bluuebunny/crossref_metadata_2025_split huggingface dataset:
Teaching microbial physiology using glucose repression phenomenon in baker's yeast as an example
Authors: Raghevendran Vijayendran , Nielsen Jens , Olsson Lisbeth 
Published: February 2007

AbstractThe yeast Saccharomyces cerevisiae has been used by human beings since ancient times for its ability to convert sugar to alcohol. Continual exposure to glucose in the natural environment for innumerable generations has probably enabled S. cerevisiae to grow in fermentative mode on sugars by switching off the genes responsible for respiration even under aerobic conditions. This phenomenon is referred to as the Crabtree effect. The present review focuses on glucose repression in S. cerevisiae from a physiological perspective. Physiological studies presented involve batch and chemostat experiments of the wild type and a mutant that lacks a trait partially responsible for the fermentative behavior. Various undergraduate student exercises have been (and can be) formulated to illustrate the concept of glucose repression.
DNA replication and transcription: An innovative teaching strategy
Authors: Fossey Annabel , Hancock Carolyn 
Published: February 2007

AbstractFirst‐year students in genetics at the University of KwaZulu‐Natal, South Africa, attend two general biology modules, one in each semester. Teaching involves four formal lectures per week of 45 min each, one 3‐h practical, and one lecture period tutorial. These students, graduating from secondary education, are well schooled in rote leaning but are limited in critical thinking and find assessment questions belonging to the higher levels of Bloom's taxonomy difficult. All students attend the formal lectures together, up to 300 students, whereas for the tutorials they are grouped into small groups, no more than 40 students in a tutorial class, allowing for innovative teaching strategies. Students find the processes of DNA replication and transcription difficult because of the sequential steps involved in the processes together with limitations imposed by the enzymes involved. Furthermore, they find the significance and relationships between the different components of the processes very difficult. A tutorial was developed in which students are requested to demonstrate replication with line drawings, which are then used in various iterations of transcription. The tutorial is administered in the presence of a tutor that guides the step by step execution of the tutorial while stimulating active participation. In the past 2 years, the presentation of this and other similar tutorials in genetics has improved overall class performance on average by 15%. Furthermore, students seem to display a greater retention from the first year to the second, which was previously rather limited. A survey among first‐year students revealed that the implementation of this tutorial facilitated studying and recall by helping students to organize thoughts, picture the sequence of events, understand fundamental concepts, and create a feeling of confidence.
A series of enzymology‐based experiments designed to mimic an applied research project
Authors: Boyce Angela , Walsh Gary 
Published: February 2007

AbstractFour mini‐practicals are described in which the effects of temperature and pH on phytase activity are assessed, as well as the enzyme's thermostability and the effect upon stability of simulated digestive tract conditions. Phytase is routinely incorporated into monogastric animal feed to ameliorate the negative nutritional and environmental consequences of its substrate, dietary phytic acid. In addition to illustrating selected basic concepts in enzymology, the combined experiments allow the students to determine the suitability of the test phytase for inclusion in animal feed. As such the practical mimics an applied research project and is particularly suited to biotechnology students undertaking courses in basic biochemistry. Students may be segregated into groups of 4, with each team member charged with undertaking one of the mini‐experiments. In this way students are given individual responsibility and learn to work as part of an integrated research grouping.
In Vitro synthesis and activity of reporter proteins in an Escherichia coli S30 extract system: An undergraduate experiment*
Authors: Higgins Pamela J. 
Published: February 2007

AbstractThis undergraduate laboratory experiment integrates multiple techniques (in vitro synthesis, enzyme assays, Western blotting) to determine the production and detection sensitivity of two common reporter proteins (β‐galactosidase and luciferase) within an Escherichia coli S30 transcription/translation extract. Comparison of the data suggests that luciferase is the more suitable reporter for this specific in vitro extract system. Simple modifications in the experimental design allow for flexibility in the use of materials and the time required to perform the study. Furthermore, extension into additional experiments and alternative techniques are also discussed.
The importance of visual literacy in the education of biochemists*
Authors: Schönborn Konrad J. , Anderson Trevor R. 
Published: February 2007

AbstractVisualization is an essential skill for all students and biochemists studying and researching the molecular and cellular biosciences. In this study, we discuss the nature and importance of visualization in biochemistry education and argue that students should be explicitly taught visual literacy and the skills for using visualization tools as essential components of all biochemistry curricula. We suggest that, at present, very little pedagogical attention has been given to this vital component of biochemistry education, although a large diversity of static, dynamic, and multimedia visual displays continues to flood modern educational resources at an exponential rate. Based on selected research findings from other science education domains and our own research experience in biochemistry education, 10 fundamental guidelines are proposed for the promotion of visualization and visual literacy among students studying in the molecular and cellular biosciences.
A mechanistic foundation for instructor‐regulated collective learning
Authors: Brooks David W. , Markwell John 
Published: February 2007

AbstractThe theory of memory and the ability to influence learning with conscious and unconscious factors, both internal and external, is reviewed. From a connectionist view of memory, the interactive compensatory model of learning is introduced, with an emphasis on the plastic components (motivation, prior knowledge, and metacognition) that can be regulated. Expert students, but not naive students, have a considerable ability to self‐regulate their learning processes and improve performance in undergraduate courses. We propose that in a class situation, there are emergent opportunities for an instructor who understands the dynamics of the learning environment to provide regulation for collective learning of multiple students and improve group learning. There are three interfaces for instructor‐regulated collective learning, and examples are provided for each to suggest how instructors may effectively provide regulation.
Identification of highly prized commercial fish using a PCR‐based methodology
Authors: Morán Paloma , Garcia‐Vazquez Eva 
Published: February 2007

AbstractWe report a practical class designed for undergraduate students of Marine Sciences as a part of the Genetics course. The class can also be included in undergraduate studies of food technology. The exercise was designed to emphasize the application of molecular biology techniques to fish species authentication and traceability. After a simple and rapid protocol for DNA extraction, PCR was used to analyze variation in size of individual 5S ribosomal gene spacer sequences in eight commercially important fishes. The resulting fragments containing these sequences were separated on agarose gels and visualized under a UV lamp. Differences in fragment length can be used to differentiate between species. This method is particularly useful in the identification of larvae, eggs, and processed food including frozen and canned products.
The development of biotechnology education in China*
Authors: Zhou Xuanwei , Lin Juan , Zhang Lei , Chen Zhonghai , Yin Yizhou , Guo Binhui , Sun Xiaofen , Tang Kexuan 
Published: February 2007

AbstractFrom the middle of the 20th century, Chinese scientists have been actively involved in biotechnology. However, biotechnology education in China is a relatively recent phenomenon. This subject has not been addressed at the undergraduate level in a serious way until recently. In the last decade, biotechnology education developed rapidly and reached a new level in Chinese universities. The Chinese scientific establishment is very much aware of the importance of biotechnology and has identified this subject as one of the priority areas. Some universities are taking positive steps toward enhancing biotechnology education. This article focuses on the emergence, as well as the problems and prospects, of biotechnology education in China.
The determination of the redox states and phosphorylation potential in living tissues and their relationship to metabolic control of disease phenotypes
Authors: Veech Richard L. 
Published: February 2007

AbstractThis paper reviews the development in the 1950s of methods to determine the redox states of the free [NAD+]/[NADH] in cytoplasm of yeast by Helmut Holzer and Feodore Lynen and in rat liver by Theodore Bucher and Martin Klingenberg. This work was extended in the 1960s in the laboratory of Hans Krebs, where the use of basic thermodynamic and kinetic principles allowed the extension of this approach to the determination of the free mitochondrial [NAD+]/NADH] in mitochondria and the redox state of the free NADP system in cytoplasm and mitochondria. This work also outlined the linkage between the redox states in the various couples to the phosphorylation state or the free [ATP]/[ADP][Pi] ratio, the central energy parameter of living cells. This work has since been extended to include other energy‐linked systems including the gradients of inorganic ions between extra and intracellular phases of the cell and the redox state of the co‐enzyme Q couple of mitochondria. This system of linked near‐equilibrium redox and phosphorylation potentials constitutes a framework of primitive metabolic control that is altered in a number of disease phenotypes. The alteration of such disease phenotypes by substrate availability is discussed, as well as the importance of a thorough grounding in basic kinetics and thermodynamics in designing new therapies to normalize the metabolic abnormalities that are the proximate cause of many common and some rare diseases states.
Engagement, exploration, explanation, extension, and evaluation (5E) learning cycle and conceptual change text as learning tools
Authors: Balci Sibel , Cakiroglu Jale , Tekkaya Ceren 
Published: February 2007

AbstractThe purpose of this study is to investigate the effects of the Engagement, Exploration, Explanation, Extension, and Evaluation (5E) learning cycle, conceptual change texts, and traditional instructions on 8th grade students' understanding of photosynthesis and respiration in plants. Students' understanding of photosynthesis and respiration in plants was measured using the test developed by Haslam and Treagust (F. Haslam, D. F. Treagust (1987) Diagnosing secondary students' misconceptions of photosynthesis and respiration in plants using a two‐tier multiple choice instrument, J. Biol. Educ. 21, 203–211). The test was administered as pre‐test and post‐test to a total of 101 8th‐grade students in three intact classes of the same school located in an urban area. The classes were randomly assigned as control and experimental groups. Students in the first experimental group (n = 33) received 5E learning cycle instruction, students in the second experimental group (n = 34) received conceptual change text instruction, and students in the control group (n = 34) received traditional instruction. Attitudes toward science and pre‐test scores were used as covariates. A quasi‐experimental design utilizing the analysis of covariance showed a statistically significant difference between the experimental and control groups in the favor of experimental groups after treatment. However, no statistically significant difference between two experimental groups (5E versus conceptual change text instruction) was found.
Molecular cloning and analysis of a DNA repetitive element from the mouse genome
Authors: Geisinger Adriana , Cossio Gabriela , Wettstein Rodolfo 
Published: February 2007

AbstractWe report the development of a 3‐week laboratory activity for an undergraduate molecular biology course. This activity introduces students to the practice of basic molecular techniques such as restriction enzyme digestion, agarose gel electrophoresis, cloning, plasmid DNA purification, Southern blotting, and sequencing. Students learn how to carry out a GenBank™ search as they are encouraged to compile most available information about their cloned sequence. The natural integration of the bench work with the use of the bioinformatics tools is considered a major advantage of this laboratory course.
Student understanding of pH: “i don't know what the log actually is, i only know where the button is on my calculator”
Authors: Watters Dianne J. , Watters James J. 
Published: February 2007

AbstractIn foundation biochemistry and biological chemistry courses, a major problem area that has been identified is students' lack of understanding of pH, acids, bases, and buffers and their inability to apply their knowledge in solving acid/base problems. The aim of this study was to explore students' conceptions of pH and their ability to solve problems associated with the behavior of biological acids to understand the source of student difficulties. The responses given by most students are characteristic of an atomistic approach in which they pay no attention to the structure of the problem and concentrate only on juggling the elements together until they get a solution. Many students reported difficulty in understanding what the question was asking and were unable to interpret a simple graph showing the pH activity profile of an enzyme. The most startling finding was the lack of basic understanding of logarithms and the inability of all except one student to perform a simple calculation on logs without a calculator. This deficiency in high school mathematical skills severely hampered their understanding of pH. This study has highlighted a widespread deficiency in basic mathematical skills among first year undergraduates and a fragmented understanding of acids and bases. Implications for the way in which the concepts of pH and buffers are taught are discussed.
Cognitive development and the complexities of the undergraduate learner in the science classroom*
Authors: Markwell John , Courtney Sean 
Published: February 2007

AbstractStudents' reactions to classroom learning and the mastery of science vary along a wide spectrum of attitudes and emotions. In particular, we argue here that how learners encounter and learn subject matter is a function of their level of cognitive development. We describe the stages of cognitive development based on the work of William Perry and demonstrate their relevance to the undergraduate science classroom. With examples drawn from biochemistry, we attempt to show that, depending on the student's developmental level, there will be different abilities to handle the range of assignments and activities s/he can expect to experience in the average classroom. The college science instructor can benefit from knowledge of these stages and can work through their implications to develop strategies and techniques to regulate collective student learning.
A descriptive analysis of computer‐assisted teaching and learning in molecular biological education
Authors: Li Guangxing , Yin Jiechao , Ren Yudong , Wang Binjie , Ren Xiaofeng 
Published: February 2007

AbstractThe role and importance of computer‐assisted teaching and learning in molecular biological‐related education and research has been emphasized and pinpointed. In this study, some benefit viewpoints and discussion are provided for applying the computer‐assisted teaching and learning more efficiently in the process of knowledge acquisition and information exchange. Meanwhile, several cultural and economic issues related to the role of computers in teaching and learning are addressed.
A course designed for undergraduate biochemistry students to learn about cultural diversity issues
Authors: Benore‐Parsons Marilee 
Published: February 2007

AbstractBiology, biochemistry, and other science students are well trained in science and familiar with how to conduct and evaluate scientific experiments. They are less aware of cultural issues or how these will impact their careers in research, education, or as professional health care workers. A course was developed for advanced undergraduate science majors to learn about diversity issues in a context that would be relevant to them, entitled “Diversity Issues in Health Care: Treatment and Research.” Learning objectives included: developing awareness of current topics concerning diversity issues in health care; learning how research is carried out in health care, including pharmaceutical research, clinical trials, and social research; and learning about health care practices. Lectures and projects included readings on laboratory and clinical research, as well as literature on legal, race, gender, language, age, and income issues in health care research and clinical practice. Exams, papers, and a service learning project were used to determine the final course grade. Assessment indicated student understanding of diversity issues was improved, and the material was relevant.
Glyceroneogenesis, the pathway that almost wasn't
Authors: Hanson Richard W. , Ballard F. John , Reshef Lea 
Published: February 2007

Abstract“What seest thou else in the dark, backward abysm of time.” Prospero in The TempestAs is true in all aspects of human endeavor, a scientific concept can appear before its time and remain unappreciated before events catch up with the concept. Such was the case of the discovery of glyceroneogenesis and the establishment of its biological importance; it took almost 40 years before the significance of this pathway became apparent and the concept of triglyceride recycling was understood by the scientific establishment. Even that may be stretching a point, because today glyceroneogenesis is hardly a household word. In this essay, we will tell the story of the discovery of glyceroneogenesis and the thought processes that led us to propose this pathway. We will also speculate on why the pathway was not more widely embraced by scientists working in lipid metabolism and why that may finally be changing. The reader is warned, however, that this story is a reconstruction of past events and, like all such attempts, suffers from the patina of nostalgia that inevitably covers all things resurrected from memory. Others may view things differently, but this is our story as we remember it.
Microarrays (DNA chips) for the classroom laboratory
Authors: Barnard Betsy , Sussman Michael , BonDurant Sandra Splinter , Nienhuis James , Krysan Patrick 
Published: February 2007

AbstractWe have developed and optimized the necessary laboratory materials to make DNA microarray technology accessible to all high school students at a fraction of both cost and data size. The primary component is a DNA chip/array that students “print” by hand and then analyze using research tools that have been adapted for classroom use. The primary adaptation is the use of a simulated cDNA target. The low density DNA array we discuss here was used to demonstrate differential expression of several Arabidopsis thaliana genes related to photosynthesis and photomorphogenesis. The methods we present here can be used with any biological organism whose sequence is known. Furthermore, these methods can be adapted to exhibit a variety of differential gene expression patterns under different experimental conditions. The materials and tools we discuss have been applied in classrooms at West High School in Madison, WI. We have also shared these materials with high school teachers attending professional development courses at the University of Wisconsin‐Madison.
Glycobiology, how to sugar‐coat an undergraduate advanced biochemistry laboratory
Authors: McReynolds Katherine D. 
Published: February 2007

AbstractA second semester biochemistry laboratory has been implemented as an independent projects course at California State University, Sacramento since 1999. To incorporate aspects of carbohydrate biochemistry, or glycobiology, into our curriculum, projects in lectin isolation and purification were undertaken over the course of two semesters. Through this modification in course content, this class now offers a diverse, hands‐on treatment of not only standard protein purification techniques but also carbohydrate techniques, specifically the study of carbohydrate‐protein interactions through hemagglutination assays, a novel commercial assay known as the Instant™Chek assay, and the generation and use of appropriate affinity chromatography matrices. Throughout the semester, the students are in charge of all aspects of their projects, from planning to execution and completion. Specific examples of student projects are highlighted such that the breadth of protein‐carbohydrate chemistry pursued in a 15‐week semester can be appreciated. The feedback of the course was very favorable, indicating that the students came away with skills necessary for them to be successful in their future careers. Most importantly, however, aspects of glycobiology have now been incorporated effectively into a mainstream undergraduate biochemistry laboratory class.
jAMVLE, A new integrated molecular visualization learning environment*
Authors: Bottomley Steven , Chandler David , Morgan Eleanor , Helmerhorst Erik 
Published: February 2007

AbstractA new computer‐based molecular visualization tool has been developed for teaching, and learning, molecular structure. This java‐based jmol Amalgamated Molecular Visualization Learning Environment (jAMVLE) is platform‐independent, integrated, and interactive. It has an overall graphical user interface that is intuitive and easy to use. The application can be downloaded free from the internet at wabri.org.au/jamvle. A cohort of 28 third year undergraduate molecular biotechnology degree students evaluated the new application through an essay‐style project. These were analyzed to identify themes expressed by students in the content of their evaluations. Most students were positive about the new jAMVLE learning environment, and five major benefits emerged from the analysis. In particular, the students perceived that jAMVLE has an appealing interface, is interactive, provides a useful integrated environment, is user friendly, and is an excellent learning tool. Overall, students found that the jAMVLE application stimulated their interest, was a more active learning environment, provided better guidance, and made learning fun.
How far is England in the process of introducing a mandatory reporting system?
Authors: Munro Eileen , Parton Nigel 
Published: February 2007

AbstractThis article argues that England is in the process of introducing a mandatory reporting system, not based on the requirement to report child abuse but on the basis of ‘a cause for concern’ for a child's welfare. It describes Section 12 of the Children Act 2004, which is fundamental to the development, and the rationale upon which it is based. The second part of the article summarizes the key criticisms that have been made of mandatory reporting systems and discusses how these are likely to apply in the English situation. Copyright © 2007 John Wiley & Sons, Ltd.