states and, then, using this to (re)design enzymes to catalyze novel reactions remain the "holy grail" of mechanistic enzymology. The necessary foundation is the free-energy profile that specifies the energies of the bound substate, product, and intervening intermediates as well as the transition states by which they are interconverted. When this free-energy profile is compared to that for the uncatalyzed reaction, strategies for establishing and enhancing catalysis can be identified. This Perspective reminds readers that the first free-energy profile determined for an enzyme-catalyzed reaction, that for triosephosphate isomerase, was published in Biochemistry in 1976 by Jeremy R. Knowles, W. John Albery, and co-workers. They used the profile to propose three steps of increasing "subtlety" that can be influenced by evolutionary pressure to increase the flux through the reaction coordinate: (1) "uniform binding" of the substrate, product, and intermediates; (2) "differential binding" of complexes so that these are isoenergetic (to minimize the energy of the intervening transition states); and (3) "catalysis of an elementary step" in which the transition state for the kinetically significant chemical step is stabilized so that flux can be determined by the rate of substrate binding or product dissociation. These papers continue to guide mechanistic studies of enzyme-catalyzed reactions and provide principles for the (re)design of novel enzymes.

Enzymes are categorized into superfamilies by sequence, structural, and mechanistic similarities. The evolutionary implications can be profound. Until the mid-1990s, the approach was fragmented largely due to limited sequence and structural data. However, in 1996, Babbitt et al. published a paper in Biochemistry that demonstrated the potential power of mechanistically diverse superfamilies to identify common ancestry, predict function, and, in some cases, predict specificity. This Perspective describes the findings of the original work and reviews the current understanding of structure and mechanism in the founding family members. The outcomes of the genomic enzymology approach have reached far beyond the functional assignment of members of the enolase superfamily, inspiring the study of superfamilies and the adoption of sequence similarity networks and genome context and yielding fundamental insights into enzyme evolution.

We are living in the Big Data era, and yet we may have serious troubles when dealing with a handful of kinetic data if we are not properly instructed. The aim of this paper, related to enzyme kinetics, is to illustrate how to determine the K m and V max of a michaelian enzyme avoiding the pitfalls in which we often fall. To this end, we will resort to kinetic data obtained by second-year Biochemistry students during a laboratory experiment using β-galactosidase as an enzyme model, assayed at different concentrations of its substrate. When these data were analyzed using conventional linear regression of double-reciprocal plots, the range of K m and V max values obtained by different students varied widely. Even worse, some students obtained negative values for the kinetic parameters. Although such a scenario could make us think of a wide inter-student variability regarding their skills to obtain reliable data, the reality was quite different: when properly analyzed (accounting for error propagation) the data obtained by all the students were good enough to allow a correct estimation of the K m (2.8 ± 0.3 mM) and V max (179 ± 27 mM/min) with a reduced intergroup standard deviation. A student-accessible discussion of the importance of weighted linear regression in biochemical sciences is provided., (© 2021 International Union of Biochemistry and Molecular Biology.)

Background: The Spearman rank correlation test under classical statistics cannot be applied when the paired data is in interval or indeterminacy is presented in the paired data., Methods: In this paper, the Spearman rank correlation test under neutrosophic statistics will be introduced. The proposed Spearman rank correlation test will be a generalization of the existing Spearman rank correlation test., Results: The proposed test is supposed to be more informative, flexible, and adequate to apply for the analysis of the measurement data. The application of the proposed test is given using the measurement of luteotropichormone data obtained from the clinical laboratory. Based on the information, the probability of accepting the null hypothesis H 0 N is 0.95, the chance of committing a type-I error is 0.05 and the chance of indeterminacy about the acceptance of H 0 N is 69%., Conclusions: From the analysis, it is noted that the proposed test is more efficient in terms of the measure of indeterminacy as compared with the existing test. From the study, it is concluded that the proposed test is more informative, applicable and useable under an indeterminate environment as compared with the existing test under classical statistics. Therefore, it is recommended to apply the proposed test in clinical laboratories for testing the correlation between instruments.

Due to over-consumption of fossil resources and environmental problems, lignocellulosic biomass as the most abundant and renewable materials is considered as the best candidate to produce biomaterials, biochemicals, and bioenergy, which is of strategic significance and meets the theme of Green Chemistry. Highly efficient and green fractionation of lignocellulose components significantly boosts the high-value utilization of lignocellulose and the biorefinery development. However, heterogeneity of lignocellulosic structure severely limited the lignocellulose fractionation. This paper offers the summary and perspective of the extensive investigation that aims to give insight into the lignocellulose prior-fractionation. Based on the role and structure of lignocellulose component in the plant cell wall, lignocellulose prior-fractionation can be divided into cellulose-first strategy, hemicelluloses-first strategy, and lignin-first strategy, which realizes the selective dissociation and transformation of a component in lignocellulose. Ultimately, the challenges and opportunities of lignocellulose prior-fractionation are proposed on account of the existing problems in the biorefining valorization., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Rosemary, oregano, pink savory, lemon balm, St. John's wort, and saffron are common herbs wildly grown and easily cultivated in many countries. All of them are rich in antioxidant compounds that exhibit several biological and health activities. They are commercialized as spices, traditional medicines, or raw materials for the production of essential oils. The whole herbs or the residues of their current use are potential sources for the recovery of natural antioxidant extracts. Finding effective and feasible extraction and purification methods is a major challenge for the industrial production of natural antioxidant extracts. In this respect, the present paper is an extensive literature review of the solvents and extraction methods that have been tested on these herbs. Green solvents and novel extraction methods that can be easily scaled up for industrial application are critically discussed.

For many students biochemistry is a demanding course because they are expected to apply previously learned foundational concepts to new biological contexts. These foundational concepts serve as a scaffold onto which to build threshold concepts such as the physical basis of interactions. Unfortunately, many students possess misconceptions or gaps in knowledge of these foundational concepts which hinder their understanding of new information. This paper describes the implementation of an iterative process to improve student foundational concept learning in an introductory biochemistry course. The process includes pre-assessment of foundational concept knowledge, introduction of interventions targeting low performing concepts and re-assessment of student learning gains. Diverse active learning strategies such as problem-based worksheets, tactile learning activities, review activities and learning cycle activities were introduced to target concepts including hydrogen bonding, pH/pKa, bond energy and chemical equilibrium. While all active learning strategies resulted in improved posttest scores compared to pretest scores, no one strategy appears to be more beneficial than another. Survey results suggest students recognized the value of utilizing the various active learning strategies in the classroom to enhance critical thinking skills, engagement during class time, and collaboration skills. The process allows instructors the breadth and flexibility to introduce diverse active learning strategies tailored to their specific student needs in an effort to improve student foundational concept learning., (© 2021 International Union of Biochemistry and Molecular Biology.)

The objective of this paper is to compare conventional, ultrasound, microwave, and French press methods for the extraction of antioxidant compounds from Decatropis bicolor in an aqueous medium. This plant is widely used in Mexican traditional medicine for breast cancer treatment. Despite that, there are few studies on D. bicolor . Two response surface designs were applied to establish the best conditions of the liberation of antioxidants from D. bicolor , which were determined by DPPH• and Ferric Reducing Antioxidant Power (FRAP) techniques. The total phenolic content was evaluated by the Folin-Ciocalteu method. The results showed that D. bicolor is a source of antioxidants (669-2128 mg ET/100 g and 553-1920 mg EFe 2+ /100 g, respectively) and phenolic compounds (2232-9929 mg EGA/100 g). Among the physical factors that were analyzed, the temperature was the determinant factor to liberate the compounds of interest by using low concentrations of the sample and short times of extraction. The French press was the most efficient method, obtaining values of antioxidant activity and phenolic compounds even higher than those reported by using extraction methods with solvents such as methanol.

Biochemical pathways and networks are central to cellular information processing. While a broad range of studies have dissected multiple aspects of information processing in biochemical pathways, the effect of spatial organization remains much less understood. It is clear that space is central to intracellular organization, plays important roles in cellular information processing and has been exploited in evolution; additionally, it is being increasingly exploited in synthetic biology through the development of artificial compartments, in a variety of ways. In this paper, we dissect different aspects of the interplay between spatial organization and biochemical pathways, by focusing on basic building blocks of these pathways: covalent modification cycles and two-component systems, with enzymes which may be monofunctional or bifunctional. Our analysis of spatial organization is performed by examining a range of 'spatial designs': patterns of localization or non-localization of enzymes/substrates, theoretically and computationally. Using these well-characterized in silico systems, we analyse the following. (i) The effect of different types of spatial organization on the overall kinetics of modification, and the role of distinct modification mechanisms therein. (ii) How different information processing characteristics seen experimentally and studied from the viewpoint of kinetics are perturbed, or generated. (iii) How the activity of enzymes (bifunctional enzymes in particular) may be spatially manipulated, and the relationship between localization and activity. (iv) How transitions in spatial organization (encountered either through evolution or through the lifetime of cells, as seen in multiple model organisms) impacts the kinetic module (and pathway) behaviour, and how transitions in chemistry may be impacted by prior spatial organization. The basic insights which emerge are central to understanding the role of spatial organization in biochemical pathways in both bacteria and eukaryotes, and are of direct relevance to engineering spatial organization of pathways in bottom-up synthetic biology in cellular and cell-free systems.

A key learning outcome for undergraduate biochemistry classes is a thorough understanding of the principles of protein structure. Traditional approaches to teaching this material, which include two-dimensional (2D) images on paper, physical molecular modeling kits, and projections of 3D structures into 2D, are unable to fully capture the dynamic 3D nature of proteins. We have built a virtual reality application, Peppy, aimed at facilitating teaching of the principles of protein secondary structure. Rather than attempt to model molecules with the same fidelity to the underlying physical chemistry as existing, research-oriented molecular modelling approaches, we took the more straightforward approach of harnessing the Unity video game physics engine. Indeed, the simplicity and limitations of our model are strengths in a teaching context, provoking questions and thus deeper understanding. Peppy allows exploration of the relative effects of hydrogen bonding (and electrostatic interactions more generally), backbone φ/ψ angles, basic chemical structure, and steric effects on a polypeptide structure in an accessible format that is novel, dynamic, and fun to use. Apart from describing the implementation and use of Peppy, we discuss the outcomes of deploying Peppy in undergraduate biochemistry courses., (© 2019 The Protein Society.)

Volume 1, Issue 1 of Mathematical Biosciences was the venue for a now-classic paper on the application of singular perturbation theory in enzyme kinetics, "On the mathematical status of the pseudo-steady state hypothesis of biochemical kinetics" by F. G. Heineken, H. M. Tsuchiya and R. Aris. More than 50 years have passed, and yet this paper continues to be studied and mined for insights. This perspective discusses both the strengths and weaknesses of the work presented in this paper. For many, the justification of the pseudo-steady-state approximation using singular perturbation theory is the main achievement of this paper. However, there is so much more material here, which laid the foundation for a great deal of research in mathematical biochemistry in the intervening decades. The parameterization of the equations, construction of the first-order uniform singular-perturbation solution, and an attempt to apply similar principles to the pseudo-equilibrium approximation are discussed in particular detail., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Background: Several studies found that physicians develop a negative attitude toward biochemistry and genetics disciplines. Many medical schools adopt an integrated system-based curriculum supplemented with clinical correlations. Medical schools in Jordan switched to the integrated curriculum; however, studies that evaluate the attitude of physicians toward biochemistry and genetics are lacking., Objectives: This study aimed to evaluate the attitude of physicians toward biochemistry and genetics including the correlation of their curricula with clinical practice., Materials and Methods: A structured questionnaire consisting of 40 statements was distributed to a random sample of 616 physicians practicing in private and governmental hospitals in Jordan. Participants earned their MD or MBBS degree from Jordan or other countries and were interns, residents, or specialists., Results: More than half of the participants admitted that biochemistry and genetics are intellectually challenging and were among their least favourite subjects (59.1%); however, many of them were familiar with some of the contemporary advances in biochemistry and genetics and their translational potential (64.0%). Most of the participants felt that modifying the medical school curriculum by integrating biochemical and genetic concepts with clinical teaching will motivate the medical students (74%). In univariate analysis, residents showed the most positive attitudes and were the most knowledgeable about the biochemical changes associated with diseases and about the contemporary advances in biochemistry or genetics ( P < 0.05). In multivariate analysis, physicians practicing in the private sector or those with more than five years of experience generally had a more positive attitude toward biochemistry and genetics ( P < 0.05)., Conclusion: Physicians in Jordan showed an overall positive attitude toward biochemistry and genetics. This was more evident among residents, physicians with more than five years of experience, or those practicing in the private sector., Competing Interests: The authors declare that there are no conflicts of interest regarding the publication of this paper., (Copyright © 2019 Mahmoud A. Alfaqih et al.)

Glucose oxidase (GOD) is an enzyme widely used in glucose monitoring systems owing to its high specificity towards glucose. However, in our previous work maltose was found to show significant interaction with GOD and based on this observation, a novel microplate-based method was developed to assess α-amylase inhibitory activity (GOD method). Concerns regarding the interaction of GOD with maltose has limited the widespread use of the GOD method in assessing α-amylase activity. The present paper provides answers to concerns regarding the interaction of GOD with maltose using HPLC studies and application of the GOD method in assessing α-amylase activity. According to the results, the newly developed GOD method can be considered as a well-suited method for the determination of α-amylase activity and as an easy method to do kinetic studies compared to other available methods., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

During Herbert Tabor's tenure as Editor-in-Chief from 1971 to 2010, JBC has published many seminal papers in the fields of chromatin structure, epigenetics, and regulation of transcription in eukaryotes. As of this writing, more than 21,000 studies on gene transcription at the molecular level have been published in JBC since 1971. This brief review will attempt to highlight some of these ground-breaking discoveries and show how early studies published in JBC have influenced current research. Papers published in the Journal have reported the initial discovery of multiple forms of RNA polymerase in eukaryotes, identification and purification of essential components of the transcription machinery, and identification and mechanistic characterization of various transcriptional activators and repressors and include studies on chromatin structure and post-translational modifications of the histone proteins. The large body of literature published in the Journal has inspired current research on how chromatin organization and epigenetics impact regulation of gene expression., (© 2019 Gottesfeld.)

Herb Tabor was the Editor-in-Chief of the Journal of Biological Chemistry (JBC) spanning the years 1971-2010. This year, Herb turns 100. What do you give a person turning 100? Our answer to this question was to dedicate two of our favorite JBC papers to Herb. Both of these papers focus on reversible phosphorylation, which we briefly review. In addition, we delve into a new finding that centers around a novel family of secreted kinases, suggesting that there are many new and exciting discoveries yet to explore., (© 2019 Worby and Dixon.)

Ca 2+ imaging of isolated cells or specific types of cells within intact tissues often reveals complex patterns of Ca 2+ signaling. This activity requires careful and in-depth analyses and quantification to capture as much information about the underlying events as possible. Spatial, temporal and intensity parameters intrinsic to Ca 2+ signals such as frequency, duration, propagation, velocity and amplitude may provide some biological information required for intracellular signalling. High-resolution Ca 2+ imaging typically results in the acquisition of large data files that are time consuming to process in terms of translating the imaging information into quantifiable data, and this process can be susceptible to human error and bias. Analysis of Ca 2+ signals from cells in situ typically relies on simple intensity measurements from arbitrarily selected regions of interest (ROI) within a field of view (FOV). This approach ignores much of the important signaling information contained in the FOV. Thus, in order to maximize recovery of information from such high-resolution recordings obtained with Ca 2+ dyes or optogenetic Ca 2+ imaging, appropriate spatial and temporal analysis of the Ca 2+ signals is required. The protocols outlined in this paper will describe how a high volume of data can be obtained from Ca 2+ imaging recordings to facilitate more complete analysis and quantification of Ca 2+ signals recorded from cells using a combination of spatiotemporal map (STM)-based analysis and particle-based analysis. The protocols also describe how different patterns of Ca 2+ signaling observed in different cell populations in situ can be analyzed appropriately. For illustration, the method will examine Ca 2+ signaling in a specialized population of cells in the small intestine, interstitial cells of Cajal (ICC), using GECIs.

Lactase is the enzyme responsible for the digestion of the disaccharide lactose, and deficiency in this enzyme causes the prevalent medical condition lactose intolerance. Management of lactose intolerance can be achieved through the administration of lactase supplements. Lactase is an appropriate platform for advanced enzymatic study because its medical application is a motivator for student learning. The following is an upper-level biochemistry laboratory sequence that integrates student inquiry and exposure to advanced laboratory techniques. Students investigate three different lactase supplements through experimentation that includes the Bradford assay, SDS-PAGE, continuous and discontinuous kinetic assays, and zymography. Upon completion of this project, students compile their results and conclusions in a scientifically formatted paper comparing supplement protein content and activity. This safe and inexpensive laboratory project enriches student understanding of key biochemical concepts while mirroring work performed in a realistic research setting. © 2018 International Union of Biochemistry and Molecular Biology, 46(6):652-662, 2018., (© 2018 International Union of Biochemistry and Molecular Biology.)

Laboratory reports written in the style of a standard scientific article are commonly used to assess student learning in biochemistry laboratory courses. While most students can complete the Materials and Methods or Results sections successfully, many have difficulty with the Introduction and Discussion. They fail to place their data in a larger experimental context or to compare their results to those previously published. To address this issue in a laboratory course focusing on l-lactate dehydrogenase, a new exercise was introduced that was designed 1) to provide more background information about l-lactate dehydrogenase; 2) to give students additional experience in using PubMed and Web of Science to locate specific papers about l-lactate dehydrogenase; 3) to introduce the major bioinformatics databases at the National Center for Biological Information, ExPASy (Swiss Institute of Bioinformatics), BRENDA (Braunschweig Enzyme Database), and the Protein Data Bank; 4) to allow students to recover detailed information about l-lactate dehydrogenases; and 5) to provide practice in reading a research article that is similar to what they do in the lab. The students completed a data sheet summarizing these activities and then prepared three laboratory reports. The lab reports improved over the course of the semester and were qualitatively better than in past years. The materials developed for this laboratory course can be adapted to similar projects that use another protein as a model system. They could also be modified for use in Course-based Undergraduate Research Experiences or research projects for undergraduate or graduate students. © 2018 International Union of Biochemistry and Molecular Biology, 46(6):619-622, 2018., (© 2018 International Union of Biochemistry and Molecular Biology.)

A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as huperphlegmine A from Huperzia phlegmaria.