bluuebunny/crossref_metadata_2025_split huggingface dataset:
Teaching receptor theory to biochemistry undergraduates
Authors: Benore‐Parsons Marilee , Sufka Kenneth J. 
Published: February 2007

AbstractReceptor:ligand interactions account for numerous reactions critical to biochemistry and molecular biology. While students are typically exposed to some examples, such as hemoglobin binding of oxygen and signal transduction pathways, the topic could easily be expanded. Theory and kinetic analysis, types of receptors, and the experimental assay techniques should be included to properly prepare students for careers in research, medicine, or professional programs. In this article we offer a range of material for teaching these concepts to students.
Development of a biochemistry laboratory course with a project‐oriented goal
Authors: Stahelin Robert V. , Forslund Raymond E. , Wink Donald J. , Cho Wonhwa 
Published: February 2007

AbstractA new course for undergraduate biochemistry laboratory has been developed in the Department of Chemistry at the University of Illinois at Chicago. The course is innovative pedagogically by giving students a set of relevant skills for biochemical research and then allowing them to apply those skills in designing and performing the procedures for a research‐like project. The course content focuses on the pharmacologically important enzyme β‐lactamase, which is involved in the hydrolysis of antibiotics such as penicillins and cephalosporins. Specifically, each student designs and performs site‐directed mutagenesis of the enzyme β‐lactamase and analyzes the effect of mutation on the catalytic function of the enzyme by an enzyme assay. This unique and valuable research experience greatly enhances their understanding of scientific reasoning and the research process. Evaluation of the progress also indicates successful linkage of skill‐building and student‐directed activities even for students with no prior experience.
Different energy sources in sports: Introductory software
Authors: Galembeck Eduardo , Macedo Denise V. , Torres Bayardo B. 
Published: February 2007

AbstractThis work describes software designed to promote the association between the content of a basic undergraduate biochemistry course and the professional activities of physical education students. The software contains three main content sections: (A) Structure of skeletal muscle, (B) Contraction mechanism, and (C) Adaptations to physical exercise. A fourth section asks questions of the students. The software offers students a brief introduction on muscle structure and function, focusing on the energy sources required by different kinds of physical activities. The software was field tested at Universidade Estadual de Campinas (Unicamp), Brazil and has been adopted by several Brazilian universities. The students are required to examine the software, to discuss its contents, and to produce a list of questions arising from their work with the software. These questions are answered during the development of the curriculum, thereby connecting biochemical knowledge with the energetic needs for the practice of sports.
Content and conflict: The use of current events to teach content in a biochemistry course*
Authors: Cornely Kathleen 
Published: February 2007

AbstractCase study exercises, based on newsworthy current events, have been written for a biochemical audience that include elements of both “content” and “conflict.” The cases have been written in such a way as to teach students basic biochemical principles. At the same time, a dilemma is posed to the students, who must use what they have learned about the issue to come to a decision to resolve the conflict. In this manner, the students learn important biochemical principles but are also asked to deal with the scientific or social conflict posed in the case.
Energy diagrams for enzyme‐catalyzed reactions: Concepts and misconcepts
Authors: Aledo J. Carlos , Lobo Carolina , del Valle Alicia Esteban 
Published: February 2007

AbstractDespite the utility that energy diagrams have as a teaching and learning tool, a survey of their use, in seven popular Biochemistry textbooks, reveals that there is certain confusion around this topic. In our opinion, this confusion arises from the reluctance of authors to consider and indicate the conditions under which the reaction being represented occurs. For an enzyme‐catalyzed reaction, it should be stressed that, under conditions where the overall reaction is spontaneous, each elementary step must exhibit a negative free energy change, and this must be properly reflected in the progression profile of the reaction.
Isolation, purification, and characterization of bovine heart and yeast cytochromes c: An integrated biochemistry laboratory experience
Authors: Hunnes Cristi H. 
Published: February 2007

AbstractThis article describes a one‐semester project‐based laboratory course for biochemistry students centered on the protein cytochrome c. Students learn a variety of protein purification techniques, including ammonium sulfate precipitation, dialysis, ultrafiltration, gel filtration chromatography, ion‐exchange chromatography, and electrophoresis, by isolating cytochrome c. The oxidation‐reduction properties of this relatively stable and forgiving protein are then characterized by UV‐visible spectroscopy and electrochemistry. Electrophoresis is utilized to assess purity and determine molecular weight. Students isolate cytochrome c from bovine heart and yeast and compare their properties.
Disciplinary differences or modes of curriculum practice? Who promised to deliver what in problem‐based learning?
Authors: Savin‐Baden Maggi 
Published: February 2007

AbstractAlthough problem‐based learning has become increasingly popular in the last five years or so, particularly in the United Kingdom, the arguments about it still seem to rage. The ones that seem to be most problematic are, first, those about the relationship between problem‐based learning and other similar active learning approaches, such as project‐based learning; and second, those arguments about sustaining problem‐based learning curricula in the face of cuts and poor university administration. Meanwhile, the blame‐it‐on‐problem‐based‐learning attitude still seems to prevail worldwide, with little real consideration of the broader concerns about some of the educational issues. For example, there seem to be too few debates about what it means to facilitate problem‐based learning or how we might develop the kinds of curriculum modes that support problem‐based learning, and even what might count as a curriculum. This article seeks to unpack two of those issues by drawing on research into facilitation and modes of curriculum practice.
The origins of molecular biology: A Pedagogical tool for the professional development of pre‐college science teachers
Authors: Silverman Philip M. 
Published: February 2007

AbstractWe examine the science and pedagogy behind a historical approach to the professional development of pre‐college science (primarily biology) teachers. Our intention is to reach professional scientists, who, as a group, are uniquely qualified to provide experience and insights essential to this approach. The underlying research for this article has been carried out during an 8‐week summer course for selected rural high school science teachers at the Oklahoma Medical Research Foundation in Oklahoma City, Oklahoma. Now configured as part of the broader Oklahoma Science Project, the Summer Course has been held during each of the past 10 years. The result of our experiences is a learning model that incorporates a research dynamic based on peer interactions and Robert K. Merton's concept of specified ignorance. This dynamic is organized around carefully chosen research topics based on simple, quantitative assays that played important roles in the development of our current understanding of genetic chemistry. These assays are starting points for rationally conceived research projects developed by the teachers themselves. We illustrate this approach with the plaque assay for bacterial viruses.
Initiation of protein biosynthesis in eukaryotes
Authors: Merrick William C. 
Published: February 2007

AbstractInitiation of protein synthesis in eukaryotes is important both mechanically, because it selects the translation reading frame, and biologically, because it is the primary site for regulation of translation. For approximately 95–98% of the cellular mRNAs, formation of an initiation complex follows a rather specific pathway that is broken down into seven discrete steps. Although almost 35 peptides in 12–14 translation initiation factors participate in this process, three appear to have dominant roles: eukaryotic initiation factor (eIF)3, in building a pool of 40S subunits; eIF2, in binding the initiator tRNA (tRNAi) to the 40S subunit; and eIF4F in activating the mRNA and binding it to the 40S subunit. This process requires both ATP and GTP. The resulting 80S initiation complex contains both the tRNAi and the mRNA, with the anticodon of the tRNAi correctly base paired with the initiating AUG code word. Regulation of translation focuses mostly on controlling the activity of either eIF2 or eIF4F and this regulation has different consequences. Reduction in eIF2 activity influences all mRNA approximately the same, whereas reduction in eIF4F activity drives competition between mRNAs.
Teaching molecular biology to undergraduate biology students: An illustration of protein expression and purification*
Authors: Sommer César Adolfo , Silva Flávio Henrique , Novo Maria Teresa Marques 
Published: February 2007

AbstractPractical classes on protein expression and purification were given to undergraduate biology students enrolled in the elective course “Introduction to Genetic Engineering.” The heterologous expression of the green fluorescent protein (GFP)* of Aequorea victoria is an interesting system for didactic purposes because it can be viewed easily during experiments. The students were provided with basic information about the molecular features and applications of the GFP in molecular biology, the available heterologous expression systems, and the theoretical and experimental details of GFP expression in Escherichia coli and its purification. E. coli BL21‐competent cells were transformed with the pET28a expression vector containing the GFP gene fused to a histidine (His) tag. During the induction of a transformed clone by isopropylthiogalactoside, a time course for GFP expression was analyzed by SDS‐PAGE, and the expression was also visualized by the increasing green fluorescence of the bacterial culture. After cellular disruption, protein purification was illustrated by affinity chromatography of the His‐tagged protein in a nickel column. Eluted fractions containing imidazole in increasing concentrations were analyzed visually and also by SDS‐PAGE, demonstrating the role of imidazole in protein recovery by competition with nonspecific proteins and the His‐tagged protein. The results obtained and the experimental factors involved in protein expression, solubilization, and folding were discussed following the laboratory experiments. These practical classes allowed several current approaches to molecular biology to be demonstrated rapidly and helped underscore some of the topics taught during the course.
A response to BIO 2010: Transforming undergraduate education for future research biologists, from the perspective of the biochemistry and molecular biology major program at Kenyon College
Authors: Slonczewski Joan L. , Marusak Rosemary 
Published: February 2007

AbstractThe National Research Council completed a major study of undergraduate biology education, BIO 2010‐Transforming Undergraduate Education For Future Research Biologists (BIO 2010), funded by the Howard Hughes Medical Institute and the National Institutes of Health. The BIO 2010 report recommends that biology pedagogy should use an interdisciplinary approach incorporating a strong basis in mathematics and physical sciences. Many of the aims of BIO 2010 can be met by an interdisciplinary major program such as that of Biochemistry and Molecular Biology at Kenyon College. The Kenyon program effectively encourages students to connect biology with chemistry and mathematics and to develop a sound basis for research in the biological sciences. A continuing challenge is to balance the needs for depth of physical and mathematical understanding and breadth of diversity in biology.
Implementing the recommended curriculum in biochemistry and molecular biology at a regional comprehensive university through a biology/chemistry double major: The minnesota state university moorhead experience*
Authors: Wallert Mark , Brisch Ellen , Chastain Chris , Malott Michelle , Provost Joseph 
Published: February 2007

AbstractMinnesota State University Moorhead (MSUM) is a regional comprehensive university that is part of the Minnesota State Colleges and Universities (MnSCU) system. The current student population consists of ∼7,600 full‐ and part‐time students who are enrolled in one of 135 majors that lead to baccalaureate degrees. MSUM is committed to excellence in science teaching and research for undergraduates. It is an institutional member of the Council on Undergraduate Research and has three faculty members participating in Project Kaleidoscope (PKAL) Faculty for the 21st Century. Fourteen years ago, MSUM renewed its effort to have faculty participate in active research. All science faculty members hired since that time have been required to establish research programs. The primary purpose for the faculty engaging in ongoing research projects is to involve undergraduates in a meaningful research experience, thus training these students to become scientists.
A colorimetric process to visualize erythrocyte exovesicles aggregates*
Authors: Saldanha Carlota , Santos Nuno C. , Martins‐Silva J. 
Published: February 2007

AbstractA biochemistry laboratory class protocol is described in order to create an opportunity for students to apply by doing the theoretical concepts underlying biomolecules and vesicles properties, together with the principles of centrifugation and colorimetric methodologies. Through simple procedures the students will i) observe the segregation of the vesicles suspensions into two separate phases (phtalate esters gradient and vesicle aggregates); ii) visualize the vesicle aggregates by protein, enzyme, and phospholipids coloration processes; and iii) discuss and explain the visualized colors by proper biochemical reactions. The aims, objectives, methodology of teaching/learning, and assessment for this laboratory class are indicated.
An introductory undergraduate course covering animal cell culture techniques
Authors: Mozdziak Paul E. , Petitte James N. , Carson Susan D. 
Published: February 2007

AbstractAnimal cell culture is a core laboratory technique in many molecular biology, developmental biology, and biotechnology laboratories. Cell culture is a relatively old technique that has been sparingly taught at the undergraduate level. The traditional methodology for acquiring cell culture training has been through trial and error, instruction when undertaking the first graduate student position, or instruction when hired for a specific industrial cell culture position. However, cell culture is an important candidate course for any biotechnology‐related training program because it is a technique that must be performed by investigators before they perform many molecular procedures, and vertebrate cell culture is becoming increasingly important for biomanufacturing of therapeutic proteins. Therefore, a cell culture techniques course is an important offering for undergraduate students who aspire to graduate training, and also undergraduate students who will seek employment with biotechnology companies immediately after graduation. Recently, a cell culture techniques course was developed and delivered to students at North Carolina State University as a component of an undergraduate Biotechnology minor curricula. Currently, the instructors at North Carolina State University are seeking to provide students with the necessary technical and critical reasoning skills to successfully perform animal cell culture.
Diphenyl carbazide restores electron transport in isolated, illuminated chloroplasts after electron transport from water has been eliminated by mild heat treatment
Authors: Dean Rob L. , Pocock Tessa 
Published: February 2007

AbstractFreshly isolated, illuminated chloroplasts oxidize water and transfer the resulting electrons through the photosynthetic electron transport chains in their thylakoid membranes to the artificial electron acceptor, dichlorophenol indophenol (DCPIP). As a consequence, DCPIP is reduced and the decline in absorbance over time can be used to measure the rate of electron transfer. When gently heated, chloroplasts lose the capacity to oxidize water and the transfer of electrons to DCPIP is eliminated. Electron transport through chloroplasts to DCPIP is restored in the presence of the artificial electron donor diphenylcarbazide (DPC). If students gain experience with the DCPIP photoreduction assay and are given information on normal chloroplast function, they should be able to predict the behavior of heat‐treated chloroplasts in a variety of experimental conditions. A number of such predictions are outlined and tested. The experiments can all be conducted with a limited repertoire of equipment and easily prepared solutions. Consequently, this work is well suited to an investigative study in which each student group, in consultation with instructors, can make and test its own prediction. The ways in which changing different variables can affect the quality of the experimental results is emphasized. Additional studies, on measurements of rates of oxygen evolution and emitted chlorophyll fluorescence, are briefly described to support the inferences that heat‐treated chloroplasts do not oxidize water and that the vectorial transfer of electrons through them to DCPIP is identical to that in untreated chloroplasts.
Estrogen regulation of the expression of a cytochrome P450 isoenzyme*
Authors: Szeberenyi Jozsef 
Published: February 2007

AbstractTerms to be familiar with before you start to solve the test: cytochrome P450 enzymes, xenobiotics, estrogens, steroid receptors, gene induction, SDS, chromatin, immunoprecipitation, immunoglobulin G (IgG), agarose gel electrophoresis, promoter, transcription factors, enhancer, histones, nonhistone proteins, PCR, Taq polymerase, primers, oligonucleotides, radioactive labeling, nondenaturing PAGE.
From gene to protein: Prostatic acid phosphatase: Structure and expression of gene and protein*
Authors: Laidler Piotr , Kuciel Radoslawa , Dulińska Joanna , Gil Dorota , Mazurkiewicz Aleksandra , Wróbel Maria 
Published: February 2007

AbstractA set of classes for medical students is designed to reinforce an understanding of the basic laboratory methods of molecular biology and protein biochemistry in the context of a clinically important problem, prostate gland pathology. Students examine the gene coding for prostatic acid phosphatase and they assay expression of the gene in different lines of prostate cancer cell cultures (LNCaP and PC‐3). The three‐dimensional structure of the expressed protein is also investigated, in relation to its catalytic function. Students are encouraged to collect data for their experiments and to perform laboratory exercises on their own. The theory and practice should stimulate the students' discussion of various fields of biochemistry and molecular biology.
A complete approach for recombinant protein expression training: From gene cloning to assessment of protein functionality*
Authors: Novo M. Teresa Marques , Soares‐Costa Andrea , de Souza Antonia Q. L. , Figueira Ana Carolina M. , Molina Gustavo C. , Palacios Carlos A. , Kull Claudia R. , Monteiro Izabel F. , Baldan‐Pineda Paulo H. , Henrique‐Silva Flavio 
Published: February 2007

AbstractA practical course was given to undergraduate biology students enrolled in the elective course “Introduction to Genetic Engineering” at the Federal University of São Carlos (UFSCar), São Paulo, Brazil. The goal of the course was to teach current molecular biology tools applied to a real research situation that could be reported by the students themselves. The purpose was to produce a plant recombinant protein and demonstrate a heretofore unreported biological activity. Cystatins, natural inhibitors of cysteine proteases, were proposed for these studies. Initially, the students searched for plant cystatin cDNA sequences in the NCBI databases and selected the Oryzacystatin I gene (ocI) from rice, Oriza sativa, as the target gene for this study. Total RNA was extracted from rice‐germinating seeds and primers containing restriction sites for NdeI and EcoRI were designed based on the ocI cDNA sequence and then used to amplify the open reading frame (ORF). RT‐PCR amplification provided a band of the expected size for ocI ORF (309 bp). The PCR product was cut with NdeI and EcoRI restriction enzymes and cloned directly in the pET28a expression vector digested with the same enzymes. A pET28‐ocI recombinant clone was selected, checked by sequencing, and used to transform Escherichia coli BL21 (DE3) expression strain. After induction of the bacteria with isopropylthiogalactoside and cellular disruption, the His‐tagged OCI protein, present mainly in the soluble fraction, was purified by affinity chromatography in a nickel column. The purified protein was successfully used to inhibit fungal growth (Trichoderma reesei). The results were discussed extensively and the students contributed to the writing of this article, of which they are co‐authors.
Bioinformatics training programs are hot but the labor market is not*
Authors: Black Grant C. , Stephan Paula E. 
Published: February 2007

AbstractBased on a survey of academic training programs and an analysis of advertised job openings, we conclude that the labor market in bioinformatics has changed dramatically from the 1990s to the early 2000s. The number of academic training programs, as well as enrollment in these programs, expanded rapidly during this period. The expansion has created a sizeable pipeline of students who will matriculate from these programs in the near future. Yet, at the same time that this expansion in training programs occurred, demand in the bioinformatics market declined and its origins have shifted largely from industry to academe. Unless conditions in industry change dramatically in the next few years, it is likely that trainees from these programs will have difficulty finding the expected jobs in industry.
A guided inquiry experiment for the measurement of activation energies in the biophysical chemistry laboratory: Decarboxylation of pyrrole‐2‐carboxylate
Authors: Hutchinson Kelly M. , Bretz Stacey Lowery , Mettee Howard D. , Smiley Jeffrey A. 
Published: February 2007

AbstractA laboratory experiment for undergraduate biophysical chemistry is described, in which the acid concentration and temperature dependences of the decarboxylation of pyrrole‐2‐carboxylate are measured using a continuous ultraviolet (UV) spectrophotometric assay. Data collection and analysis are structured using principles of guided inquiry. Data leading to the calculation of multiple rate constants at varying temperatures and acid concentrations can be collected within one laboratory period, using inexpensive reagents and standard instrumentation. These experiments permit determination of activation energies that are lower at high acid concentration, indicative of a subtle change in the reaction mechanism with decreasing pH. The reaction is readily observable by students as they collect UV spectrophotometry data, and the decarboxylation reaction is related to biologically relevant enzymatic reactions.