bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermostable glucoamylase‐type enzyme from Bacillus acidocaldarius RP1*
Authors: Natalia Dessy , Yuliani Yuyu , Ermayadhie Yusdiana , Putra Redha , Sindumarta Muliawati 
Published: February 2007

AbstractWe present an experiment that enables student to understand the properties of thermostable glucoamylase‐type enzyme produced by thermophilic Bacillus acidocaldarius RP1 isolated from Cimanggu Hot Spring, West Java, Indonesia. In addition, the students also gain experience working with a thermostable microorganism and some techniques frequently used in biochemistry, e.g. ultrasonication, ammonium sulfate fractionation, and spectrophotometric analysis. The glucoamylase‐type enzyme activities were detected both as cell‐associated and in the culture supernatant. The 20–40% saturated ammonium sulfate fraction of glucoamylase‐type enzyme exhibited an optimum temperature of 65 °C and an optimum pH of 4.5. The enzyme showed a Vmax of 600 milliunits/mg and Km of 11.7 mg/ml.
Kinetic studies with alkaline phosphatase in the presence and absence of inhibitors and divalent cations
Authors: Dean Rob L. 
Published: February 2007

AbstractA very robust and inexpensive kinetic assay for determining rates of hydrolysis of p‐nitrophenyl phosphate by the enzyme alkaline phosphatase is presented. The reaction increases in rate with increase in pH. The enzyme is competitively inhibited by the reaction products, uncompetitively inhibited by L‐phenylalanine, and responds to the presence of two cofactors, magnesium and zinc ions. The reaction rate increases as Mg2+ concentration is increased from 1–5 mM. With increasing Zn2+ concentration, the reaction rate is stimulated and then depressed. Experimental work on the interaction between Mg2+ and Zn2+ in the reaction is suggested for more capable students.
A collaborative, investigative recombinant DNA technology course with laboratory*
Authors: Pezzementi Leo , Johnson Joy F. 
Published: February 2007

AbstractA recombinant DNA technology course was designed to promote contextual, collaborative, inquiry‐based learning of science where students learn from one another and have a sense of ownership of their education. The class stressed group presentations and critical reading and discussion of scientific articles. The laboratory consisted of two research projects: random cDNA cloning and in vitro expression and site‐directed mutagenesis of cholinesterase. Students prepared a poster and wrote a scientific paper peer‐reviewed by scientists at a nearby university. Multiple methods were used to evaluate the course. Evaluation data were consistent and positive. Students learned to read, present, and discuss scientific articles in depth, work collaboratively in small teams, and perform genetic engineering experiments. The students also outperformed all biology majors on the molecular biology/genetics subtest of the Major Field Achievement Test. The course has an extensive website at http://panther.bsc.edu/∼lepezzem/bi405_html/bi405.html.
Comparison of the interaction of cobalt bovine carbonic anhydrase II with acetazolamide and methazolamide and the reaction of apoenzyme with cobalt(II) complexes of acetazolamide and methazolamide: Spectrophotometric study
Authors: Rubio Silvia , Borrás Consuelo , Alzuet Gloria , Borrás Joaquin 
Published: February 2007

AbstractThe metalloenzyme carbonic anhydrase (CA) is an attractive choice for a research‐based bioinorganic laboratory course. In this project the interaction of cobalt bovine carbonic anhydrase II (CoBCAII) with acetazolamide and methazolamide and the reaction of apoenzyme with cobalt(II) complexes of acetazolamide and methazolamide is studied by UV‐visible spectroscopy. Prior to this spectroscopic study students are given native BCAII, and they prepare apoBCAII and CoBCAII. A major aim is to provide experience in handling metalloproteins and in the study of metal complexes‐protein interactions.
Assessment of verbal communication in science education: A comparison of small and large classes*
Authors: Haworth Ian S. , Garrill Ashley 
Published: February 2007

AbstractClear verbal communication is a key skill for the modern scientist. In this article we describe two model science courses, one given to a small class and the other to a large class, in which verbal communication is emphasized as a key learning objective. Both courses use a form of problem‐based learning (PBL) with an end point that involves students communicating their results and ideas verbally. Hence, assessment of verbal communication is necessary. We describe several different approaches to this challenge and highlight their applicability to small and large class sizes. We then show that, with careful application of these methods, a good relationship can be obtained between scores on verbal assessment exercises and scores on written examinations. On this basis, we argue that the verbal assessment can give an accurate reflection of the student's ability and can therefore be used as a method of formative evaluation in addition to being a component of the overall grade.
Crime scene investigation: An exercise in generating and analyzing DNA evidence*
Authors: Lounsbury Karen M. 
Published: February 2007

AbstractThe goal of this project is to introduce students to molecular biology techniques using an experimental setting that inspires both scientific and personal interest. The project is designed as a small group apprenticeship for gifted high school juniors or seniors who can spend full time in a sponsor's laboratory for at least 1 week. The students begin by examining evidence from a mock crime scene that consists of hair samples from the crime scene and from five potential suspects. Students extract DNA from the hair samples and amplify a hypervariable region within the mitochondrial genome using the polymerase chain reaction. Amplified products are then sequenced and compared with the crime scene sequence using DNA alignment software. In consecutive projects, students from four different schools successfully identified the suspect who matched the crime scene evidence. This project is a valuable learning tool not only due to the comprehensive introduction to molecular biology techniques but also because it helps the students to connect scientific exploration with well publicized media events and provides a window into potential career opportunities in the field of molecular biology.
Concepts and skills in the biochemistry/molecular biology lab
Authors: Boyer Rodney 
Published: February 2007

AbstractMost colleges and universities throughout the world now offer a Biochemistry/Molecular Biology (BMB) lab course that is designed for undergraduate students in the molecular life sciences, chemistry, and related fields. To best serve our students, we must introduce them to the most current concepts, skills, and methods available. Suggestions for teaching a modern BMB lab are given here.
On the convenience of using a computer simulation to teach enzyme kinetics to undergraduate students with biological chemistry‐related curricula
Authors: González‐Cruz Javier , Rodríguez‐Sotres Rogelio , Rodríguez‐Penagos Mireya 
Published: February 2007

AbstractEnzyme kinetics is a difficult subject for students to learn and for tutors to teach. During the practicals included in the biochemical courses at the Faculty of Chemistry of Universidad Nacional Autónoma de México, we found that the students acquire good training in the calculations to obtain kinetic parameters such as Km, Vmax, optimum pH, etc., but, when they are questioned about the significance of the values and their relationship to enzyme catalysis, many confusing ideas arise. To provide extended practice opportunities that could aid in the learning process we developed computer software that simulates an enzyme assay for lactate dehydrogenase, named enzsimil, that was used as well as the practical sessions. We tested three different levels of guidance to work with enzsimil, scripts where the students had to follow detailed (guided), intermediate (semiguided), or minimal (unguided) instructions, and for comparison, one group had a session of solving problems in class extracted from the program (class), and one more group had no additional sessions (control). After their respective sessions, the students either wrote a report or completed their script and undertook a laboratory practical. At the end, an exam was applied to all students. The reports and exams were graded, and the performance of the experimental groups was subjected to a statistical analysis. In addition, we carefully read the answers trying to identify the more common errors and misconceptions. The study revealed that there are statistically significant benefits in the use of the program. The semiguided scheme was more convenient to help the student in the short term for the preparation of better reports, while in the long term, both the semiguided and unguided groups performed equally well. These results are discussed in terms of the convenience of guided or unguided teaching strategies in computer‐assisted learning.
Purification of colored photosynthetic proteins for understanding protein isolation principles
Authors: Bes M. Teresa , Sancho Javier , Peleato M. Luisa , Medina Milagros , Gómez‐Moreno Carlos , Fillat María F. 
Published: February 2007

AbstractThe purification of a protein is the essential initial step in the study of its physical and biological properties and is one of the most common procedures in biochemistry. This article describes a method for teaching purification skills through the partial isolation of ferredoxin‐NADP+ reductase and ferredoxin from a single cell batch. The method has been used for several years in an introductory biochemistry course using spinach leaves as cellular source. The protocol gives a complete picture of the preparation of a crude extract and the subsequent isolation of both electron transport proteins on a laboratory scale. It introduces students to the use of different techniques for the purification and detection of proteins and allows them to develop a number of valuable experimental and analytical skills without necessarily resorting to complicated or expensive equipment.
Fermentable and non‐fermentable sugars: A simple experiment of anaerobic metabolism
Authors: Paulino Tony P. , Cardoso Mauro , Bruschi‐Thedei Giuliana C. M. , Ciancaglini Pietro , Thedei Geraldo 
Published: February 2007

AbstractThe main objective of this class experiment is to show the time‐dependent consumption of a fermentable sugar (glucose) in the presence and absence of a non‐fermentable sugar (xylose) by bacteria in anaerobic conditions. The observation of the pH decrease due to acid production and the turbidity increase as a result of cell multiplication, both in function of time, enables an interesting discussion regarding the metabolic pathways and the products of anaerobic fermentation of carbohydrates. Also the time‐dependent disappearance of glucose due to its metabolic consumption is compared with the non‐disappearance of xylose and permits a discussion of the function of glycolysis and pentose phosphate pathways as metabolic routes.This work was supported by the Universidade de Uberaba, Fundaçao de Amparo à Pesquisa do Estado de São Paulo, and Conselho Nacional de Pesquisas (Brazil).
Isolation of chicken immunoglobulins (IgY) from egg yolk*
Authors: Goldring J. P. Dean , Coetzer Theresa H. T. 
Published: February 2007

AbstractSeparating individual proteins from complex mixtures of molecules is the basis of many biochemical investigations. The method describes the separation of immunoglobulin Y (IgY) from chicken eggs using a series of physical and chemical separation techniques. The separation is rapid, and the success of each step is readily viewed on an SDS‐polyacrylamide gel. IgY identity can be confirmed on a Western blot probed with enzyme‐labeled anti‐IgY antibodies. The method is a good illustration of protein separation when there is no enzyme activity to follow.
It is time to update “the graduate”
Authors: Gundersen Larry E. 
Published: February 2007

AbstractWhile leaders of the commercial biotechnology industry are impressed with the numbers and quality of science graduates, they complain that they must invest time to further train them about basic aspects of this highly regulated work environment. The addition of a small number of recommended courses would augment the students' preparation for and participation in commercial research and development (R&D). These courses include a basic understanding of the R&D process and the laws and regulations that impact this process, such as Good Laboratory Practices (GLPs) and current Good Manufacturing Practices (cGMPs). Finally it is suggested that the most likely and capable teachers of these principles are working in the biotechnology industry, and it will involve active collaboration between academia and industry to best prepare graduates for success in biotechnology R&D.
Lesson plan for protein exploration in a large biochemistry class*
Authors: Honey David W. , Cox James R. 
Published: February 2007

AbstractThe teaching of structural concepts plays a prominent role in many chemistry and biology courses. When it comes to macromolecular systems, a thorough understanding of noncovalent interactions lays a strong foundation for students to understand such things as protein folding, the formation of protein‐ligand complexes, and the melting of the DNA double helix. The incorporation of computer‐based molecular graphics into the biochemistry curriculum has given students unique opportunities in visualizing the structure of biological molecules and recognizing the subtle aspects of noncovalent interactions. This report describes a series of visualization‐based assignments developed to facilitate protein exploration in a large biochemistry class. A large enrollment can present special challenges for students to benefit from hands‐on use of visualization software. Three of the assignments are described in detail along with a description of an on‐line teaching tool used to manage the assignments and to coordinate the student groups participating in these exercises.
Achievement of original results in an essentially practical course in molecular biology for undergraduate students
Authors: Possik Patricia Abrão , Malagó Junior Wilson , Torres Bayardo Baptista , Henrique‐Silva Flávio 
Published: February 2007

AbstractWe discuss a proposal for an experimental, laboratory‐based course in molecular biology aimed at familiarizing undergraduate students with scientific research. The main advantage of this course is that it provides students with good laboratory training through the development of a scientific project and the achievement of original results. The course was implemented experimentally, with students actively involved from the elaboration to the execution of a scientific project, which included the amplification, cloning, and sequencing of DNA. The project consisted of the isolation of microsatellite arrays from ostrich using a polymerase chain reaction‐based identification of microsatellite arrays (PIMA) technique. The group successfully identified three putative microsatellites and presented its results to the National Congress of Genetics. Additionally, graduate students participated in teaching activities as tutors, monitoring class experiments and assisting the groups. An evaluation of the discipline revealed a highly positive feedback from graduate and undergraduate students.
An undergraduate biochemistry laboratory course with an emphasis on a research experience
Authors: Caspers Mary Lou , Roberts‐Kirchhoff Elizabeth S. 
Published: February 2007

AbstractIn their junior or senior year, biochemistry majors at the University of Detroit Mercy are required to take a two‐credit biochemistry laboratory course. Five years ago, the format of this course was changed from structured experiments to a more project‐based approach. Several structured experiments were included at the beginning of the course because not all students were familiar with computer‐based statistics and graphics programs or fundamental biochemical techniques. Finally, students were given an enzyme purification assignment and a test/control project. In the latter project, students were provided with tissue from test and control animals and were expected to propose and test a parameter that they hypothesized might be different between the two tissues. For both projects, student teams were required to search the literature, submit and orally defend their proposals, perform the experiments, and submit a report. For all experiments except the test/control project, students submitted a written report in the style of a journal paper. A poster presentation was required for the test/control project. In course evaluations, the students cited a high degree of satisfaction with the project‐based approach.
Self or help? A comparison of a personalized system of instruction biochemistry class to a standard lecture‐based biochemistry class
Authors: Ocorr Karen , Osgood Marcy P. 
Published: February 2007

AbstractFor the past eight years the University of Michigan has offered two different styles of biochemistry courses each semester, one a standard lecture‐based and discussion‐section (SLB) course and one a self‐paced, non‐lecture Personalized System of Instruction (PSI) course. We tracked student responses to selected exam questions that were used in both courses for three semesters. Data on student grade point average, student satisfaction, and perceived effort in the courses were also gathered. In two of the three semesters that we monitored students there were no significant differences in performance on test questions between the two courses. In one of the three semesters there was a small but nevertheless significant difference between the two courses with junior and senior PSI students outperforming their SLB counterparts by 10 points. Student grade point average, overall satisfaction, and perceived effort were similar for both courses. Our study indicated that the PSI format works as well as the SLB model does for students in biochemistry and may be especially beneficial for more experienced students.
Evaluation of a web‐based resource to support a molecular biology practical class—does computer‐aided learning really work?
Authors: Gibbins Sue , Sosabowski Michael Hal , Cunningham Jim 
Published: February 2007

AbstractIn view of the increasing usage of information technology in learning and teaching there is an increasing need for meaningful evaluation of the effectiveness of information technology‐based media. The aim of this study was to investigate whether a web‐based computer‐aided learning (CAL) package enhances the learning outcomes of a laboratory‐based molecular biology class. A multiplex PCR practical exercise to detect genetically modified sequences in soybean DNA was carried out by students using either traditional (non‐electronic) teaching and learning resources or a web‐based CAL resource. The learning outcomes were evaluated by pre‐ and post‐class subject‐based comparative tests with self‐assessed confidence ratings and questionnaires. Scores relating to four modes of student learning style were assessed by questionnaire and these were correlated with the effectiveness of the support resource used. There was a significantly greater improvement in knowledge‐based test performance and self‐assessed confidence rating by students using CAL‐based learning support versus those using traditional resources. Learning style score did not correlate with the enhancement in performance by students supported by the CAL package, although one learning style did favor a response to the traditional support package. We conclude that compared with a non‐electronic alternative, the use of CAL can enhance learning and teaching outcomes in a laboratory‐based molecular biology class.
Influence of enzyme conformational changes on catalytic activity investigated by circular dichroism spectroscopy
Authors: Rigos Carolina Fortes , Santos Hérica de Lima , Thedei Geraldo , Ward Richard John , Ciancaglini Pietro 
Published: February 2007

AbstractEnzyme activity is dependent on native conformational integrity. Here we present a simple laboratory exercise based on dichroism spectroscopy in which the change in enzyme structure induced by denaturation is correlated with the loss of catalytic activity. The results of circular dichroism spectra show that enzyme denaturation by either trifluoroethanol (enhancement of α‐helix structure) or guanidinium chloride (reduction of α‐helix and enhancement of random coil structure) leads to a concomitant reduction in enzyme activity, which demonstrates the relationship between structure and catalytic activity of the enzyme. This simple experimental approach demonstrates that only a single native protein (enzyme) conformation has the ability to catalyze substrate hydrolysis.
The ames test
Authors: Szeberenyi Jozsef 
Published: February 2007

AbstractTerms to be familiar with before you start to solve the test: Polycyclic aromatic hydrocarbons, microsomal fraction, histidine operon, mutation, induction, repression, translation, Ca2+ channel, Ca2+ ATPase, steroid receptor, cytochrome P450, cytochrome c, direct and indirect carcinogen, procarcinogen, mutagenic compounds, tumor initiation, tumor promoter, complete and incomplete carcinogens, apoptosis.
Implementing the recommended curriculum in biochemistry & molecular biology at a Large State University: THE TEXAS A&M EXPERIENCE
Authors: Gunn J. Martyn 
Published: February 2007

AbstractThis article discusses how the biochemistry curriculum at Texas A&M University, a large, state‐assisted research university, fulfills the American Society for Biochemistry and Molecular Biology‐recommended guidelines. In addition, the research requirement for our degree, changes we are making to the curriculum, and the effect our large service teaching function has on implementing the guidelines are discussed.
Labeling of proteins with fluorescent probes: Photophysical characterization of dansylated bovine serum albumin
Authors: Levi Valeria , González Flecha F. Luis 
Published: February 2007

AbstractFluorescence spectroscopy is a widely used technique in biophysical studies. One of the strategies frequently used consists of labeling biomolecules with fluorescent probes, which have distinctive photophysical properties. This methodology allows the study of a wide variety of structural features of the biomolecule. We describe a simple laboratory activity for undergraduate Biophysical Chemistry courses. The experimental work includes two activities: labeling BSA with dansyl chloride and analyzing the resulting absorption and fluorescence spectra. The discussion of these activities helps students to understand the basis of fluorescence spectroscopy with emphasis in the application to biological systems.
Rates of electron transport in the thylakoid membranes of isolated, illuminated chloroplasts are enhanced in the presence of ammonium chloride
Authors: Dean Rob L. , Miskiewicz Ewa 
Published: February 2007

AbstractThe rate of flow of electrons from water to an artificial electron acceptor, dichlorophenolindophenol (DCPIP), through photosystem II in the thylakoid membranes of isolated chloroplasts is greatly enhanced in the presence of 10 mM ammonium chloride. Rate enhancement depends on irradiance levels. Uncoupling reagents like ammonium chloride prevent the formation of a proton gradient across the thylakoid membrane and consequently remove a constraint on the rate of electron transport. The mode of action of ammonium chloride is explained. Evidence obtained using an oxygen electrode that DCPIP itself also partially uncouples the system is presented as background information for instructors. Suggestions on how this reaction may be used in laboratory classes for students from high school to the senior undergraduate level are included.