bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractRestriction 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

AbstractThis 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

AbstractThe 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

AbstractWe 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

AbstractA 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

AbstractWe 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

AbstractThis 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

AbstractWe 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

AbstractPCR 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

AbstractRedox 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

AbstractSymbiosis 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

AbstractIn 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

AbstractAn 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

AbstractTerms 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

AbstractGood 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

AbstractNature 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

AbstractThe 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

AbstractNeuroglobin (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

AbstractThe 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

AbstractThe 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

AbstractCourses 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.