bluuebunny/crossref_metadata_2025 huggingface dataset:
What we know about facilitative glucose transporters: Lessons from cultured cells, animal models, and human studies
Authors: Gorovits Naira , Charron Maureen J.
Published: February 2007

Glucose uptake by all cells in the organism by glucose transport proteins is among the most essential processes in life. The process of glucose uptake into tissues is performed by glucose transporters. This review focuses on the biology of facilitative glucose transporters (GLUTs). The knowledge that has accumulated for more than a decade with respect to the regulation of GLUT expression and function in various experimental conditions points to the great potential for GLUTs to be utilized as targets for designing therapies for treatment of diseases related to impaired regulation of glucose homeostasis including type 2 diabetes.
Substrate channeling: Molecular bases
Authors: Milani Mario , Pesce Alessandra , Bolognesi Martino , Bocedi Alessio , Ascenzi Paolo
Published: February 2007

Substrate channeling (or tunneling) is the process of non‐covalent direct transfer of a reaction intermediate from the active site of one enzyme to the catalytic center of a second enzyme without prior dissociation into the bulk solvent. Substrate channeling can occur within protein matrix tunnels or along electrostatic highways crossing the surface of multifunctional enzymes, of tightly associated multienzyme complexes, or of transient multienzyme complexes. Substrate channeling has been proposed (i) to decrease the transit time of reaction intermediates, (ii) to prevent the loss of reaction intermediates by diffusion, (iii) to protect labile reaction intermediates from solvent, (iv) to sequester reaction intermediates that are toxic to the cell, (v) to circumvent unfavorable equilibria, (vi) to forestall the entrance of reaction intermediates into competing metabolic pathways, (vii) to prevent the build‐up of excess reaction intermediates, and (viii) to closely regulate a block of consecutive reactions within a metabolic pathway or in a multistep catalytic cycle. The three‐dimensional structures of Escherichia coli carbamoyl‐phosphate synthetase and Leishmania major dihydrofolate reductase‐thymidylate synthase beautifully exemplify the concept of substrate channeling.
Implementing the American Society for Biochemistry and molecular biology recommended curriculum in a biochemistry and molecular biology degree program Hosted Jointly by a chemistry and biology department: The richmond experience
Authors: Bell Ellis
Published: February 2007

The design of a curriculum for a Biochemistry and Molecular Biology degree program has to consider many factors including how the curriculum satisfies the recommended curriculum published by the American Society for Biochemistry and Molecular Biology (ASBMB) that emphasizes a combination of content and student skills. This article discusses how the University of Richmond, a medium‐sized, private, predominantly undergraduate institution, has created an interdepartmental program based in the biology and chemistry departments that attempts to fulfill the guidelines of ASBMB. In addition, some of the benefits and problems associated with the creation of an interdepartmental program are discussed together with efforts to create a “research‐rich” environment for student learning.
Salt fractionation of plasma proteins: A procedure to teach principles of protein chemistry
Authors: Spadaro A. C. C. , Assis‐Pandochi A. I. , Lucisano‐Valim Y. M. , Rothschild Z.
Published: February 2007

A two‐step laboratory exercise in biochemistry is proposed, comprising salt fractionation of plasma proteins and protein quantification. This exercise targets mainly undergraduate students, namely in the second year of Pharmacy, who are up to this point more used to deal with physical and chemical properties of micromolecules than macromolecules. The exercise requires simple equipment usually available in basic laboratories. Students work in small teams or alone depending on the laboratory conditions. Questions are proposed to check and reinforce the essential concepts involved as a preparation for detailed comprehension of protein chemistry. After salt fractionation, protein samples can be stored before quantification, allowing a two‐period schedule for the laboratory work. Exercises as proposed here are very useful to guide students to a detailed analysis of fundamental aspects determining structure and physicochemical properties of proteins.
Incorporation of ethical and societal issues in biochemistry into a senior seminar course
Authors: Caspers Mary Lou , Roberts‐Kirchhoff Elizabeth S.
Published: February 2007

In their senior year, biochemistry majors at the University of Detroit Mercy take a senior seminar course entitled “Recent Advances in Biochemistry Related to Societal Issues.” Students read papers selected from the current literature and take turns presenting these papers to the class. Papers are grouped into units dealing with molecular biology, protein structure/function, apoptosis/cancer/AIDS, and neurochemistry. The ethical/societal implications of the research are also discussed. In addition, a term paper dealing with societal issues and written in dialogue format by teams of students is required. The students present their dialogue papers as skits to an audience composed of faculty as well as junior biochemistry, chemistry, and biology majors. Based upon a survey taken at the beginning, at midterm, and at the end of the semester, the familiarity of the students with the ethical/societal issues related to the subjects covered increased significantly. Also, in course evaluations administered at the end of the semester, students expressed a high degree of satisfaction with this course.
Implementing the recommended curriculum in a biochemistry and molecular biology degree program in a biochemistry and molecular biology department: THE MISSISSIPPI STATE EXPERIENCE
Authors: Boyle John A.
Published: February 2007

Biochemistry and molecular biology are relatively new disciplines that have evolved from chemistry and biology. Undergraduate programs in these areas are also new, and their structures may reflect their evolutionary path. Some programs will be dominated by chemistry, others by biology. The American Society for Biochemistry and Molecular Biology (ASBMB) has provided a recommended curriculum that attempts to address the diverse needs of students in these areas. Mississippi State University is a research‐intensive university and has a Department of Biochemistry and Molecular Biology. The departmental curriculum provides a broad core of courses that meet the suggested ASBMB standards. In addition, use of appropriate electives allows students to design flexible programs unique to their specific career goals. This report is the second in a series illustrating how different departments are implementing the new ASBMB‐recommended curriculum in biochemistry and molecular biology.
Demonstration of the principles of restriction endonuclease cleavage reactions using thermostable Bfl I from Anoxybacillus flavithermus
Authors: Sharma Prince , D'Souza David R. , Bhandari Deepali , Parashar Vijay , Capalash Neena
Published: February 2007

Restriction enzymes are basic tools in recombinant DNA technology. To shape the molecular biology experiments, the students must know how to work with these molecular scissors. Here, we describe an integrated set of experiments, introduced in the “Advances in Molecular Biology and Biotechnology” postgraduate course, which covers the important aspects about restriction endonucleases: preparation of cell‐lysate, one‐column partial‐purification, assay, effect of temperature, buffers, Mg2+ ions and glycerol on activity, and quality control of two‐column partially purified enzyme. Examples of study questions, which help students understand the theoretical basis of the experiments, have been given.
Biochemistry in undergraduate health courses: Structure and organization
Authors: Silva Irani F. , Batista Nildo A.
Published: February 2007

This article describes the following aspects of teaching biochemistry in undergraduate health courses: objectives, number of hours, time in which the subject is studied, selection of content, teaching strategies, and evaluation methodologies used. Fifty‐three courses distributed in 13 areas within the health field and offered by 12 institutions were analyzed for this matter. An exploratory research was developed, with data obtained from documentation analysis, form completion, and interviews with teachers involved. For the analysis of data, both quantitative and qualitative approaches were used. The analysis of teaching plans for the subjects under investigation shows that their inclusion in the curriculum occurs early in the professional education. The subject focus is intradisciplinary, and there is a great diversity in terms of number of hours, even if one looks at the same professional field. There is a tendency to standardize objectives, centralizing the teaching in “biochemical knowledge,” which is frequently not related to the specific proposal of professional education. We also noticed that there is a certain degree of similarity in the contents, even though some specific content is seen in the courses of dentistry and veterinary medicine. From the value given to lectures, one could see an evidence of transmission of pre‐established content. Thus, there seems to be a need to stimulate the use of more active learning methodologies. As for evaluation, this study suggests an increased emphasis on the formative approach to assessing students.
Caring for students: A teacher's view
Authors: Rangachari P. K.
Published: February 2007

The asymmetry in power relations that exist between physicians and patients also exist between teachers and students. Thus, the dimensions of student care are analogous to those of patient care. The interactions between teachers and students are analyzed using the framework of the principles of beneficence (non‐maleficence), autonomy, and justice, which have been generally applied to physician‐patient interactions.
A curriculum skills matrix for development and assessment of undergraduate biochemistry and molecular biology laboratory programs
Authors: Caldwell Benjamin , Rohlman Christopher , Benore‐Parsons Marilee
Published: February 2007

We have designed a skills matrix to be used for developing and assessing undergraduate biochemistry and molecular biology laboratory curricula. We prepared the skills matrix for the Project Kaleidoscope Summer Institute workshop in Snowbird, Utah (July 2001) to help current and developing undergraduate biochemistry and molecular biology program designers to determine which laboratory techniques, skills, and theories to include in a 4‐year plan. The skills matrix can be used to evaluate and assess the types of laboratory skills as well as the level at which they are taught in biochemistry and molecular biology curricula. The matrix can foster better communication between faculty in chemistry, biology, math, and physics as they share curricular information. As an example of utility of the skills matrix, we used it to survey several commonly used biochemistry laboratory manuals to evaluate the skills covered in each text.
A simple method for detecting genetically modified maize in common food products
Authors: Brinegar Chris , Levee Darcy
Published: February 2007

A commercially available leaf DNA extraction and amplification kit has been adapted for the detection of genetically modified material in common food products containing maize. Amplification using published primer pairs specific for the Bacillus thuringiensis delta‐endotoxin and maize invertase genes results in a 226‐bp invertase PCR product in all samples (an internal positive control) plus a 184‐bp product in samples that are genetically modified with the endotoxin gene. The ease and rapidity of DNA extraction and PCR make this exercise especially suitable for advanced‐placement high school or lower division college biology students.
Using cytochome c to monitor electron transport and inhibition in beef heart submitochondrial particles*
Authors: Melin Amanda D. , Lohmeier‐Vogel Elke M.
Published: February 2007

We present a two‐part undergraduate laboratory exercise. In the first part, electron transport in bovine heart submitochondrial particles causing reduction of cytochrome c is monitored at 550 nm. Redox‐active dyes have historically been used in most previous undergraduate laboratory exercises of this sort but do not demonstrate respiratory inhibition by antimycin A and rotenone. By using cytochrome c instead of redox‐active dyes, it is possible to observe inhibition of electron transport in the presence of the aforementioned respiratory inhibitors. In the second part, students are asked to design a soluble redox chain between NADH and cytochrome c using catalytic amounts of redox‐active dyes. The students are also responsible for designing the assays and control. The entire experiment can be performed in 3 h with single‐beam spectrophotometers that are currently used in most undergraduate teaching laboratories. This exercise is suitable for large undergraduate classes of over 200 students and can be performed either by a single student or a student pair.
Outcomes of a research‐driven laboratory and literature course designed to enhance undergraduate contributions to original research
Authors: Rasche Madeline E.
Published: February 2007

This work describes outcomes of a research‐driven advanced microbiology laboratory and literature research course intended to enhance undergraduate preparation for and contributions to original research. The laboratory section was designed to teach fundamental biochemistry and molecular biology techniques in the context of an original research project. Site‐directed mutants of a gene of interest were constructed, and the effects of mutations on the resulting enzymes were analyzed. Students were also introduced to the literature surrounding their project, electronic literature databases, and preparation of computer‐generated slides for oral presentations. Student progress was evaluated through a laboratory report written as scientific manuscript, an oral presentation, a 10‐page written review, and an essay examination. In the semester following the laboratory course, four of the 14 undergraduates joined the host laboratory to continue their projects as individual undergraduate researchers. Quantifiable outcomes of the course and subsequent undergraduate research included i) production of eight new site‐directed mutants and preliminary characterization of the corresponding enzymes, ii) training of four individual undergraduate researchers prior to joining the laboratory, iii) publication of a manuscript with results from two undergraduate researchers, and iv) presentation of two posters with undergraduate co‐authors at a national meeting. This research‐driven approach may be applicable to enhance undergraduate contributions to other original research projects that have defined goals achievable within the timeframe of a single semester.
Facilitating student understanding of buffering by an integration of mathematics and chemical concepts
Authors: Curtright Robert , Emry Randall , Heaton Ruth M. , Markwell John
Published: February 2007

We describe a simple undergraduate exercise involving the titration of a weak acid by a strong base using a pH meter and a micropipette. Students then use their data and carry out graphical analyses with a spreadsheet. The analyses involve using mathematical concepts such as first‐derivative and semi‐log plots and provide an opportunity for collaboration between biochemistry and mathematics instructors. By focusing on titration data, rather than the titration process, and using a variety of graphical transformations, we believe that students achieve a deeper understanding of the concept of buffering.
Sex determination using PCR
Authors: Kima Peter E. , Rasche Madeline E.
Published: February 2007

PCR has revolutionized many aspects of biochemistry and molecular biology research. In the following exercise, students learn PCR by isolating their own DNA, amplifying specific segments of the X and Y chromosomes, and estimating the sizes of the PCR products using agarose gel electrophoresis. Based on the pattern of PCR products, students can distinguish between male and female samples and determine the gender of an unknown DNA donor. The exercise is presented for upper division undergraduate majors in microbiology, biochemistry, and molecular biology, but can be adapted to different academic levels and disciplines. The use of student samples in the exercise can enhance learning of these techniques by making PCR and agarose gel electrophoresis directly relevant to the students.
Oxidation‐reduction calculations in the biochemistry course
Authors: Feinman Richard D.
Published: February 2007

Redox calculations have the potential to reinforce important concepts in bioenergetics. The intermediacy of the NAD+/NADH couple in the oxidation of food by oxygen, for example, can be brought out by such calculations. In practice, students have great difficulty and, even when adept at the calculations, frequently do not understand their significance. The causes of this problem are identified with 1) the context in which redox calculations are presented and 2) the confusion over the formalism of the redox potential, particularly the meaning of the sign that refers to direction of current flow but is frequently confused with thermodynamic sign. A method is described for teaching redox calculations that is straight‐forward and simple for students to perform but, at the same time, brings out the key concepts. The primacy of the free energy is emphasized and the method is used to reinforce an understanding of respiration.
The ribosomal RNA is a useful marker to visualize rhizobia interacting with legume plants
Authors: Rinaudi Luciana , Isola María C. , Giordano Walter
Published: February 2007

Symbiosis between rhizobia and leguminous plants leads to the formation of nitrogen‐fixing root nodules. In the present article, we recommend the use of the ribosomal RNA (rRNA) isolated from legume nodules in an experimental class with the purpose of introducing students to the structure of eukaryotic and prokaryotic ribosomes and of demonstrating rhizobia colonization and nodule occupancy. We consider that this activity might help students previously trained in molecular biology handling to experience a richer way of learning some concepts and methodology in molecular plant‐microbe interactions.
The microarray revolution: Perspectives from educators
Authors: Brewster Jay L. , Beason K. Beth , Eckdahl Todd T. , Evans Irene M.
Published: February 2007

In recent years, microarray analysis has become a key experimental tool, enabling the analysis of genome‐wide patterns of gene expression. This review approaches the microarray revolution with a focus upon four topics: 1) the early development of this technology and its application to cancer diagnostics; 2) a primer of microarray research, designed to guide the beginner; 3) a highlight of the Genome Consortium for Active Teaching (GCAT), a worldwide consortium of faculty who are integrating microarrays into the undergraduate teaching laboratory; and 4) the use of microarrays in the biotechnology industry with a look forward to future applications. A central theme within this review is the profound relevance of new, bioinformatics‐based, technologies to undergraduate students within the biosciences.
An enzymatic clinical chemistry laboratory experiment incorporating an introduction to mathematical method comparison techniques
Authors: Duxbury Mark
Published: February 2007

An enzymatic laboratory experiment based on the analysis of serum is described that is suitable for students of clinical chemistry. The experiment incorporates an introduction to mathematical method‐comparison techniques in which three different clinical glucose analysis methods are compared using linear regression and Bland‐Altman difference plots. The experiment may also be undertaken using simple glucose solutions by general biochemistry students.
An in‐gel enzyme assay*
Authors: Szeberenyi Jozsef
Published: February 2007

Terms to be familiar with before you start to solve the test: signal transduction, growth factor signalling, nerve growth factor (NGF), epidermal growth factor (EGF), mitogen‐activated protein kinases (MAPKs), extracellular signal‐regulated kinases (ERKs), MAPK/ERK kinase (MEK), SDS‐PAGE, [γ‐32P]ATP, autoradiography, caspases, protein kinases, phosphatidylinositol 3‐kinase (PI3K), gene induction, alternative splicing.
Agarose gel electrophoresis system in the classroom: Detection of DNA strand breaks through the alteration of plasmid topology
Authors: De Mattos J. C. P. , Dantas F. J. S. , Caldeira‐de‐Araújo A. , Moraes M. O.
Published: February 2007

Good quality scientific teaching depends on the ability of researchers to translate laboratory experiments into high school and undergraduate classes, bridging the advanced and basic science with common knowledge. A fast‐growing field in biomedical sciences is oxidative stress, which has been associated to several diseases, including cancer and neurodegenerative disorders. We suggest herein a simple methodology for exploring DNA damage as an introductory pathway to these themes. The potential of natural or artificial products to induce DNA strand breaks can be easily tested in supercoiled plasmids incubated with selected products followed by agarose gel electrophoresis. This is designed to detect single and double strand breaks caused by reactive oxygen species generated by the products being tested. The altered topology of the damaged plasmid migrates slowly in the gel, creating a new band. We further introduce the quantitation of supercoiled DNA forms using densitometry of the gel with a digital camera; the values can then be used to estimate the number of breaks per genome using Poisson distribution. The system is inexpensive, rapid, and does not need high‐cost equipment and supplies and can be performed in high schools and undergraduate classes with a minimal structure.
Calculation of theoretical yields in metabolic networks*
Authors: Shastri Avantika , Morgan John
Published: February 2007

Nature has created elaborate networks of reactions to convert substrates into the building blocks of living cells as well as a myriad of natural products. The biosynthetic pathways responsible for each metabolite produced have a certain material and energetic “cost” associated with them. The theoretical calculation of these costs aid in analyzing metabolic pathways and engineering metabolic changes in cells. Depending on the complexity and structure of the metabolic system under consideration, different approaches need to be taken for the calculations. In this article, a systematic method to calculate theoretical yields is described for simple linear and cyclic pathways. A published error in the theoretical cost calculations for photorespiration is corrected (J. N. Siedow and D.A. Day (2000) Biochemistry and Molecular Biology of Plants, American Society of Plant Physiologists, Rockville, MD, pp. 676–726). A matrix‐vector formulation of the stoichiometric pathways is presented for more complex systems.
Student‐designed enzyme‐linked metabolite assay kits
Authors: Hancock D. , Johnston J. , Dimauro J. , Denyer G.
Published: February 2007

The extensive use of commercial kits in molecular biology and biochemistry has prompted us to design a series of practical sessions to help students become familiar with the uses and limitations of pre‐packaged assay systems. To facilitate an understanding of these assay systems and to promote reflection on their appropriate use, students manufacture their own kit for one of four enzyme‐linked metabolite assays. To do this they must investigate the role of each of the components in the assay, optimize the conditions where possible, check for cross reactivity, and then work this assay up for a few related “real” samples. Students make up all the buffers, the standard solution, instructions, and even the packaging. The kit is checked for accuracy by the producers, “marketed” to other students, and evaluated by their peers. By going through this process, students learn the benefits and pitfalls of commercial kits as well as reinforcing the basic principles of metabolite measurement and gaining experience with assay design, troubleshooting, and problem solving.
Neuroglobin and cytoglobin: Two new entries in the hemoglobin superfamily*
Authors: Ascenzi Paolo , Bocedi Alessio , de Sanctis Daniele , Pesce Alessandra , Bolognesi Martino , Marden Michael C. , Dewilde Sylvia , Moens Luc , Hankeln Thomas , Burmester Thorsten
Published: February 2007

Neuroglobin (Ngb) and cytoglobin (Cygb) are two newly discovered intracellular members of the vertebrate hemoglobin (Hb) family. Ngb, predominantly expressed in nerve cells, is of ancient evolutionary origin and is homologous to nerve‐globins of invertebrates. Cygb, present in many different tissues, shares common ancestry with myoglobin (Mb) and can be traced to early vertebrate evolution. Ngb and Cygb display the classical three‐on‐three α‐helical globin fold and are endowed with a hexa‐coordinate heme Fe atom, in both their ferrous and ferric forms, having the heme distal HisE7 residue as the endogenous sixth ligand. Reversible intramolecular hexa‐ to penta‐coordination of the heme Fe atom modulates Ngb and Cygb ligand‐binding properties. In Ngb and Cygb, ligand migration to/from the heme distal site may be assisted by protein/matrix tunnel cavity systems. The physiological roles of Ngb and Cygb are poorly understood. Ngb may protect neuronal cells from hypoxic‐ischemic insults, may act as oxidative stress‐responsive sensor protein, and may sustain NO/O2 scavenging and/or reactive oxygen species (ROS) detoxification. Cygb, located in the cytoplasm of fibroblasts, chondroblasts, osteoblasts, and hepatic stellate cells, has been hypothesized to be involved in collagen synthesis. In neurons, Cygb, located in both cytoplasm and nucleus, may provide O2 for enzymatic reactions, and may be involved in a ROS (NO)‐signaling pathway(s). Here, we review current knowledge on Ngb and Cygb in terms of their structure, function, and evolutionary links to the well‐known human HbA and Mb.
The effect of carbon source and fluoride concentrations in the streptococcus mutans biofilm formation*
Authors: Paulino Tony P. , Andrade Ricardo O. , Bruschi‐Thedei Giuliana C. M. , Thedei Geraldo , Ciancaglini Pietro
Published: February 2007

The main objective of this class experiment is to show the influence of carbon source and of different fluoride concentrations on the biofilm formation by the bacterium Streptococcus mutans. The observation of different biofilm morphology as a function of carbon source and fluoride concentration allows an interesting discussion regarding the metabolic pathways that lead to cavity development, about the role of fluoride on this disease prevention, and also on the importance of biofilm formation to the cariogenic potential of this bacterium, one of the main responsible for this multifatorial disease appearance. On addition to that, the low execution cost and the simple technical apparatus makes this experiment easy to perform.
Glutamine metabolism: Role in acid‐base balance*
Authors: Taylor Lynn , Curthoys Norman P.
Published: February 2007

The intent of this review is to provide a broad overview of the interorgan metabolism of glutamine and to discuss in more detail its role in acid‐base balance. Muscle, adipose tissue, and the lungs are the primary sites of glutamine synthesis and release. During normal acid‐base balance, the small intestine and the liver are the major sites of glutamine utilization. The periportal hepatocytes catabolize glutamine and convert ammonium and bicarbonate ions to urea. In contrast, the perivenous hepatocytes are capable of synthesizing glutamine. During metabolic acidosis, the kidney becomes the major site of glutamine extraction and catabolism. This process generates ammonium ions that are excreted in the urine to facilitate the excretion of acids and bicarbonate ions that are transported to the blood to partially compensate the acidosis. The increased renal extraction of glutamine is balanced by an increased release from muscle and liver and by a decreased utilization in the intestine. During chronic acidosis, this adaptation is sustained, in part, by increased renal expression of genes that encode various transport proteins and key enzymes of glutamine metabolism. The increased levels of phosphoenolpyruvate carboxykinase result from increased transcription, while the increase in glutaminase and glutamate dehydrogenase activities result from stabilization of their respective mRNAs. Where feasible, this review draws upon data obtained from studies in humans. Studies conducted in model animals are discussed where available data from humans is either lacking or not firmly established. Because there are quantitative differences in tissue utilization and synthesis of glutamine in different mammals, the review will focus more on common principles than on quantification.
A phytase enzyme‐based biochemistry practical particularly suited to students undertaking courses in biotechnology and environmental science
Authors: Boyce Angela , Casey Anne , Walsh Gary
Published: February 2007

Courses in introductory biochemistry invariably encompass basic principles of enzymology, with reinforcement of lecture‐based material in appropriate laboratory practicals. Students undertaking practical classes are more enthusiastic, and generally display improved performance, when the specific experiments undertaken show direct relevance to their core degree area. Herein is described an enzyme‐based practical of particular relevance to students undertaking primary degrees in biotechnology, environmental science, nutrition, as well as animal and veterinary science. The practical entails assay of phytase, an enzyme that is now routinely included in monogastric animal feed in order to ameliorate the negative nutritional and environmental consequences of its substrate, dietary phytic acid. The practical is technically straightforward, requiring relatively basic laboratory equipment and reagents that are both easily obtained and relatively inexpensive. To be an effective digestive supplement, the enzyme must display a combination of physicochemical properties, which provide sufficient scope for an interesting and multifaceted post‐laboratory discussion.
The human side of science education: Using McGregor's theory Y as a framework for improving student motivation*
Authors: Markwell John
Published: February 2007

Student motivation is correlated with learning. Douglas McGregor's Theory X and Theory Y as a basis for understanding and improving motivation in the business world can be directly applied to the science classroom. Teachers with a Theory Y perspective (students naturally want to learn) provide increased motivation for students and promote more active learning than Theory X‐style teachers who do not view students as active learners. Many teachers are not aware of their Theory X/Theory Y orientation and how this bias may be impacting their interaction with students. This article explores the benefits of moving from a Theory X to a more Theory Y style of teaching.
European doctorate in biotechnology: Added value for european academia and industry
Authors: Bryce C. F. A. , Aghion J. , Bos P. , Celada F. , Griffin M. , Hull R.
Published: February 2007

It has long been recognized that educational programs and degrees are not equivalent across Europe. Add to this the fact that Europe consists of many different cultures and languages, then it is not surprising that the free circulation of scientists and their job market in the European Union is severely restricted. This is one of several debated causes for the crisis in European biotechnology, which is in danger of succumbing to the competition of North America, Japan, and some of the developing countries. The Universities (even those tradition‐ridden), the European University Association, and the European Commission are aware of the danger and plans are in preparation for sweeping organizational and cultural changes. The problem is how long will it take and how long can we afford to wait? A number of biotechnologists and scientists from several institutions and many countries decided, instead of waiting, to make a preliminary move in the right direction. With the help of the European Commission and using European Molecular Biology Organization, European Federation of Biotechnology, and the European University Rectors as references, the European Association for Higher Education in Biotechnology was founded in 1995 by representatives of universities and research institutes. It awards the additional title of European Doctor to PhD graduates showing excellence in biotechnology and/or related Life Science subjects and who are willing to fulfil a program of studies that is both international and interdisciplinary. The present article reports on the first 9 years of this adventure.
A biochemistry and molecular biology course for secondary school teachers*
Authors: Fernández‐Novell J. M. , Cid E. , Gomis R. , Barberà A. , Guinovart J. J.
Published: February 2007

This article describes a course for reinforcing the knowledge of biochemistry in secondary school science teachers. The Department of Biochemistry and Molecular Biology of the University of Barcelona designed a course to bring these teachers up to date with this discipline. In addition to updating their knowledge of biochemistry and molecular biology, this course aims to provide teachers with a set of relevant laboratory practices that can be applied in their practical lessons.
Quantification of DNA by agarose gel electrophoresis and analysis of the topoisomers of plasmid and M13 DNA following treatment with a restriction endonuclease or DNA topoisomerase I
Authors: Tweedie John W. , Stowell Kathryn M.
Published: February 2007

A two‐session laboratory exercise for advanced undergraduate students in biochemistry and molecular biology is described. The first session introduces students to DNA quantification by ultraviolet absorbance and agarose gel electrophoresis followed by ethidium bromide staining. The second session involves treatment of various topological forms of DNA with a restriction endonuclease and with a DNA topoisomerase. This session introduces students to the concept of DNA topoisomers, to the properties of different forms of DNA, and to the activity of restriction endonucleases and topoisomerases toward these forms. The exercise also involves measuring the size of linear duplex fragments of DNA by comparison of mobility with a ladder of double stranded DNA of known sizes.
Theme‐based tests: Teaching in context
Authors: Anderson Gretchen L. , Heck Marsha L.
Published: February 2007

Theme‐based tests provide an assessment tool that instructs as well by providing a single general context for a broad set of biochemical concepts. A single story line connects the questions on the tests and models applications of scientific principles and biochemical knowledge in an extended scenario. Theme‐based tests are based on a set of interrelated journal articles or a fictional story derived from popular culture or local events that interweaves biochemical principles into a story line. Theme‐based tests engage students during an exam and promote their creativity.
Quantifying the activation of the small molecular weight G‐protein ras
Authors: Chapman Katharine , Hall David J.
Published: February 2007

Low molecular weight guanine‐nucleotide binding proteins are molecular switches involved in a wide range of cellular functions in eukaryotes. Ras is activated when a membrane receptor is bound by a ligand and the GDP bound to the Ras protein is exchanged for GTP. Once GTP is bound, the Ras three‐dimensional conformation changes and binds the kinase Raf. This protein‐protein interaction can be used to “pull‐down” activated Ras from a cell lysate. The amount of activated Ras is quantitated through immunoblotting and densitometry. This procedure is excellent as a multiweek investigational laboratory.
The biological activity of the large‐T protein of SV40 virus*
Authors: Szeberenyi Jozsef
Published: February 2007

Terms to be familiar with before you start to solve the test: SV40 virus, malignant transformation, in vitro DNA synthesis, template, primer, DNA polymerase, radioactive labeling, autoradiography, dideoxynucleoside triphosphates, heat denaturation, nondenaturing PAGE.
Screening a library of household substances for inhibitors of phosphatases: An introduction to high‐throughput screening
Authors: Taylor Ann T. S.
Published: February 2007

Library screening methods are commonly used in industry and research. This article describes an experiment that screens a library of household substances for properties that would make a good “drug,” including enzyme inhibition, neutral pH, and nondenaturing to proteins, using wheat germ acid phosphatase as the target protein. An adaptation of the experiment appropriate for lower level biochemistry or outreach is also described.

This work was supported by Wabash College through the Haines Fund for the Study of Biochemistry and the National Science Foundation through Grant DUE 0126242.
A guided discovery approach for learning metabolic pathways
Authors: Schultz Emeric
Published: February 2007

Learning the wealth of information in metabolic pathways is both challenging and overwhelming for students. A step‐by‐step guided discovery approach to the learning of the chemical steps in gluconeogenesis and the citric acid cycle is described. This approach starts from concepts the student already knows, develops these further in a logical manner using easy‐to‐remember memory devices, and significantly reduces student learning demand. This approach incorporates the use of PowerPoint, web access, and a digital whiteboard to enhance student learning and retention.
Bioinformatics: Current practice and future challenges for life science education
Authors: Hack Catherine , Kendall Gary
Published: February 2007

It is widely predicted that the application of high‐throughput technologies to the quantification and identification of biological molecules will cause a paradigm shift in the life sciences. However, if the biosciences are to evolve from a predominantly descriptive discipline to an information science, practitioners will require enhanced skills in mathematics, computing, and statistical analysis. Universities have responded to the widely perceived skills gap primarily by developing masters programs in bioinformatics, resulting in a rapid expansion in the provision of postgraduate bioinformatics education. There is, however, a clear need to improve the quantitative and analytical skills of life science undergraduates. This article reviews the response of academia in the United Kingdom and proposes the learning outcomes that graduates should achieve to cope with the new biology. While the analysis discussed here uses the development of bioinformatics education in the United Kingdom as an illustrative example, it is hoped that the issues raised will resonate with all those involved in curriculum development in the life sciences.
Physical models enhance molecular three‐dimensional literacy in an introductory biochemistry course*
Authors: Roberts Jacqueline R. , Hagedorn Eric , Dillenburg Paul , Patrick Michael , Herman Timothy
Published: February 2007

This article reports the results of a recent study to evaluate the usefulness of physical models of molecular structures as a new tool with which to teach concepts of molecular structure and function. Of seven different learning tools used by students in this introductory biochemistry class, the use of the physical models in a laboratory was rated as most useful. These results suggest that physical models can play an important role in capturing the interest of students in the subject of molecular structure and function. These physical models often stimulate more sophisticated questions in the minds of students, which can then be more appropriately explored using computer visualization tools.
Test: Construction of genomic libraries
Authors: Szeberényi Jozséf
Published: February 2007

Terms to be familiar with before you start to solve the test: genomic library, gel filtration, restriction endonuclease, plasmid, sticky ends, blunt ends, ligation, recombinant DNA, bacterium transformation, denaturation and renaturation of DNA, satellite DNA, telomere, centromere, unique and repetitive sequences.
Discovering an accessible enzyme: Salivary α‐amylase : Prima digestio fit in ore: A didactic approach for high school students
Authors: Marini Isabella
Published: February 2007

Human salivary α‐amylase is used in this experimental approach to introduce biology high school students to the concept of enzyme activity in a dynamic way. Through a series of five easy, rapid, and inexpensive laboratory experiments students learn what the activity of an enzyme consists of: first in a qualitative then in a semi‐quantitative way. They also learn how some environmental effectors can influence it. The choice of a “human body” enzyme and not an anonymous commercial enzyme is a very attractive one for students. This laboratory approach will be integrated with theoretical knowledge about α‐amylase, starch, their physiological meaning, and biotechnological applications.
Development and evaluation of a peer‐tutoring program for graduate students*
Authors: Copeland H. Liesel , Kinzy Terri Goss
Published: February 2007

Many interdisciplinary Ph.D. programs admit students of different educational backgrounds who receive a first year of a general curriculum education. However, student preparation for this curriculum varies, and methods are needed to provide academic support. Graduate student peer tutoring was piloted as an initiative funded by a National Institutes of Health (NIH) Initiative for Minority Student Development award to the University of Medicine and Dentistry of New Jersey–Robert Wood Johnson Medical School (UMDNJ‐RWJMS) and is now offered to all students in the interdisciplinary Molecular Biosciences Ph.D. program between Rutgers, The State University of New Jersey, and UMDNJ‐RWJMS. Tutoring occurs individually or in small groups and has grown over the past 5 years in the number of students tutored and hours of tutoring. The program was evaluated by surveying and interviewing both tutors and students concerning process variables (e.g. awareness, frequency) and impact variables (e.g. perceived benefits, motivators), as well as by assessing changes in exam scores for the four core courses of the first‐year graduate curriculum.
Concepts of protein sorting or targeting signals and membrane topology in undergraduate teaching*
Authors: Tang Bor Luen , Teng Felicia Yu Hsuan
Published: February 2007

The process of protein biogenesis culminates in its correct targeting to specific subcellular locations where it serves a function. Contemporary molecular and cell biology investigations often involve the exogenous expression of epitope‐ or fluorescent protein‐tagged recombinant molecules as well as subsequent analysis of protein‐protein interactions in vitro and in vivo. Fundamental knowledge of targeting signals that direct a polypeptide to various organelles or membrane domains is essential for the proper design of such recombinant molecules. A fundamental concept of membrane compartmentalization is also often useful for the interpretation of the preliminary results of interaction screens. Knowledge in targeting signals and post‐translational dynamics of proteins should therefore be given sufficient emphasis in an undergraduate biochemistry or molecular biology curriculum. Such knowledge is essential, particularly for undergraduates or fresh graduates embarking on research projects in a cell and molecular biology laboratory.
Vitamin E: Textbooks require updating
Authors: Azzi Angelo , Zingg Jean‐Marc
Published: February 2007

Vitamin E was discovered in 1922, but in more than 60 years many new findings have added to the early one. However, its description in many textbooks has not been proportionally updated. The result is an inaccurate, incomplete, and often incorrect description of the function of this vitamin. In some other textbooks, vitamin E is absolutely neglected. In almost all books the existence of vitamin E deficiency diseases is ignored. Recent findings on vitamin E molecular functions and its related diseases are described in this article.
Evolution of innate immune systems*
Authors: Suckale Jakob , Sim Robert B. , Dodds Alister W.
Published: February 2007

Innate immunity is the oldest form of defense and is found to some degree in all species. It predates the adaptive immune system, consisting of antibodies, B cells, T cells, and the major histocompatibility antigens. These are found only in higher vertebrates and have been the focus of the majority of immunological research, particularly in mice and humans, over the years. Knowledge of immunity in lower vertebrate and invertebrate species is now increasing rapidly, shedding light on the evolution of immunity and in many cases adding to our understanding of the mammalian system. Several recurring structural, genetic, and developmental mechanisms are common features in these processes in both the cellular and the molecular aspects of innate immunity.
Facilitating understanding of the purine nucleotide cycle and the one‐carbon pool: Part I: The purine nucleotide cycle
Authors: Arinze Ifeanyi J.
Published: February 2007

Some metabolic processes are readily understood because they are circumscribed in metabolic pathways that have clearly identifiable beginning points, end products, and other features. Other metabolic pathways that do not appear to be straightforward pose difficulties for students. One such metabolic process, the purine nucleotide cycle, is discussed here.
Allosteric modulation of monomeric proteins*
Authors: Ascenzi Paolo , Bocedi Alessio , Bolli Alessandro , Fasano Mauro , Notari Stefania , Polticelli Fabio
Published: February 2007

Multimeric proteins (e.g. hemoglobin) are considered to be the prototypes of allosteric enzymes, whereas monomeric proteins (e.g. myoglobin) usually are assumed to be nonallosteric. However, the modulation of the functional properties of monomeric proteins by heterotropic allosteric effectors casts doubts on this assumption. Here, the allosteric properties of sperm whale myoglobin, human serum albumin, and human α‐thrombin, generally considered as molecular models of monomeric proteins, are summarized.
Facilitating understanding of the purine nucleotide cycle and the one‐carbon pool: Part II: Metabolism of the one‐carbon pool
Authors: Arinze Ifeanyi J.
Published: February 2007

Some metabolic processes such as glycolysis, gluconeogenesis, and lipogenesis are readily understood because they are circumscribed in metabolic pathways that have clearly identifiable beginning points, end products, and other features. Other metabolic pathways that do not appear to be straightforward pose difficulties for students. In part I of this two‐part series, one such metabolic process, the purine nucleotide cycle, was discussed (I. J. Arinze (2005) Biochem. Mol. Biol. Educ. 33, 165–168). In the present article, the focus is on the metabolism of one‐carbon fragments, the so‐called one‐carbon pool. As with the first article in this series, the intent of this article is to facilitate teaching and learning of this rather complex area of metabolism.