bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular modeling of heme proteins using MOE: Bio‐inorganic and structure‐function activity for undergraduates*S
Authors: Ray Gigi B. , Cook J. Whitney
Published: February 2007

A biochemical molecular modeling project on heme proteins suitable for an introductory Biochemistry I class has been designed with a 2‐fold objective: i) to reinforce the correlation between protein three‐dimensional structure and function through a discovery oriented project, and ii) to introduce students to the fields of bioinorganic and coordination chemistry. Students are asked to identify several unknown heme proteins based on a careful analysis of covalent and noncovalent interactions at the active site of each protein, focusing on amino acid reactivity and H‐bonding networks. Starting with the three‐dimensional crystal structures of four unknown proteins, students isolate and examine the coordination environment of the iron center in order to predict the relative reactivity toward dioxygen (O2) or hydrogen peroxide (H2O2). The central question of the project is to determine how the same iron protoporphyrin IX cofactor can be used by four different proteins to carry out diverse reactions, from electron transfer, to reversible oxygen binding to hydrogen peroxide activation. Pedagogical reasons for implementation of this biomolecular discovery‐based activity and student evaluations are discussed. In addition to developing many of the three‐dimensional visualization skills needed to successfully learn biochemistry, students also learn to use the versatile MOE molecular modeling program (Molecular Operating Environment), become familiar with metalloprotein reactivity, and are introduced to computational biochemistry research.
Isolation of Caenorhabditis elegans genomic DNA and detection of deletions in the unc‐93 gene using PCR
Authors: Lissemore James L. , Lackner Laura L. , Fedoriw George D. , De Stasio Elizabeth A.
Published: February 2007

PCR, genomic DNA isolation, and agarose gel electrophoresis are common molecular biology techniques with a wide range of applications. Therefore, we have developed a series of exercises employing these techniques for an intermediate level undergraduate molecular biology laboratory course. In these exercises, students isolate genomic DNA from the nematode Caenorhabditis elegans and use PCR to detect deletions in the C. elegans unc‐93 gene. In advance of the exercises, wild‐type and three different unc‐93 deletion mutant strains are grown, harvested, and frozen by the instructor. In one approach, students isolate genomic DNA from each strain using a genomic DNA isolation kit and use agarose gel electrophoresis to analyze the DNA and to estimate its concentration. PCRs using primers directed to two different regions of the unc‐93 gene are carried out on the genomic DNA from wild‐type and mutant strains, and the PCR products are analyzed by agarose gel electrophoresis. Students analyze the gel to determine the approximate location and size of deletions in the three mutant strains. Alternatively, students may lyse single nematodes and carry out PCR in one laboratory session. These exercises should be easily adaptable to detection of well characterized deletions in any organism.
Developing students' awareness of public understanding of science: A matter of survival?
Authors: Castanho Miguel A. R. B.
Published: February 2007

Biochemists and life scientists in general are now encountering a paradox regarding the public image of their work; society demands and encourages pursuit of more knowledge but at the same time is suspicious and fears the novelties it brings. At this historical moment, we are experiencing a delicate balance between the birth of a new era and a downsizing the status of biochemistry. The future can go either way, and it is up to scientists to become deeply involved to make the first scenario overturn the second. This task demands awareness and engagement in scientific communication and the promotion of science. However, the work ahead demands continuous commitment for more than one generation. If we want to leave a legacy of a well regarded and prosperous science to our students, we must let them know why public understanding is crucial, indeed vital, and show them how to cope with and actually embrace it. This may actually be a survival skill for them!
Hinari and Agora: Providing access for researchers in developing countries
Authors: Long Maurice
Published: February 2007

This article briefly describes two schemes, Health InterNetwork Access to Research Initiative (HINARI) and Access to Global Online Research in Agriculture (AGORA), which enable up to date scientific and clinical literature to be distributed via the World Wide Web to individuals in developing countries at zero or minimal cost as a result of agreements between publishers.
Using the discussion board in the undergraduate biochemistry classroom: Some lessons learned*
Authors: Markwell John
Published: February 2007

The discussion board feature that is included with most course management software packages is a potentially valuable tool to augment instructor‐student interactions in science lecture courses and increase student motivation. However, many teachers seem to have been frustrated that students do not readily make use of this feature when it is added to the course resources. The author has been using a discussion board in undergraduate biochemistry lecture courses for six years and has learned to use it to evolve a system that students use and that seems to increase interaction with students while requiring less time than traditional face‐to‐face meetings outside of the lecture. The aspects that the author emphasizes for efficient discussion board use are timing, creating a safe virtual environment for the students, “seeding” with simulated questions, setting boundaries, and being self‐conscious about the attitude that the instructor projects to the students.
Methionine and derivatives: Exploring chirality at sulfur
Authors: Bentley Ronald
Published: February 2007

Chiral molecules, both small and large, play important roles in biochemistry, molecular biology, and related biosciences. The central position of carbon atoms in determining chirality has received considerable attention. Less well known is the fact that chirality is also possible for sulfur atoms in certain compounds. This article introduces the role of sulfur chirality in metabolic reactions by considering methionine derivatives with chiral sulfur atoms, S‐adenosylmethionine and its decarboxylated product, methionine S‐oxide, and methionine sulfoximine.
Preparing the senior or graduating student for graduate research
Authors: Tang Bor Luen , Gan Yunn Hwen
Published: February 2007

Senior undergraduates in the honors or graduation year with an intention to further their career in science would soon face the real world of scientific research as a junior scientist. It is important to acquaint these students with and adequately prepare them for the key aspects of a scientist's professional life. These include technical capacities indispensable for continuous and intense appraisal of data and knowledge as well as awareness that would ensure proper professional conduct within the laboratory. We have designed and conducted a module called “Scientific Critique” in the fourth year for Biochemistry majors. The module emphasizes scientific literature review and critique. It also incorporates techniques in preparing research grant proposals and an exercise in peer review of grant proposals as well as lectures and presentations on scientific integrity and research ethics. Positive response and feedback from students are indicative of an appreciation for the module contents, and we believe it of value to include such contents in any senior undergraduate life sciences curriculum.
Critical analysis on the use of poster display as an alternative evaluation method in basic biochemistry
Authors: Fernandes Patricia M. B. , Rodrigues Silas P. , Lindsey George
Published: February 2007

This article describes the use of poster preparation and display as an assessment tool and includes feedback from the students and academics concerned. This alternative approach has been used for four years since 2000 for biological science students studying biochemistry. The object of this approach was to get away from traditional teaching evaluation strategies, which promote passive learning and superficial memorization. Creating and presenting posters based on published manuscripts require students to understand, critically analyze, and disseminate the data, thereby promoting the understanding and retention of the material presented.
Immunoprecipitation and characterization of membrane protein complexes from yeast*S
Authors: Parra‐Belky Karlett , McCulloch Kathryn , Wick Nicole , Shircliff Rebecca , Croft Nicolas , Margalef Katrina , Brown Jamie , Crabill Todd , Jankord Ryan , Waldo Eric
Published: February 2007

In this undergraduate biochemistry laboratory experiment, the vacuolar ATPase protein complex is purified from yeast cell extracts by doing immunoprecipitations under nondenaturing conditions. Immunoprecipitations are performed using monoclonal antibodies to facilitate data interpretation, and subunits are separated on the basis of their molecular size by SDS‐PAGE. Both integral membrane and peripheral subunits are detected in Coomassie Blue‐stained gels, and the identity of several subunits are confirmed by Western blots. Western blots serve to illustrate reproducibility and authenticity of the results and help students understand that they could use immunoblotting to detect subunits that are not visualized by Coomassie stain. The molecular mass of the subunits is estimated by their migration relative to molecular marker proteins in the same gel and used to estimate the size of the entire complex. Just like in biochemistry research, students learn to integrate several techniques to solve the subunit composition of a protein complex. These experiments are an alternative to classical protein purification techniques and can be adapted to study most protein complexes composed of membrane‐bound and peripheral subunits from yeast. Instructors can use this approach to teaching proteomics and introduce students to systems biology. Because numerous yeast proteins are epitope tagged, instructors could use commercially available antibodies to study a protein complex of interest.
Digital learning material for student‐directed model building in molecular biologyS
Authors: Aegerter‐Wilmsen Tinri , Coppens Marjolijn , Janssen Fred , Hartog Rob , Bisseling Ton
Published: February 2007

The building of models to explain data and make predictions constitutes an important goal in molecular biology research. To give students the opportunity to practice such model building, two digital cases had previously been developed in which students are guided to build a model step by step. In this article, the development and initial evaluation of a third digital case is described. It concerns the selection of bristles during Drosophila development. To mimic a real research situation in a more realistic way, students are given much more freedom while building their models and can thus follow their own model‐building approach. At the same time, however, students are provided with a sufficient amount of support to ensure that they can build their models without the requirement of intensive supervision.
A docking interaction study of the effect of critical mutations in ribonuclease a on protein‐ligand binding
Authors: Mukherjee Sayan , De Soumya , Ghosh Zhumur , Dasgupta Swagata
Published: February 2007

Enzymes with ribonucleolytic activity play a pivotal role in gene expression and cellular homeostasis by altering the levels of cellular RNA. Ribonuclease A has been the most well studied of such enzymes whose histidine residues (His12 and His119) play a crucial role in the catalytic mechanism of the protein. The ligands chosen for this study, 2′CMP and 3′CMP, act as competitive substrate analog inhibitors of this enzyme. Using molecular graphics software freely available for academic use, AutoDock and PyMol, we demonstrate that substitution of either histidine residue by alanine causes marked changes in the distances between these critical residues of the enzyme. The ligands in the docked conformation (particularly on mutation of His119 to Ala) compensate for the altered free energy and hydrogen bonding abilities in these new protein‐ligand complexes.
Simplifying structure analysis projects with customizable chime‐based templates*
Authors: Thompson Scott E. , Sears Duane W.
Published: February 2007

Structure/function relationships are fundamental to understanding the properties of biological molecules, and thus it is imperative that biochemistry students learn how to analyze such relationships. Here we describe Chime‐based web page templates and tutorials designed to help students develop their own strategies for exploring macromolecular three‐dimensional structures like those on our course website. The templates can easily be customized for any structure of interest, and some templates include a Command Entry Line and a Message Recall Box for more refined macromolecular exploration using RasMol/Chime image modification commands. The tutorials present students with an integrated overview of the image modification capabilities of the Chime plug‐in and its underlying RasMol‐based command structure as accessed through the Command Entry Line. The tutorial also illustrates how RasMol/Chime command syntax addresses specific formatted structural information in a standard Protein Data Bank file. Judging by the high quality of structure‐based presentations given by students who have used these templates and tutorials, it appears that these resources can help students learn to analyze complex macromolecular structures while also providing them with convenient tools for creating scientifically meaningful and visually effective molecular images to share with others. (The templates, tutorials, and our course website can be viewed at the following URLs, respectively: tutor.lscf.ucsb.edu/instdev/sears/biochemistry/presentations/demos‐downloads.htm, tutor.lscf.ucsb.edu/instdev/sears/biochemistry/tutorials/pdbtutorial/frontwindow.html, and tutor.lscf.ucsb.edu/instdev/sears/biochemistry/.)
Modular laboratory courses: An alternative to a traditional laboratory program
Authors: Caprette David R. , Armstrong Sarah , Beason K. Beth
Published: February 2007

Our modular laboratory teaching program is characterized by two major features. First, each course is taught independently and not linked with a particular lecture course. Second, each course is designed to be completed within one‐half semester or less. The modular organization has allowed incorporation of the latest technology, reduction of class sizes, and a greater number of choices to permit students to pursue their own interests. Full‐time laboratory teaching personnel work together on the organization of the program as well as design and teach individual courses. The program has distinct and separate instructional goals, namely introduction, reinforcement, and advancement of fundamental scientific capacities. Such focus has facilitated efforts to coordinate laboratory courses within the biological sciences and among other departments in natural sciences and engineering, raising expectations as students progress through a program.
Use of solid phase extraction in the biochemistry laboratory to separate different lipids
Authors: Flurkey William H.
Published: February 2007

Solid‐phase extraction (SPE) was used to demonstrate how various lipids and lipid classes could be separated in a biochemistry laboratory setting. Three different SPE methods were chosen on their ability to separate a lipid mixture, consisting of a combination of a either a fatty acid, a triacylglycerol, a mono‐ or diacylglycerol, phospholipid, cholesterol, or cholesteryl ester into distinct lipid fractions. These mini‐scale SPE methods used aminopropyl‐bonded silica columns or silica Sep‐Pak cartridges suitable for completion in a 2‐ to 3‐h time block. Thin‐layer chromatography of the isolated lipid fractions was used to show separation characteristics and to evaluate the utility and reproducibility of each SPE method.
Poem: A is for alanine
Authors: Crowther Gregory J.
Published: February 2007

The poem below presents a brief review of amino acid abbreviations and structures. Among the featured facts are the following: histidine has a pKa close to the normal pH of the cytosol and therefore is an effective intracellular buffer, the R group of isoleucine is hydrophobic, and many protein kinases add a phosphate at the ‐OH site of tyrosine.

This work is just one of many science songs and poems that may be used for educational purposes. A comprehensive database of over 2,000 songs is available online at www.science‐groove.org/MASSIVE/.
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

We 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

Cytochrome 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

We 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

International 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

We 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

A 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

A 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

Health 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.
The yeast two‐hybrid system
Authors: Szeberényi József
Published: February 2007

Terms to be familiar with before you start to solve the test: transcription factors, enhancer, promoter, RNA polymerase, expression plasmid, terminator, histidine, transfection, cell culture, fusion proteins, RNA splicing.
Biomolecules in the computer: Jmol to the rescue
Authors: Herráez Angel
Published: February 2007

Jmol 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

The 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

Bioinformatics 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

We 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

Terms 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

The 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

Hydrogen‐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

The 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

A 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

An 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

Highly 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

We 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

This 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.
Note on the determination of the ignition point in forest fires propagation using a control algorithm
Authors: Bergmann M. , Séro‐Guillaume O. , Ramezani S.
Published: February 2007

This paper is devoted to the determination of the origin point in forest fires propagation using a control algorithm. The forest fires propagation are mathematically modelled starting from a reaction diffusion model. A volume of fluid (V.O.F.) formulation is also used to determine the fraction of the area which is burnt. After having developed the objective functional and its derivative, results from an optimization process based on the simplex method is presented. It is shown that the ignition point and the final time of the fire propagation are precisely recovered, even for a realistic, non‐horizontal, terrain. Copyright © 2007 John Wiley & Sons, Ltd.
CJZ3, a lomerizine derivative, reverses P‐glycoprotein‐mediated multidrug‐resistance in doxorubicin‐resistant human myelogenous leukemia (K562/DOX) cells
Authors: Ji Bian‐Sheng , He Ling , Liu Guo‐Qing
Published: February 2007

P‐glycoprotein‐mediated drug efflux can yield a multidrug‐resistance (MDR) phenotype that is associated with a poor response to cancer chemotherapy. The development of safe and effective MDR‐reversing agents is an important approach in the clinic. The aim of this study was to examine the effects of CJZ3, a lomerizine derivative, on the inhibition of P‐gp function and P‐gp‐mediated MDR in K562/DOX cells and parental K562 cells. Incubation of K562/DOX cells with CJZ3 caused a marked increase in accumulation and uptake and a notable decrease in efflux of Rh123, No such results were found in parental K562 cells. The inhibitory effect of the agent on P‐gp function was reversible, but it persisted for at least 90 min after removal of 2.5 &µM CJZ3 from the incubation medium. The doxorubicin‐induced cytotoxicity, apoptosis, and cell‐cycle perturbations were significantly potentiated by CJZ3. The intracellular accumulation of doxorubicin was enhanced in the presence of various concentrations of CJZ3. The CJZ3 exhibited potent effects in vitro in the reversal of P‐gp‐mediated MDR, suggesting that the compound may be an effective MDR reversing agent in cancer chemotherapy. Drug Dev. Res. 67:862–869, 2006. © 2007 Wiley‐Liss, Inc.
Non‐viral gene therapy for diabetic retinopathy
Authors: Oshitari Toshiyuki
Published: February 2007

Diabetic retinopathy results from vascular abnormalities, such as an increase in the permeability of retinal vessels, and retinal neurodegeneration, which are irreversible changes that occur early in the course of diabetic retinopathy. To block the vascular and neuronal complications associated with the development and progression of diabetic retinopathy, a reasonable strategy would be to prevent the increased vascular permeability and to block the neuronal cell death. The purpose of this review is to present the non‐viral strategies being used to block the neurovascular abnormalities and neuronal cell death that are observed in the early stages of diabetic retinopathy in order to prevent the onset or the progression of the diabetic retinopathy. Some of the non‐viral gene therapeutic techniques being used are electroporation of selected genes, injections of antisense oligonucleotides, and injections of small interference RNAs. The results obtained by these methods are discussed as is the potential of these therapeutic strategies to prevent the onset or the progression of the neurovascular abnormalities in diabetic retinopathy. Drug Dev. Res. 67:835–841, 2006. © 2007 Wiley‐Liss, Inc.
Synaptic transmission is impaired at neuronal autonomic synapses in agrin‐null mice
Authors: Gingras Jacinthe , Rassadi Siamak , Cooper Ellis , Ferns Michael
Published: February 2007

Neuronal synapse formation is a multistep process regulated by several pre‐ and postsynaptic adhesion and signaling proteins. Recently, we found that agrin acts as one such synaptogenic factor at neuronal synapses in the PNS by demonstrating that structural synapse formation is impaired in the superior cervical ganglia (SCG) of z+ agrin‐deficient mice and in SCG cultures derived from those animals. Here, we tested whether synaptic function is defective in agrin‐null (AGD−/−) ganglia and began to define agrin's mechanism of action. Our electrophysiological recordings of compound action potentials showed that presynaptic stimulation evoked action potentials in ≈40% of AGD−/− ganglionic neurons compared to 90% of wild‐type neurons; moreover, transmission could not be potentiated as in wild‐type or z+ agrin‐deficient ganglia. Intracellular recordings also showed that nerve‐evoked excitatory postsynaptic potentials in AGD−/− neurons were only 1/3 the size of those in wild‐type neurons and mostly subthreshold. Consistent with these defects in transmission, we found an ≈40–50% decrease in synapse number in AGD−/− ganglia and cultures, and decreased levels of differentiation at the residual synapses in culture. Furthermore, surface levels of acetylcholine receptors (AChRs) were equivalent in cultured AGD−/− and wild‐type neurons, and depolarization reduced the synaptic localization of AChRs in AGD−/− but not wild‐type neurons. These findings provide the first direct demonstration that agrin is required for proper structural and functional development of an interneuronal synapse in vivo. Moreover, they suggest a novel role for agrin, in stabilizing the postsynaptic density of nAChR at nascent neuronal synapses. © 2007 Wiley Periodicals, Inc. Develop Neurobiol, 2007
A screen for neurotransmitter transporters expressed in the visual system ofDrosophila melanogasteridentifies three novel genes
Authors: Romero‐Calderón Rafael , Shome Ratula M. , Simon Anne F. , Daniels Richard W. , DiAntonio Aaron , Krantz David E.
Published: February 2007

The fly eye provides an attractive substrate for genetic studies, and critical transport activities for synaptic transmission and pigment biogenesis in the insect visual system remain unknown. We therefore screened for transporters inDrosophila melanogasterthat are down‐regulated by genetically ablating the eye. Using a large panel of transporter specific probes on Northern blots, we identified three transcripts that are down‐regulated in flies lacking eye tissue. Two of these,CG13794andCG13795, are part of a previously unknown subfamily of putative solute carriers within the neurotransmitter transporter family. The third, CG4476, is a member of a related subfamily that includes characterized nutrient transporters expressed in the insect gut. Using imprecise excision of a nearby transposable P element, we have generated a series of deletions in theCG4476gene. In fast phototaxis assays,CG4476mutants show a decreased behavioral response to light, and the most severe mutant behaves as if it were blind. These data suggest an unforeseen role for the “nutrient amino acid transporter” subfamily in the nervous system, and suggest new models to study transport function using the fly eye. © 2007 Wiley Periodicals, Inc. Develop Neurobiol, 2007