bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementing the American Society for Biochemistry and molecular biology recommended curriculum in a biochemistry and molecular biology degree program in a genetics and biochemistry department: The Clemson University experience
Authors: Zimmerman James K. 
Published: February 2007

AbstractThis article describes the undergraduate biochemistry degree program at a medium‐sized, “state‐supported,” land‐grant university and how this degree program implements the curriculum recommended by the Educational and Professional Development Committee of the American Society for Biochemistry and Molecular Biology.The abbreviation used is: ASBMB, American Society for Biochemistry and Molecular Biology.
DNA isolation from a dried blood sample, PCR amplification, and population analysis: Making the most of commercially available kits
Authors: DeLong Frost Laura , Peart Sharifa T. 
Published: February 2007

AbstractA 3‐week undergraduate molecular biology laboratory exercise combining commercially available kits is described. The laboratory involves DNA extraction from a human dried blood sample, amplification of an Alu‐repeat sequence found on chromosome 8, and analysis of the genetic and allelic frequency in the class population using Hardy‐Weinberg statistics. The use of the prepared kits provides a means for the instructor of an undergraduate biochemistry course to explore molecular biology techniques on a limited budget and with a minimal time investment.
Teaching structural bioinformatics at the undergraduate level
Authors: Centeno Nuria B. , Villà‐Freixa Jordi , Oliva Baldomero 
Published: February 2007

AbstractUnderstanding the basic principles of structural biology is becoming a major subject of study in most undergraduate level programs in biology. In the genomic and proteomic age, it is becoming indispensable for biology students to master concepts related to the sequence and structure of proteins in order to develop skills that may be useful in a wide range of applications. Within this context, this article shows a scheme for teaching structural biology based on hands‐on computer approaches, including computational genomics, and structural bioinformatics tools. The students learn to use most of the leading computer programs available for the complete path that goes from sequence to structure and eventually function. During the course, they are taught to build models of proteins based on sequence and structure information. The students are also provided with a critical point of view on automatic procedures and learn to discern between likely and unlikely structures of their final models.
Assessment in a problem‐based learning course: Twelve tips for constructing multiple choice questions that test students' cognitive skills
Authors: Azer Samy A. 
Published: February 2007

AbstractFor over 35 years, multiple choice questions (MCQs) have been used in the assessment of students in medical, dental, nursing, and physiotherapy courses. MCQs enable educators to test a broad range of topics in the curriculum. However, the educational goals of MCQs used currently are to test factual knowledge rather than a deeper understanding or use of information. They do not focus on testing cognitive skills, and many of them test small print in textbooks. With the introduction of problem‐based learning in medical and health professional courses and a full shift from a traditional lecture‐based curriculum to a student‐centered program, many schools are currently reviewing their assessment tools and introducing new strategies that reflect the philosophy of the new curriculum. However, there is limited information in the literature to guide question writers and provide them with guidelines to construct new styles of MCQs that test higher‐order thinking skills. This article provides 12 practical tips to help question writers in creating MCQs that test cognitive skills.
Preparing undergraduates to participate in the post‐genome era: A capstone laboratory experience in proteomics*
Authors: Eberhardt Eric S. , Hansen Johanna , Riservato Luke , Cole Melissa , Smaglo Brandon , Szaniawski Paul 
Published: February 2007

AbstractProteomics is one of the important new disciplines to emerge from the genome sequencing projects of the last decade. In order to introduce our students to the techniques and promise of this emerging field, a capstone laboratory experience has been developed. The exercise involves multiple aspects of proteomics research including microbial culturing methods, two‐dimensional gel electrophoresis techniques, matrix‐assisted laser desorption‐ionization time‐of‐flight mass spectrometry, and database mining. Over a 12‐week semester, students design their own experiments and apply a proteomic approach to investigate the heat shock response in Escherichia coli. In the trial presented in this article, students successfully identified several major heat shock proteins. The laboratory outlined here can be readily adapted to explore a wide variety of responses in metabolic pathways or responses resulting from other environmental insults or stresses. Additionally, the laboratory can be modified to explore the proteomes of organelles, tissues, and other model organisms.
Contribution of each complex of the mitochondrial respiratory chain in the generation of the proton‐motive force*
Authors: Garcia‐Vallve Santiago 
Published: February 2007

AbstractA new parameter is presented for considering the contribution from each complex of the mitochondrial respiratory chain to the creation of the electrochemical gradient. This parameter is the proton gradient generated in each complex per pair of electrons transported (ΔH+/2e−) and may be calculated as the sum of the electrons taken up from the N‐side and the electrons released at the P‐side. The ΔH+/2e− values take into account all the electrons taken up and released in each complex and differentiate between the contribution from protons that are translocated from the N‐side to the P‐side and the contribution of scalar protons. Using these values, the P/O ratios for the oxidation of NADH and succinate are predicted to be 2.5 and 1.5, respectively.
A spectroscopic‐based laboratory experiment for protein conformational studies*
Authors: Ramos Carlos Henrique I. 
Published: February 2007

AbstractThis article describes a practical experiment for teaching basic spectroscopic techniques to introduce the topic of protein conformational change to students in the field of molecular biology, biochemistry, or structural biology. The spectroscopic methods employed in the experiment are absorbance, for protein concentration measurements, and fluorescence and circular dichroism, for probing protein conformational changes.
Supplementing introductory biology with on‐line curriculum*
Authors: McGroarty Estelle , Parker Joyce , Heidemann Merle , Lim Heejun , Olson Mark , Long Tammy , Merrill John , Riffell Samuel , Smith James , Batzli Janet , Kirschtel David 
Published: February 2007

AbstractWe developed web‐based modules addressing fundamental concepts of introductory biology delivered through the LON‐CAPA course management system. These modules were designed and used to supplement large, lecture‐based introductory biology classes. Incorporating educational principles and the strength of web‐based instructional technology, choices were made about knowledge presentation, representation, and construction (W. A. Nelson, D. B. Palumbo (1992) J. Educ. Media Hypermedia 1, 287–299). Knowledge presentation focused on big and connecting ideas. Knowledge representation provided students the opportunity to interact with concepts in several ways using multiple representations. For knowledge construction, we facilitated students' active and meaningful interactions with content using interwoven high‐level questions. Students' extended responses to a questionnaire indicated that these modules influenced the students learning in meaningful ways. (For access to demonstration modules, go to demo.lon‐capa.org/cgi‐bin/signon.pl?hhmi.)
Innovative tools for scientific and technological education in italian secondary schools
Authors: Santucci Annalisa , Mini Roberta , Ferro Elisa , Martelli Paola , Trabalzini Lorenza 
Published: February 2007

AbstractThis paper describes the project “Biotech a Scuola” (“Biotech at School”), financed by the Italian Ministry of Education within the SeT program (Special Project for Scientific‐Technological Education). The project involved the University of Siena, five senior and junior secondary schools in the Siena area, and a private company. Twenty‐three teachers from diverse fields and 318 students from 15 classes were involved. The aim of the project was to improve scientific‐technological teaching by providing schools with the support and materials necessary to understand some fundamental aspects of biotechnology. With this project we propose a model of close cooperation among various educational sectors with the goal of teaching junior and senior high school students some of the theory and practice of modern biotechnology.
Adjusting a biochemistry course for physical education majors: A case study
Authors: da Costa Caetano , Torres Bayardo B. 
Published: February 2007

AbstractThe purpose of this study was to investigate and analyze the events responsible for curricular characteristics that lead to positive outcomes in university teaching using a biochemistry course taught to physical education students as a model. The research was carried out as a case study, supported by questionnaires, classroom observation, document analysis, and interviews. The overall analyses of obtained data were validated by means of triangulation protocols, which proved the following reasons for the course achievements: 1) teaching staff deeply committed to the course; 2) contents adaptation to students' careers; 3) gradual adjustment of the teaching strategies and evaluation tools; 4) valorization of formative evaluation; and 5) providing a suitable affective milieu.
An introduction to mass spectrometry applications in biological research
Authors: Finehout Erin J. , Lee Kelvin H. 
Published: February 2007

AbstractMass spectrometry involves the measurement of the mass‐to‐charge ratio of ions. It has become an essential analytical tool in biological research and can be used to characterize a wide variety of biomolecules such as sugars, proteins, and oligonucleotides. In this review, a brief history of mass spectrometry is discussed, and the basic principles of the technology are introduced. A summary of some current applications is provided, as are examples of recently published research. The current methods used to identify, quantify, and characterize proteins and peptides are then reviewed. The range of applications of mass spectrometry is considerable and only promises to grow as the technology continues to improve.
Protein transport into the rough endoplasmic reticulum
Authors: Szeberenyi Joszef 
Published: February 2007

AbstractTerms to be familiar with before you start to solve the test: in vitro protein synthesis, endoplasmic reticulum, [35S]methionine labeling, ribosomes, aminoacyl‐tRNA synthase, microsomes, signal recognition particle (SRP),1The abbreviations used are: SRP, signal recognition particle; NEM, N‐ethylmaleimide; MCQ, multiple‐choice question.
SRP receptor, protease, detergent, SDS‐PAGE, autoradiography, protein glycosylation, peptidyl transferase, protein kinases, signal peptide, signal peptidase.
Virtual bioinformatics distance learning suite*
Authors: Tolvanen Martti , Vihinen Mauno 
Published: February 2007

AbstractDistance learning as a computer‐aided concept allows students to take courses from anywhere at any time. In bioinformatics, computers are needed to collect, store, process, and analyze massive amounts of biological and biomedical data. We have applied the concept of distance learning in virtual bioinformatics to provide university course material over the Internet. Currently, we provide two fully computer‐based courses, “Introduction to Bioinformatics” and “Bioinformatics in Functional Genomics.” Here we will discuss the application of distance learning in bioinformatics training and our experiences gained during the 3 years that we have run the courses, with about 400 students from a number of universities. The courses are available at bioinf.uta.fi.
Gene amplification by PCR and subcloning into a GFP‐fusion plasmid expression vector as a molecular biology laboratory course*
Authors: Bornhorst Joshua A. , Deibel Michael A. , Mulnix Amy B. 
Published: February 2007

AbstractA novel experimental sequence for the advanced undergraduate laboratory course has been developed at Earlham College. Utilizing recent improvements in molecular techniques for a time‐sensitive environment, undergraduates were able to create a chimera of a selected gene and green fluorescent protein (GFP) in a bacterial expression plasmid over the course of a single semester in a weekly 3‐h laboratory period. Students designed PCR primers for amplification of the selected gene using computational DNA sequence analysis tools. During the experimental portion of the course, students amplified and ligated the target DNA into a commercially available GFP expression vector. Following transformation of the ligation product, plasmids were harvested from the resulting bacterial colonies and were analyzed by restriction digestion to confirm the creation of the chimeric GFP‐DNA. This course gave students valuable experience with commonly used molecular techniques in an authentic research project. In addition, students gained experience with experimental design and execution. The techniques presented here are flexible and can be generalized for use with almost any DNA sequence and expression vector. This series also serves as an example of how faculty can adapt their ongoing research projects to the undergraduate laboratory.
cAMP Regulation of the lactose operon
Authors: Szeberenyi Jozsef 
Published: February 2007

AbstractTerms to be familiar with before you start to solve the test: lactose operon, adenylate cyclase, cAMP, catabolite activator protein (CAP), expression plasmid, lac operator, lac repressor, lactose, glucose, promoter, cis‐ and trans‐acting factors.
Lucenz simulator: A tool for the teaching of enzyme kinetics
Authors: Clark Alan G. 
Published: February 2007

AbstractA program has been developed that will produce simulated enzyme kinetic data suitable for inclusion in problem sets for undergraduates. Mechanisms simulated include one‐ and two‐substrate reactions and various types of inhibition. The effects of variation of pH and temperature may be modeled, as may the effects of random errors on the experimental procedure. The graphical output is suitable for use in lecture demonstrations.
The use of item analysis for improvement of biochemical teaching
Authors: Nagata Ryoichi 
Published: February 2007

AbstractItem analysis was used to find out which biochemical explanations need to be improved in biochemical teaching, not which items are to be discarded, improved, or reusable in biochemical examinations. The analysis revealed the basic facts of which “less able” students had more misunderstanding than “able” students. Identifying these basic facts helps biochemistry teachers to improve their teaching.
An interactive introduction to protein structure
Authors: Lee W. Theodore 
Published: February 2007

AbstractTo improve student understanding of protein structure and the significance of noncovalent interactions in protein structure and function, students are assigned a project to write a paper complemented with computer‐generated images. The assignment provides an opportunity for students to select a protein structure that is of interest and detail three to five noncovalent interactions important for protein structure and/or function. The assignment is designed to provide a hands‐on learning experience for students in a moderately large introductory biochemistry class.
Characterization of the CCR5 chemokine receptor gene
Authors: Thomas John C. 
Published: February 2007

AbstractThe life cycle of retroviruses is an essential topic of modern cell biology instruction. Furthermore, the process of HIV viral entry into the cell is a question of great interest in basic and clinical biology. This paper describes how students can easily recover their own DNA, amplify a portion of the CCR5 chemokine receptor gene, characterize wild‐type and mutant genotypes, and provide a timely backdrop for learning the many molecular facets of the HIV virus. This exercise can easily lead to current and ongoing discussions of the relevance of mutant alleles in the CCR5 co‐receptor and possible HIV tolerance. Student laboratory reports often discussed the potential importance of structure to the function of CCR5 protein within the context of HIV infection and resistance. Discussions of structure linked to function are key components of student assessment.
Slow‐binding inhibition: A theoretical and practical course for students
Authors: Goliĉnik Marko , Stojan Jure 
Published: February 2007

AbstractTyrosinase (EC 1.14.18.1) catalyzes the oxidation of L‐3,4‐dihydroxyphenylalanine (L‐DOPA) to 2,3,5,6‐tetrahydro‐5,6‐dioxo‐1H‐indole‐2‐carboxylate (dopachrome), according to the classical Michaelis‐Menten kinetic mechanism. The enzyme is strongly but slowly inhibited by α‐amino‐β‐[N‐(3‐hydroxy‐4‐pyridone)] propionic acid (L‐mimosine), a toxic plant amino acid. Easily available reagents and simple spectrophotometric detection of the product make the experimental characterization and kinetic analysis of tyrosinase action convenient and interesting for teaching purposes. In the present article, we present a theoretical and practical guide to the kinetic analysis of slow‐binding inhibition. The effect of L‐mimosine on tyrosinase is established by progress curve measurements, carried out on a conventional spectrophotometer equipped with a rapid kinetic accessory. In the analysis, we recommend a classical linearization approach but we also took advantage of a more reliable nonlinear regression method to avoid subjective bias. A multistep procedure starts by careful inspection of the curves to discriminate between candidate mechanisms. Next, the evaluation of initial and steady‐state velocities provides information on the enzyme catalytic and Michaelis‐Menten constants, as well as the corresponding inhibition constants. Subsequently, an appropriate mathematical derivation enables estimation of the isomerization rate constants characteristic for a slow‐binding inhibitor. To conclude, we suggest simultaneous multivariable regression, using all the progress curve data, to cross‐check the proposed reaction mechanism and evaluated kinetic constants.
Bioinformatics in undergraduate education: Practical examples
Authors: Boyle John A. 
Published: February 2007

AbstractBioinformatics has emerged as an important research tool in recent years. The ability to mine large databases for relevant information has become increasingly central to many different aspects of biochemistry and molecular biology. It is important that undergraduates be introduced to the available information and methodologies. We present a problem‐based approach for incorporation of bioinformatics into existing courses. Examples of exercises are presented along with resources available on the World‐Wide Web.
A rapid PCR‐RFLP method for monitoring genetic variation among commercial mushroom species*
Authors: Martin Presley , Muruke Masoud , Hosea Kenneth , Kivaisi Amelia , Zerwas Nick , Bauerle Cynthia 
Published: February 2007

AbstractWe report the development of a simplified procedure for restriction fragment length polymorphism (RFLP) analysis of mushrooms. We have adapted standard molecular techniques to be amenable to an undergraduate laboratory setting in order to allow students to explore basic questions about fungal diversity and relatedness among mushroom species. The streamlined protocols allowed students to practice important molecular techniques within the context of self‐designed investigative projects. This laboratory experience provided opportunities for students to practice strategies for examining molecular diversity among species.
Solving an ethical issue involved in experimentation with animals in a brazilian teaching laboratory*
Authors: Loureiro Natália I. V. , Viana Henrique V. , Rodrigues Carlos R. , Cabral Lúcio Mendes , Silva Thaís D. N. , Cardoso Fernanda Serpa , Santos Dilvani Oliveira , Castro Helena C. 
Published: February 2007

AbstractChanges are occurring within Brazilian institutes of higher education; currently several universities are reviewing their course offerings and teaching approaches to determine if they meet the needs of today's undergraduate students. When changes are made to the curriculum of experimental courses, there should be an understood guarantee that all efforts to avoid ethical and biosafety issues have been diligently considered. Ethical considerations lead us to create an alternative experimental session to be conducted that eliminated the use of rats, the conventional in vivo model employed for learning metabolism of glycogen in our university. To avoid possible biosafety issues, we prepared an alternative sample to simulate human urine, which we called guarurine. Using our new method, it is possible to verify positive results imitating a diabetic and starving people samples for detection of glucose and ketone. The alternative tool described herein is not only particularly suited to bypass the ethics of using animals for teaching, but also permits the discussion of significant aspects of pathological and physiological situations such as diabetics and starvation in a simple, safe, and interesting way.
Introductory course based on a single problem: Learning nucleic acid biochemistry from AIDS research
Authors: Grover Neena 
Published: February 2007

AbstractIn departure from the standard approach of using several problems to cover specific topics in a class, I use a single problem to cover the contents of the entire semester‐equivalent biochemistry classes. I have developed a problem‐based service‐learning (PBSL) problem on HIV/AIDS to cover nucleic acid concepts that are typically taught in the second semester of a biochemistry class. Use of research articles on a specific topic allows developing problems such as one discussed here. The implementation of this problem is similar to teaching literature‐based courses but is tailored to undergraduate work. Details of designing and setting up this problem, along with the pros and cons of this approach, are discussed here.
A new literary metaphor for the genome or proteome
Authors: Pappas Gus 
Published: February 2007

AbstractPreviously, the idea of a blueprint has been used to explain the genome. The concept of a play's cast of characters, the Dramatis Personae, is a more fluid metaphor that allows for mutations and time‐dependent phenomena to be taken into account. It also provides an educational and mnemonic exercise for students.
Use of visible light‐based photodynamic therapy to bacterial photoinactivation
Authors: Paulino Tony P. , Magalhães Prislaine P. , Thedei Geraldo , Tedesco Antônio C. , Ciancaglini Pietro 
Published: February 2007

AbstractThe main focus of this laboratory exercise was to investigate the photodynamic therapy (PDT) acting over Streptococcus mutans. A handheld photopolymerizer and a classical photosensitizer (Rose Bengal) were used to induce photodynamic response. In this way, a suspension of S. mutans was treated with different concentrations of Rose Bengal (0–10 μmol/liter), irradiated with a light (400–600 nm) for 20 s, and then cell viability was evaluated. It was observed that the light (per se) is not toxic, and in the dark, Rose Bengal is toxic only to the cells tested at concentrations above 5.0 μmol/liter. Under light exposure, concentrations of Rose Bengal above 0.5 μmol/liter killed all S. mutans. Therefore, for the purpose of our work, the photoactivation of Rose Bengal using the handheld photopolymerizer was efficient in bacteria inactivation.