bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chile: Begehrte Schnecken
Authors: Vasquez Nelson , Kronberg Inge 
Published: February 2007

AbstractMeeresschnecken werden in Europa nur wenig verzehrt. In anderen Kontinenten ist besonders die algenfressende Haliotis (Meerohr) beliebt, die je nach der Fleischfarbe als rosa, grüne, rote, schwarze oder weiße Abalone gehandelt wird. Eine ähnliche große Meeresschnecke ist die chilenische Abalone (Concholepas concholepas), die zu den Raubschnecken (Muricidae) gehört, also eigentlich eine “falsche” Abalone ist. Sie wird in Chile und Peru als “loco” gesammelt und gegessen. Seit über 20 Jahren spielt auch der Export eine wachsende Rolle und hat zu einem Rückgang der Bestände geführt. Die Erforschung ihrer Biologie und Managementpläne unter Beteiligung der Küstenbewohner sollen das Problem lösen.
The Relevance of student seminars on clinically related subjects in a biochemistry course for medical and nutrition students
Authors: Hermes‐Lima Marcelo , Muniz Karinne C. , Coutinho Iracema S. 
Published: February 2007

AbstractThe aim of this study was to determine the value of a system of seminars on clinically related biochemistry topics for undergraduate students in medicine and nutrition at the University of Brasília, Brazil. During the second semester of 1998 (1998–2), the teaching staff decided to establish new and stricter rules for the seminar method and to adopt a system of peer tutoring, whereby former good to excellent students of the class Bioquímica e Biofísica helped in the planning and preparation of the oral presentations. The average performance grades for the seminars in the first semester of 1998 (1998–1) (7.19 ± 1.42) were significantly lower than those for the following semesters (ranging from 8.10 to 8.91), indicating some degree of success with the new system. We also conducted, by means of questionnaires, an evaluation (scores ranging from 0 to 4) of each student seminar (14 topics) in relation to the overall biochemistry learning experience connected to the clinical expectations of the students. All seminars but one averaged above 3.0. Moreover, when asked whether (i) the seminars were relevant to a more clinical approach to biochemistry and whether (ii) the oral presentations could be viewed as valid tools for the understanding of biochemistry, 96% (n = 188) and 80.6% (n = 150) of the students, respectively, answered, “yes.” The students also scored the work of the peer tutors high (ranging from 3.38 to 3.90, out of 4). A seminar system for a clinically related biochemistry course may also open the minds of students about the relevance of biochemistry to their future medical or nutritional practices.
Integrating internet assignments into a biochemistry/molecular biology laboratory course
Authors: Kaspar Roger L. 
Published: February 2007

AbstractA main challenge in educating undergraduate students is to introduce them to the Internet and to teach them how to effectively use it in research. To this end, an Internet assignment was developed that introduces students to websites related to biomedical research at the beginning of a biochemistry/molecular biology laboratory course. The basic sites introduced cover many subjects, include searching for specific DNA sequences, restriction enzyme mapping, RNA folding, analyzing three‐dimensional protein images, and literature searches. These newly learned Internet skills are incorporated into other aspects of the laboratory course. In the example illustrated here, students sequence DNA inserts from randomly chosen bacterial colonies prepared from a human cDNA plasmid library. The obtained DNA sequence is used to search on‐line data bases introduced in the initial Internet assignment to determine whether the cDNAs have already been identified. The sequencing “wet‐lab” module, coupled with the Internet assignment, gives students experience in four areas. 1) purifying plasmid DNA, 2) performing restriction endonuclease digests on the plasmid DNA, 3) sequencing double‐stranded DNA, and 4) comparison of obtained sequence data to known DNA sequences in the human genome data base in a way that simulates a research experience.
Practical studies on urine demonstrating principles of clinical and veterinary significance
Authors: Ryan J. Philip , Irwin Jane A. 
Published: February 2007

AbstractUrine is a versatile and variable fluid that can be readily used in practical classes to demonstrate important biochemical and physiological principles. It can be readily adjusted to simulate a wide variety of medical conditions. This paper describes a range of easily performed experiments and includes some background on clinical and veterinary aspects. The experiments can be adapted for veterinary medicine, animal science, or medical students of biochemistry or physiology. To avoid any possibility of health risks posed by real urine samples, the experiments may be carried out on simulated samples. These experiments are ideal for laboratories with small resources.
Evaluation of molecular visualization software for teaching protein structure differing outcomes from lecture and lab: Differing outcomes from lecture and lab
Authors: White Brian , Kim Stella , Sherman Katerina , Weber Nicole 
Published: February 2007

AbstractIn this study we measured the learning outcomes resulting from using molecular visualization software in lecture and in the teaching laboratory of a large introductory‐level undergraduate biology majors' course. The study was initially carried out in the Fall semester of 1999; the results of this study were used to devise an expanded laboratory component that was evaluated in a second study carried out in the Fall of 2000. In both studies, students (n = 175 and 161) attended two 50‐min lectures that used molecular visualization software to explain protein structure and function and the gene‐protein connection. Students also used this software during one 3‐h laboratory session as a tool for exploring these topics. Students completed open‐ended pre‐ and post‐surveys that involved a related but unfamiliar task. Survey responses were scored for correctness, as well as by the type(s) of explanations used in the response. We found the following eight types of responses that students employed to explain protein structure and function: genetics, protein structure, chemical interactions, amino acid sequence, purpose/teleology, extrinsic factors, miscellaneous, and none. In both studies, the frequencies of correct answers, as well as the frequencies of each response type, showed significant changes as a result of lecture and/or lab. The effects of lecture were highly similar in both studies. The changes in the expanded lab resulted in significant changes in outcome. Overall, the curriculum effectively communicated several core concepts in protein biochemistry and expanded the conceptual “toolkit” that students applied to problems of protein structure and function. Lecture increased students' understanding of the role of amino acid sequence, whereas lab tended to increase their understanding of three‐dimensional structure and the gene‐protein connection. Our results demonstrate that exposure to molecular visualization, even for a relatively brief time, can improve students' understanding of protein structure and function. In addition, we demonstrate the differing and largely non‐overlapping effects of lecture and lab, suggesting that effective use of molecular visualization should involve both types of activities.
Investigating plant galactomannans
Authors: Mulimani Veerappa H. , Prashanth Sirigeri J. 
Published: February 2007

AbstractThis paper presents a review of biological importance and occurrence of galactomannan in plants. Its chemical composition and structure are reviewed, and a short laboratory practical exercise on the isolation and determination of D‐mannose/D‐galactose ratio of plant galactomannan is presented.
Understanding heterologous protein overproduction under the T7 promoter: A practical exercise
Authors: Christodoulou Evangelos , Vorgias Constantinos E. 
Published: February 2007

AbstractBecause various genome projects have been advanced many genes are known, and large amounts of proteins are required to elucidate their function. Most biomolecular research laboratories have a need to overexpress a certain gene, or a part of it, in eukaryotic or prokaryotic expression systems. It is therefore important for young students to become familiar with the technology of heterologous gene expression systems. Gene expression in eukaryotic cells is rather complicated and costly and is therefore not ideally suited to exercises for students. The goal of this paper is to describe an experimental example of a well known and broadly used prokaryotic system, the pET system, that works under the strong T7 promoter. The clones described in this paper are suitable for the practical exercise and are available upon request.
An experiment illustrating the effect of saline stress and ions on the malate dehydrogenase activity in vegetal tissues*
Authors: González‐Moreno Sergio , Perales‐Vela Hugo , Alvarez Martha O. Salcedo 
Published: February 2007

AbstractThis paper describes a simple, rapid, and economic protocol to evaluate the effect of saline stress and Na+, K+, Ca2+, and Mg2+ions on malate dehydrogenase activity in crude extracts from the leaves and roots ofVigna radiata. The main objectives of this work are to illustrate the effect of an environmental stress factor, as well as thein vitroeffect of some ions on an enzymatic activity, while introducing the students to the use of Michaelis‐Menten kinetics and a graphic procedure to calculate kinetics constants.
On the H+/2e− stoichiometry of the respiratory chain *
Authors: Guerra Guadalupe , Martínez Federico , Pardo Juan Pablo 
Published: February 2007

AbstractTo calculate the number of ATP molecules synthesized during oxidative phosphorylation, and to understand the yield and efficiency of this process, it is necessary to know the H+/2e− stoichiometry of the respiratory complexes, as well as the H+/ATP ratio for the ATP synthase. However, in most biochemistry textbooks, this topic is treated poorly. For example, several books simply mention that mitochondrial respiratory complexes pump protons across the membrane, without any reference to the number of protons translocated per pair of electrons [1–4]. Stryer's textbook [5] mentions a 4H+/2e−, 2H+/2e−, 4H+/2e− stoichiometry for complex I, III, and IV, respectively, but most recent editions of the biochemistry textbooks of Nelson and Cox [6] and Voet et al. [7] cite a 4, 4, 2 stoichiometry [6, 7]. Several years ago Hinkle et al. [8] proposed a 4, 2, 4 stoichiometry for the “effective” pumping of protons across the membrane; interestingly, these values are identical to the number of charges moved across the inner mitochondrial membrane by respiratory complexes I, III, and IV. The present work describes several arguments in favor of the stoichiometry of 4, 2, 4 for complex I, III, and IV, respectively.
Introduction to interpretation of stochastic parameters: Computer‐intensive procedures for evaluation of data in enzyme kinetics
Authors: Tenekedjiev Kiril , Kolev Krasimir 
Published: February 2007

AbstractComputer simulation of a simple enzyme kinetic model is used to train medical students in interpretation of the stochastic nature of experimentally estimated model parameters. The principles for identification of parameters and estimation of their confidence intervals with the help of Monte Carlo procedures are introduced in a simplified and easily perceivable form.
An innovative selection and training program for problem‐based learning (PBL) workshop leaders in biochemistry*
Authors: Platt Terry , Barber Eugene , Yoshinaka Antoine , Roth Vicki 
Published: February 2007

AbstractWe describe here a novel and effective structure to support the replacement of traditional recitation sections in a large upper level biochemistry course with small student‐led problem‐based learning (PBL) groups (“workshops”) that employ a cooperative learning approach. This is part of an ongoing campus‐wide effort to establish and maintain such workshops as a viable and integral component of many undergraduate courses at the University of Rochester. In biochemistry, for each workshop group of 8–10 students, we rely on a student leader, usually recruited from the previous year's pool of top students, whose function is both to guide and to inspire the group effort. A crucial component of our approach is that these leaders participate in a semester‐long credit‐bearing training course co‐taught by the course instructors and an educational specialist. In this course, leaders review the preceding and upcoming weeks' workshops and study selected aspects of learning theory, group dynamics, and diversity training. Overall our workshop leaders feel that they benefit substantially from this training by improving their pedagogical skills in the context of biochemistry, by putting theories about group leadership and learning into practice, and by solidifying their working biochemical knowledge. We believe that the important features of implementing our model (the incorporation of a problem‐based learning approach into a student‐led small group format) are: 1) the teamwork as co‐equals between the course instructors and the educational specialists, 2) the concurrent iterative training of the workshop leaders in a credit‐bearing course of study, 3) the built‐in leader turnover (normally a frustrating occurrence) as a beneficial component of the course, and 4) the enthusiasm and commitment to biochemistry displayed to current students by their peer leaders.
A programmable $25 thermal cycler for PCR
Authors: Betsch David F. , Blais Brian S. 
Published: February 2007

AbstractThis article describes the construction of a safe, programmable, automatic thermal cycler for PCR that can be easily constructed by persons with basic soldering and mechanical skills for under $25 in parts and a modest computer such as IBM 486, all of which are readily available. The cycler relies on the heating provided by an incandescent light bulb and cooling by simple convection.
A laboratory exercise in comparative DNA analysis
Authors: Brown Lesley R. 
Published: February 2007

AbstractThis report describes a laboratory exercise that is used in an upper level biochemistry course at a small liberal arts college. The laboratory exercise was designed with three major learning objectives in mind. The first objective is that students learn how to isolate and purify plasmid DNA. The second is that they understand this process on a molecular level. Last, they analyze their DNA samples using a variety of biochemical and biophysical methods. By comparing and contrasting the results, they are to draw conclusions about which methods would be best under a given set of experimental conditions.
Determination of the molecular size of BSA by fluorescence anisotropy
Authors: González Flecha F. Luis , Levi Valeria 
Published: February 2007

AbstractThis work describes a laboratory experiment to illustrate the usefulness of fluorescence anisotropy in the field of biophysics. Fluorescence anisotropy of dansyl‐labeled BSA was determined in media of increasing glycerol concentrations. The Perrin equation was fitted to the experimental data, obtaining the molecular volume of the protein. The simplicity of the experiment and data analysis helped the students to focus on the relationship between probe anisotropy and rotational diffusion. Additionally, this laboratory exercise has the advantage of using a protein and a probe that are inexpensive and very common in many laboratories.
The regulation of the function of the tumor suppressor protein p53
Authors: Szeberenyi Jozsef 
Published: February 2007

AbstractTerms to be familiar with before you start to solve the test: Tumor suppressor proteins; p53 protein; p53‐positive and p53‐negative tumors; transcription factors; protein phosphorylation; retinoblastoma protein; Go phase; apoptosis; chaperone; transfection; expression plasmid; cDNA; papillomavirus; Western blot analysis; γ‐irradiation; mitotic index; [3H]thymidine labeling.
Adapting a biochemistry course to distance education
Authors: Yokaichiya Daniela K. , Galembeck Eduardo , Torres Bayardo B. 
Published: February 2007

AbstractInternet‐based distance education seems to be an attractive alternative to offer courses dealing with specific topics that are not conveniently explored in undergraduate courses. This is a good way to provide access to the recent and updated discoveries in this research area and to reach people who could not take the classes in the traditional mode. Using the communication advantages available via the Internet, we adapted the course “Biochemistry of Nutrition,” first offered as a summer course to be entirely carried out at distance. The adaptation explored the use of online tools such as E‐mail communication among students and teachers, computer conferencing in small groups to discuss specific subjects, and texts and software downloads to be used as main references. Graduate students had their first real experience as teachers, which proved to be very productive for both the development of the Internet version of the course and their integration with undergraduate students.
The zymogen‐enteropeptidase system: A practical approach to study the regulation of enzyme activity by proteolytic cleavage*
Authors: Pizauro João M. , Ferro Jesus A. , de Lima Andréa C. F. , Routman Karina S. , Portella Maria Célia 
Published: February 2007

AbstractThe present research describes an efficient procedure to obtain high levels of trypsinogen and chymotrypsinogen by using a simple, rapid, and easily reproducible method. The extraction process and the time‐course of activation of zymogens can be carried out in a single laboratory period, without sophisticated equipment. The main objective was to prepare a laboratory class that would stimulate student interest in enzyme regulation, exploring the fact that the catalytic activity of some enzymes is regulated by different mechanisms. The regulation of proteolytic enzymes requires the synthesis of an inactive zymogen and its being irreversibly “switched on” by specific proteolytic cleavage.
An hypothesis‐driven, molecular phylogenetics exercise for college biology students
Authors: Parker Joel D. , Ziemba Robert E. , Cahan Sara Helms , Rissing Steven W. 
Published: February 2007

AbstractThis hypothesis‐driven laboratory exercise teaches how DNA evidence can be used to investigate an organism's evolutionary history while providing practical modeling of the fundamental processes of gene transcription and translation. We used an inquiry‐based approach to construct a laboratory around a nontrivial, open‐ended evolutionary question about the relationship of five species ofDrosophila. In the course of answering this question, students at the early college biology level learn how the information in DNA can be extracted and used by both the cell and scientists. This dual proximate‐ultimate approach introduces students to the techniques of PCR, DNA sequencing, and phylogenetic sequence analysis while simultaneously providing a concrete pen‐and‐paper model of the cellular processes of transcription and translation. The laboratory has been successfully employed over 3 years with first‐year college students and has proven its versatility by being easily adapted to a “dry lab” form with advanced high school students.
Formation and detoxification of reactive oxygen species
Authors: Kuciel Radosława , Mazurkiewicz Aleksandra 
Published: February 2007

AbstractA model of reactive oxygen species metabolism is proposed as a laboratory exercise for students. The superoxide ion in this model is generated during the reaction of oxidation of xanthine, catalyzed by xanthine oxidase. The effect of catalase, superoxide dismutase, and allopurinol on superoxide ion generation and removal in this system is also determined, using cytochrome c as a probe.
Thermodynamic properties of peptide folding
Authors: Sigman Jeffrey A. 
Published: February 2007

AbstractInter‐ and intramolecular forces and thermodynamics are concepts usually presented early within introductory biochemistry and have relevance to many topics throughout the remainder of the course. For this reason, it is important to have a good foundation in these concepts so they can be applied to many systems. To this end, a group problem has been developed that allows students to analyze thermodynamic data and, using their knowledge of inter‐ and intramolecular forces, gain an understanding of the elements involved in the thermodynamic stability and folding of a peptide.
An introductory bioinformatics exercise to reinforce gene structure and expression and analyze the relationship between gene and protein sequences
Authors: Almeida Craig A. , Tardiff Daniel F. , De Luca Jane P. 
Published: February 2007

AbstractWe have developed an introductory bioinformatics exercise for sophomore biology and biochemistry students that reinforces the understanding of the structure of a gene and the principles and events involved in its expression. In addition, the activity illustrates the severe effect mutations in a gene sequence can have on the protein product. Students search GenBank for the wild‐type nucleotide sequence of the Caenorhabditis elegans unc‐22 gene, the amino acid sequence of its gene product, and the nucleotide sequence of the transposon Tc5. The nucleotide sequences are manipulated using two programs in the Lasergene® software package from DNASTAR®. The first program, EditSeq®, enables students to experience the meticulous process required to precisely locate and remove intron sequences from the wild‐type unc‐22 allele to generate a cDNA sequence. The unc‐22(r466) allele is generated by inserting the sequence of the transposon Tc5 into the appropriate location of the third exon in unc‐22. The open reading frames of both cDNAs are located and then translated. MegAlign®, the second program, aligns the wild‐type sequence of the UNC‐22 protein and the wild‐type and mutant protein sequences that were constructed. The degree of sequence similarity between the aligned proteins allows students to verify their success in processing the gene, as well as to visualize the truncated protein product from the Tc5 mutant allele. Student feedback and possible modifications to the exercise as well as supplemental exercises are also discussed.
Immunoassay for visualization of protein‐protein interactions on Ni‐nitrilotriacetate support: Example of a laboratory exercise with recombinant heterotrimeric Gαi2β1γ2 Tagged by Hexahistidine from sf9 Cells
Authors: Bavec Aljosa 
Published: February 2007

AbstractWe have developed an in vitro assay for following the interaction between the αi2 subunit and β1γ2 dimer from sf9 cells. This method is suitable for education purposes because it is easy, reliable, nonexpensive, can be applied for a big class of 20 students, and avoid the commonly used kinetic approach, which does not allow visualization of protein‐protein interaction.
Simple protocol for secondary school hands‐on activity: Electrophoresis of pre‐stained nucleic acids on agar‐agar borate gels
Authors: Britos Leticia , Goyenola Guillermo , Oroño Silvia Umpiérrez 
Published: February 2007

AbstractAn extremely simple, inexpensive, and safe method is presented, which emulates nucleic acids isolation and electrophoretic analysis as performed in a research environment, in the context of a secondary school hands‐on activity. The protocol is amenable to an interdisciplinary approach, taking into consideration the electrical and chemical parameters of the electrophoretic system. Furthermore, the laboratory is framed in a more comprehensive pedagogical setting, which addresses the methodological aspects of a pivotal scientific enterprise such as the Human Genome Project. In this setting, the hands‐on activity is complemented with animations, paper models, and discussions. Additionally, our results indicate that the use of borate buffer and agar‐agar gels suits many of the experiments included in college‐level laboratory activities, which currently make use of more expensive agarose gels and TBE or TAE buffers.