bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic interrelationships software application: Interactive learning tool for intermediary metabolism*
Authors: Verhoeven Adrie J. M. , Doets Mathijs , Lamers Jos M. J. , Koster Johan F. 
Published: February 2007

AbstractWe developed and implemented the software application titled Metabolic Interrelationships as a self‐learning and ‐teaching tool for intermediary metabolism. It is used by undergraduate medical students in an integrated organ systems‐based and disease‐oriented core curriculum, which started in our medical faculty in 2001. The computer program provides an interactive environment in which students learn to integrate the major metabolic pathways as well as their hormonal control mechanisms as far as they depend on nutritional status. Students can explore the time‐ and tissue‐dependent changes in mammalian intermediary metabolism during a feeding‐fasting cycle. Starting from a whole‐body view of interorgan nutrient fluxes, the student can make excursions to individual organs and, from there, to increasing levels of molecular detail and to explanatory animations. The application is well received by students and staff.
Cytochrome P450 enzymes in drug metabolism and chemical toxicology: An introduction
Authors: Furge Laura Lowe , Guengerich F. Peter 
Published: February 2007

AbstractCytochrome P450 (P450) enzymes include a family of related enzymes that are involved in metabolism of vitamins, steroids, fatty acids, and other chemicals. This review presents a brief historical overview of the discovery and characterization of P450 enzymes extending from intermediary metabolism to the fields of drug metabolism and toxicology. Introductions to P450 enzyme structure and function are also presented. The goals of this review are to 1) provide an introduction to a few of the many aspects of P450 research relating to humans, 2) introduce additional ways of thinking about metabolism, 3) provide some basic examples of P450 enzymology, and 4) provide applications to topics widely taught in undergraduate courses in biochemistry.
Middle/high school students in the research laboratory: A summer internship program emphasizing the interdisciplinary nature of biology
Authors: McMiller Tracee , Lee Tameshia , Saroop Ria , Green Tyra , Johnson Casonya M. 
Published: February 2007

AbstractWe describe an eight‐week summer Young Scientist in Training (YSIT) internship program involving middle and high school students. This program exposed students to current basic research in molecular genetics, while introducing or reinforcing principles of the scientific method and demonstrating the uses of mathematics and chemistry in biology. For the laboratory‐based program, selected students from Baltimore City Schools working in groups of three were teamed with undergraduate research assistants at Morgan State University. Teams were assigned a project that was indirectly related to our laboratory research on the characterization of gene expression in Caenorhabditis elegans. At the end of the program, teams prepared posters detailing their accomplishments, and presented their findings to parents and faculty members during a mini‐symposium. The posters were also submitted to the respective schools and the interns were offered a presentation of their research at local high school science fairs.
A new three‐dimensional educational model kit for building DNA and RNA molecules: Development and evaluation*
Authors: Beltramini Leila Maria , Araújo Ana Paula Ulian , de Oliveira Tales Henrique Gonçalves , dos Santos Abel Luciano Douglas , da Silva Aparecido Rodrigues , dos Santos Neusa Fernandes 
Published: February 2007

AbstractInternational specialized literature focused on research in biology education is sadly scarce, especially regarding biochemical and molecular aspects. In this light, researchers from this Centre for Structural Molecular Biotechnology developed and evaluated a three‐dimensional educational model named “Building Life Molecules DNA and RNA.” The development of the model and its evaluation as a potential tool in the teaching‐learning process were based on a pilot study involving 226 learners and teachers. Questionnaires were elaborated, containing simple and objective questions, similar to those used in research on science teaching, to orient the evaluation process. Our results show that the model has high educational potential, aiding participants in their conceptual understanding of these molecular structures and their functions, DNA semiconservative replication, and RNA transcription. In addition, it was observed that this model leads students to critical associations of these concepts with actual scientific themes of molecular biology and biotechnology, such as cloning, transgenic organisms, and the genome.
A nitrogen balance experiment using simulated urine samples
Authors: Sadighi Mehri , Reichman Nurit , Wilson Kaye , Carne Alan , Thompson Mary P. 
Published: February 2007

AbstractWe describe an undergraduate laboratory experiment that combines the advantages of problem‐based learning with the need for biochemistry students to become proficient in practical laboratory skills. It also avoids the need to obtain ethical approval for recruiting volunteers and eliminates any possible biosafety issues with the handling and disposal of large amounts of urine. Simulated human urine samples are prepared that contain urea, uric acid, and creatinine at concentrations that represent the levels expected in 2 liters of urine collected over 24 h from subjects on various protein diets or during different physiological states. The students measure the nitrogen‐containing compounds in the “urine samples” using specific colorimetric assays and use the data they generate to derive knowledge about nitrogen balance and the excretory metabolism of amino acids.
Phylogenetics exercise using inherited human traits
Authors: Tuimala Jarno 
Published: February 2007

AbstractA bioinformatics laboratory exercise based on inherited human morphological traits is presented. It teaches how morphological characters can be used to study the evolutionary history of humans using parsimony. The exercise can easily be used in a pen‐and‐paper laboratory, but if computers are available, a more versatile analysis can be carried out. The exercise introduces students to the basics of bioinformatics laboratory work, shows them possible problems associated in data acquisition, and most importantly, teaches them basic group working skills, such as the appropriate distribution of work. An open and student‐oriented approach, in which group work is designed to support the learning of individual students, was adapted. The exercise is devised in two sessions that cover collection of data, analysis using parsimony, and a combined matrix analysis in a parsimony framework. The exercise, or parts of it, has successfully been applied in bioinformatics courses intended for second to third year biology majors and in adult education.
Evolution of protein lipograms: A bioinformatics problem
Authors: White Harold B. , Dhurjati Prasad 
Published: February 2007

AbstractA protein lacking one of the 20 common amino acids is a protein lipogram. This open‐ended problem‐based learning assignment deals with the evolution of proteins with biased amino acid composition. It has students query protein and metabolic databases to test the hypothesis that natural selection has reduced the frequency of each amino acid specifically in the enzymes required for its biosynthesis. Student groups work in parallel on different amino acids and share strategies. Aside from content objectives that integrate knowledge of protein structure, function, synthesis, and evolution, this problem incorporates oral and written presentations, statistical analysis, and substantial decision making. The point of the problem described here is that a deficiency or absence of a particular amino acid in a protein may be more than a chance occurrence and may be driven by natural selection. The challenge is to demonstrate the difference.
Human salivary α‐amylase (EC.3.2.1.1) activity and periodic acid and schiff reactive (PAS) staining: A useful tool to study polysaccharides at an undergraduate level
Authors: Fernandes Ruben , Correia Rossana , Fonte Rosália , Prudêncio Cristina 
Published: February 2007

AbstractHealth science education is presently in discussion throughout Europe due to the Bologna Declaration. Teaching basic sciences such as biochemistry in a health sciences context, namely in allied heath education, can be a challenging task since the students of preclinical health sciences are not often convinced that basic sciences are clinically valuable (J. R. Rudland, S. C. Rennie (2003) The determination of the relevance of basic sciences learning objectives to clinical practice using a questionnaire survey, Med. Educ. (Oxf.) 37, 962–965; E. C. Wragg (2003) How can we determine the relevance of basic sciences learning objectives to clinical practice?, Med. Educ. (Oxf.) 37, 948–949). Thus, nowadays teachers are compelled to use their imagination to be able to elaborate laboratory sessions aiming for the understanding of theoretical concepts that are also clinically related: in other words, basic concepts and skills that underlie the competencies demanded of the future health professional. In the present work, we describe a set of laboratory sessions implemented in the discipline of biochemistry, belonging to the first year of several courses of allied health professionals, which can also be implemented in other health sciences courses. These sessions focus on the characteristics and properties of carbohydrates. The exercises we propose include two different laboratory practical sessions based on a histopathological routine technique known as periodic acid and Schiff reactive that is currently used to detect sugar metabolic and tumor diseases (J. M. T. Rivera, C. T. López, B. C. Segui (2001) Bioquímica Estructural: Conceptos y Tests, Tebar Flores, Madrid). The methodology described enables the demonstration of some biochemical properties of polysaccharides, namely animal and vegetable, and the catalytic activity of the human salivary α‐amylase (EC.3.2.1.1) enzyme. A further comparison between α‐amylase activity in vitro and in situ is also possible by the proposed methodology. Additionally, to this extent, a comparison between the results of the learning improvement that occurred after the implementation of this tool is presented.
Biomolecules in the computer: Jmol to the rescue
Authors: Herráez Angel 
Published: February 2007

AbstractJmol is free, open source software for interactive molecular visualization. Since it is written in the Java™ programming language, it is compatible with all major operating systems and, in the applet form, with most modern web browsers. This article summarizes Jmol development and features that make it a valid and promising replacement for Rasmol and Chime in the development of educational materials, as well as in basic investigation of biomolecular structure. The description is set up by comparison with the well known abilities of Rasmol and Chime. Jmol is suitable for molecular model display and analysis in biochemistry, molecular biology, organic and inorganic chemistry, crystallography, and materials science.
Tactile teaching: Exploring protein structure/function using physical models*
Authors: Herman Tim , Morris Jennifer , Colton Shannon , Batiza Ann , Patrick Michael , Franzen Margaret , Goodsell David S. 
Published: February 2007

AbstractThe technology now exists to construct physical models of proteins based on atomic coordinates of solved structures. We review here our recent experiences in using physical models to teach concepts of protein structure and function at both the high school and the undergraduate levels. At the high school level, physical models are used in a professional development program targeted to biology and chemistry teachers. This program has recently been expanded to include two student enrichment programs in which high school students participate in physical protein modeling activities. At the undergraduate level, we are currently exploring the usefulness of physical models in communicating concepts of protein structure and function that have been traditionally difficult to teach. We discuss our recent experience with two such examples: the close‐packed nature of an enzyme active site and the pH‐induced conformational change of the influenza hemagglutinin protein during virus infection.
Intrageneric primer design: Bringing bioinformatics tools to the class
Authors: Lima André O. S. , Garcês Sérgio P. S. 
Published: February 2007

AbstractBioinformatics is one of the fastest growing scientific areas over the last decade. It focuses on the use of informatics tools for the organization and analysis of biological data. An example of their importance is the availability nowadays of dozens of software programs for genomic and proteomic studies. Thus, there is a growing field (private and academic) with a need for bachelor of science students with bioinformatics skills. In consideration of this need, described here is a problem‐based class in which students are asked to design a set of intrageneric primers for PCR. The exercise is divided into five classes of 1 h each, in which students use freeware bioinformatics tools and data bases available through the Internet. Besides designing the set of primers, the students will consequently learn the significance and use of the major bioinformatics procedures, such as searching a data base, conducting and analyzing sequence multialignment, comparing sequences with a data base, and selecting primers.
A simple assay to quantify metallothionein helps to learn about bioindicators and environmental health
Authors: Linde Ana R. , Garcia‐Vazquez Eva 
Published: February 2007

AbstractWe present a laboratory practice aimed to clarify and discuss the concept of bioindicator molecules in environmental health. It has been implemented as a hands‐on laboratory exercise in postgraduate courses in public health (in Brazil) and in a course entitled Biology Applied to Natural Resources Sustainability (in Spain) but can be useful for undergraduate studies. By simple, repeatable, and low cost spectrophotometry methodology, students detect minimal concentrations (nmol) of metallothionein in biological samples obtained from sites with various status of pollution. They can also expose experimental fish or mollusks to heavy metals in aquarium conditions and then detect metallothionein. This method is excellent for didactic purposes because it can be developed even in modest laboratories with basic equipment for molecular biology.
The effect of α‐amanitin on RNA polymerase II ubiquitination*
Authors: Szeberenyi Jozsef 
Published: February 2007

AbstractTerms to be familiar with before you start to solve the test: RNA polymerase II, transcription, α‐amanitin, protein ubiquitination, synchronization of cell cultures, affinity adsorption, SDS‐polyacrylamide gel electrophoresis, Western blotting, protein phosphorylation, protein kinases, in vitro transcription, plasmid, promoter, general and regulatory transcription factors, autoradiography.
Working in partnership: user perceptions of intensive home visiting
Authors: Kirkpatrick Sue , Barlow Jane , Stewart‐Brown Sarah , Davis Hilton 
Published: February 2007

AbstractThe aim of this study was to explore the perceptions of vulnerable women about the value of intensive home visiting in pregnancy and the first year of life delivered by health visitors trained to work in partnership with families.Twenty in‐depth interviews were conducted with women who had completed the home visiting programme and agreed to be interviewed. The data were fully transcribed and analysed thematically.Despite initial concerns and negative preconceptions about health and social service professionals, participating women greatly valued the relationships that were established with their home visitors and identified a number of ways in which they had benefited. These included increased confidence, improved mental health, better parenting, improved relationships and changes in their attitudes toward professionals.These findings demonstrate the potential of intensive home visiting delivered in partnership with mothers in reaching and helping vulnerable and ‘hard‐to‐reach’ families. They highlight the importance of establishing a trusting relationship between helper and provider, and the need for home visitors to have the necessary skills and qualities to establish such relationships. Copyright © 2007 John Wiley & Sons, Ltd.
Ionic Hydrogen Bonds Controlling Two‐Dimensional Supramolecular Systems at a Metal Surface
Authors: Payer Dietmar , Comisso Alessio , Dmitriev Alexandre , Strunskus Thomas , Lin Nian , Wöll Christof , DeVita Alessandro , Barth Johannes V. , Kern Klaus 
Published: February 2007

AbstractHydrogen‐bond formation between ionic adsorbates on an Ag(111) surface under ultrahigh vacuum was studied by scanning tunneling microscopy/spectroscopy (STM/STS), X‐ray photoelectron spectroscopy (XPS), near‐edge X‐ray absorption fine structure (NEXAFS), and molecular dynamics calculations. The adsorbate, 1,3,5‐benzenetricarboxylic acid (trimesic acid, TMA), self‐assembles at low temperatures (250–300 K) into the known open honeycomb motif through neutral hydrogen bonds formed between carboxyl groups, whereas annealing at 420 K leads to a densely packed quartet structure consisting of flat‐lying molecules with one deprotonated carboxyl group per molecule. The resulting charged carboxylate groups form intermolecular ionic hydrogen bonds with enhanced strength compared to the neutral hydrogen bonds; this represents an alternative supramolecular bonding motif in 2D supramolecular organization.
Structure, Formation, and Dynamics of Mo12 and Mo16 Oxothiomolybdenum Rings Containing Terephtalate Derivatives
Authors: Lemonnier Jean‐François , Floquet Sébastien , Marrot Jérôme , Terazzi Emmanuel , Piguet Claude , Lesot Philippe , Pinto André , Cadot Emmanuel 
Published: February 2007

AbstractThe influence of rigid or semirigid dicarboxylate anions, terephtalate (TerP2−), isophtalate (IsoP2−), and phenylenediacetate (PDA2−) on the self‐condensation process of the [Mo2O2S2]2+ dioxothio cation has been investigated. Three new molybdenum rings, [Mo12O12S12(OH)12(TerP)]2− ([Mo12TerP]2−), [Mo16O16S16(OH)16(H2O)4(PDA)2]4− ([Mo16(PDA)2]4−), and [Mo16O16S16(OH)16(H2O)2(IsoP)2]4− ([Mo16(IsoP)2]4−) have been isolated and unambiguously characterized in the solid state by single‐crystal X‐ray studies and in solution by various NMR methods and especially by diffusion‐correlated NMR (1H DOSY) spectroscopy, which was shown to be a powerful tool for the characterization and speciation of templated molybdenum ring systems in solution. Characterization by FT‐IR and elemental analysis are also reported. The dynamic and thermodynamic properties of both the sixteen‐membered rings were studied in aqueous medium. Specific and distinct behaviors were revealed for each system. The IsoP2−/[Mo2O2S2]2+ system gave rise to equilibrium, involving mono‐templated [Mo12IsoP]2− and bis‐templated [Mo16(IsoP)2]4− ions. Thermodynamic parameters have been determined and showed that the driving‐force for the formation of the [Mo16(IsoP)2]4− is entropically governed. However, whatever the conditions (temperature, proportion of reactants), the PDA2−/[Mo2O2S2]2+ system led only to a single compound, the [Mo16(PDA)2]4− ion. The latter exhibits dynamic behavior, consistent with the gliding of both the stacked aromatic groups. Stability and dynamics of both Mo16 rings was related to weak hydrophobic or π–π stacking inter‐template interactions and inner hydrogen‐bond network occurring within the [Mo16(IsoP)2]4− and [Mo16(PDA)2]4− ions.
Reactivity of Aldehydes with Semi‐Stabilised Arsonium Ylide Anions: Synthesis of Terminal (E)‐1,3‐Dienes
Authors: Habrant Damien , Stengel Bruno , Meunier Stéphane , Mioskowski Charles 
Published: February 2007

AbstractA study of the reactivity of semi‐stabilised arsonium ylide anions in olefination reactions is presented. The different ylide anions were generated by the addition of nBuLi to various arsonium halide derivatives: [Ph2As(R)R′]+X−, where R and R′ are methyl, allyl, prenyl or benzyl groups. By using diallyldiphenylarsonium bromide (R=R′=allyl) an olefination protocol was optimised allowing the efficient transformation of aliphatic aldehydes into terminal 1,3‐dienes with a high selectivity for the E isomer (E/Z ratios ranging from 90:10 to 97:3). The olefination reactions of aldehydes with dissymmetric arsonium halides (R≠R′) are very chemoselective; with arsonium ylide anions the benzyl moiety is more reactive than the allyl moiety which is much more reactive than prenyl and methyl groups. Based on the experimental results, a mechanism is proposed for the reaction.
Ionic Interaction as a Powerful Driving Force for the Formation of Heterobidentate Assembly Ligands
Authors: Gulyás Henrik , Benet‐Buchholz Jordi , Escudero‐Adan Eduardo C. , Freixa Zoraida , van Leeuwen Piet W. N. M. 
Published: February 2007

AbstractAn ionic interaction has been used for the first time to assemble monophosphane ligands. NMR spectroscopy and X‐ray studies show that cationic and anionic triphenylphosphane derivatives form ion pairs and subsequently act as a ligand in various transition‐metal complexes. The position of the ionic functional groups allows both cis and trans coordination of the novel assembly ligand in square‐planar transition‐metal complexes.
Highly Chemo‐ and Stereoselective Intermolecular Coupling of Diazoacetates To Givecis‐Olefins by Using Grubbs Second‐Generation Catalyst
Authors: Hodgson David M. , Angrish Deepshikha 
Published: February 2007

AbstractHighly stereoselective formation ofcis‐2‐ene‐1,4‐diesters by homo‐ and heterocoupling of α‐diazoacetates in the presence of Grubbs second‐generation catalyst is demonstrated. The dual reactivity of the catalyst in alkene metathesis and diazocoupling has been exploited in the synthesis of 12–26‐membered macrocyclic dienyl dilactones by one‐pot carbene dimerisation/ring‐closing metathesis.
Screening of a Modular Sugar‐Based Phosphite–Oxazoline Ligand Library in Asymmetric Pd‐Catalyzed Heck Reactions
Authors: Mata Yvette , Pàmies Oscar , Diéguez Montserrat 
Published: February 2007

AbstractWe have synthesised a library of phosphite–oxazoline ligands derived from readily available D‐glucosamine. These ligands have been successfully screened in the palladium‐catalysed Heck reaction of several substrates with high regio‐ (up to 99 %) and enantioselectivities (ee's up to 99 %) as well as with improved activities under standard thermal conditions. The results indicate that the catalytic performance is highly affected by the oxazoline and biarylphosphite substituents and the axial chirality of the biaryl moiety of the ligand. The Heck reactions were also performed under microwave irradiation conditions, allowing a considerably shorter reaction time (full conversion in minutes) maintaining the excellent regio‐ and enantioselectivities.
Time domain 3D fundamental solutions for saturated poroelastic media with incompressible constituents
Authors: Kamalian Mohsen , Gatmiri Behrouz , Sharahi Morteza Jiryaei 
Published: February 2007

AbstractThis paper presents simple time domain fundamental solutions for the three‐dimensional (3D) well known u–p formulation of saturated porous media, neglecting the compressibility of fluid and solid particles. At first, the corresponding boundary integral equations as well as the explicit Laplace transform domain fundamental solutions are obtained in terms of solid displacements and fluid pressure. Subsequently, the closed form time domain fundamental solutions are derived by analytical inversion of the Laplace transform domain solutions. Finally, a set of numerical results are presented which demonstrate the accuracies and some salient features of the derived analytical transient fundamental solutions. Copyright © 2007 John Wiley & Sons, Ltd.