bluuebunny/crossref_metadata_2025_split huggingface dataset:
From problem‐based learning to interrupted lecture: Using case‐based teaching in different class formats
Authors: Hodges Linda C. 
Published: February 2007

AbstractAlthough many examples of using problem‐based learning and case studies in teaching science occur in the literature, instructors may still have questions about when, why, and how to use these strategies, especially in different class settings. In this article, I describe my experience in using these pedagogical methods in three different class formats: a small biochemistry survey course, which I taught entirely as problem‐based learning; a small organic chemistry class in which I used some case‐based teaching with students working collaboratively in groups; and a large lecture‐style biochemistry survey course in which I used cases as homework and in‐class exercises. In each instance I describe the apparent benefits and drawbacks of each approach, drawing on the literature of how these methods may best promote learning. As part of this discussion I pose questions for instructors to help them decide which form of case‐based teaching best fits with their particular teaching goals and class contexts.
Often ignored facts about the control of the 2‐oxoglutarate dehydrogenase complex
Authors: Strumilo Slawomir 
Published: February 2007

AbstractInformation about the control of the activity of the 2‐oxoglutarate dehydrogenase complex (OGDHC), a key enzyme in the citric acid cycle, is not well covered in the biochemical education literature, especially as it concerns the allosteric regulation of OGDHC by adenine nucleotide and ortophosphate. From experimental work published during the last 25 years, the following basic view is clear: (a) animal OGDHC is very sensitive to ADP, Pi, and Ca2+; (b) these positive effectors increase the affinity of OGDHC to 2‐oxoglutarate; (c) OGDHC is inhibited by ATP, NADH, and succinyl‐CoA; (d) the ATP effect is realized mainly via opposition to ADP activation; (e) NADH, in addition to inhibiting the dihydrolipoamide dehydrogenase component of the enzyme complex (competitively versus NAD+) decreases the affinity of 2‐oxoglutarate dehydrogenase to its substrate; (f) bacterial and plant OGDHC are activated by AMP instead of ADP. These main effects form the basis of short term regulation of OGDHC. It is desirable that such information should reach biochemistry students.
SigrafW: An easy‐to‐use program for fitting enzyme kinetic data
Authors: Leone Francisco Assis , Baranauskas José Augusto , Furriel Rosa Prazeres Melo , Borin Ivana Aparecida 
Published: February 2007

AbstractSigrafW is Windows‐compatible software developed using the Microsoft® Visual Basic Studio program that uses the simplified Hill equation for fitting kinetic data from allosteric and Michaelian enzymes. SigrafW uses a modified Fibonacci search to calculate maximal velocity (V), the Hill coefficient (n), and the enzyme‐substrate apparent dissociation constant (K). The estimation of V, K, and the sum of the squares of residuals is performed using a Wilkinson nonlinear regression at any Hill coefficient (n). In contrast to many currently available kinetic analysis programs, SigrafW shows several advantages for the determination of kinetic parameters of both hyperbolic and nonhyperbolic saturation curves. No initial estimates of the kinetic parameters are required, a measure of the goodness‐of‐the‐fit for each calculation performed is provided, the nonlinear regression used for calculations eliminates the statistical bias inherent in linear transformations, and the software can be used for enzyme kinetic simulations either for educational or research purposes.Persons interested in receiving a free copy of the software should contact Dr. F. A. Leone.
The mitochondrial phosphate‐to‐oxygen ratio is not an integer
Authors: Silverstein Todd 
Published: February 2007

AbstractFor many years, mitochondrial phosphate‐to‐oxygen ratios were believed to be integral values: 3 for ATP/NADH and 2 for ATP/FADH2. The chemiosmotic theory has demonstrated that this need not be the case because coupling sites do not directly synthesize ATP. Coupling between coupling site redox reactions and ATP synthesis occurs via proton pumping and proton flow, respectively. Most recent measurements support phosphate‐to‐oxygen ratios of ∼2.5 ATP/NADH and 1.5 ATP/FADH2; these values match those expected from chemiosmotic calculations. Faculty members who teach metabolism are encouraged to reflect these developments in their lecture notes.
One hundred years of American Women in biochemistry *
Authors: Wolfson Adele J. 
Published: February 2007

AbstractThe occasion of ASBMB's 100th anniversary provides an opportunity to consider the history and accomplishments of women biochemists over the past century. American women in biochemistry have ranged from the highly visible, such as Nobel Prize winners Gert Cori and Gertrude Elion, to those who contributed in relative obscurity to equally dramatic breakthroughs. Women with Ph.D.s in biochemistry established departments of public health, nutrition, and home economics when more prestigious academic departments were not open to them. As in all fields of science, women have made great progress in biochemistry in recent years, and ASBMB reflects that progress; the past, current, and incoming presidents of the Society are all women. The data and biographical information presented here should provide a basis for inclusion of more women in recounting the history of biochemistry.
Thoughts on the teaching of metabolism
Authors: Metzger Robert P. 
Published: February 2007

AbstractSystems biology, metabolomics, metabolic engineering, and other recent developments in biochemistry suggest that future biochemists will require a detailed familiarity with the compounds and pathways of intermediary metabolism and their biochemical control. The challenge to the biochemistry instructor is the presentation of metabolic pathways in a manner that allows student creativity in learning the pathways and their components. One approach that does permit the use of problem solving for the study of metabolic pathways involves following the fate of 13C, 14C, or 15N labels, presented originally in the structure of an important metabolic starting compound, through relevant metabolic pathways. This method allows the presentation and study of problems in which such an isotopic label can be traced through two or more metabolic pathways, thus illustrating how these pathways are interconnected. The understanding that all the pathways of intermediary metabolism are interconnected provides opportunities to discuss their metabolic control by such mechanisms as signaling, feedback inhibition, location in organelles, coenzyme levels, and coenzyme recycling rates. The method is illustrated by following the fate of 14C labels through anaerobic glycolysis, gluconeogenesis, and fatty acid transport, β‐oxidation, and ketone body formation. Cholesterol biosynthesis and heme formation are used to show that presentations of long and complex pathways can demonstrate important biochemical concepts by following the fate of an isotopic label using only the most important intermediates. Problems based on tracing radioactive labels through one or more metabolic pathways allow the use of cooperative learning techniques.
An exercise to estimate differential gene expression in human cells
Authors: Chaudhry M. Ahmad 
Published: February 2007

AbstractThe expression of genes in cells of various tissue types varies considerably and is correlated with the function of a particular organ. The pattern of gene expression changes in diseased tissues, in response to therapy or infection and exposure to environmental mutagens, chemicals, ultraviolet light, and ionizing radiation. To better understand the disease at the molecular level, the alterations in gene expression can provide clues to identify the cellular pathways involved. There are a wide variety of techniques that have been developed to study differential gene expression. Most of these methodologies are technically challenging. We developed an exercise to examine and quantify differential gene expression based on reverse transcription‐PCR. Our goal was to have this technique successfully performed by college level students. This technique is easy to perform and does not require the use of radioactive substances. We examined the ionizing radiation‐induced changes in gene expression in human cells. After exposure to ionizing radiation, total RNA was isolated at 4, 8, 12, and 24 h. The RNA was converted to cDNA and subjected to PCR amplification using gene‐specific primers and commercially available β‐actin internal standards in a multiplex format. The differences in gene expression were quantified with freely available imaging software. This technique should have a wide application to investigate differential gene expression in a variety of organisms and under various experimental and treatment conditions.
Using yeast to easily determine mitochondrial functionality with 1‐(4,5‐dimethylthiazol‐2‐yl)‐3,5‐diphenyltetrazolium bromide (MTT) assay
Authors: Sánchez Norma Silvia , Königsberg Mina 
Published: February 2007

AbstractMitochondrial respiration is an important topic in biochemical courses, but at the same time it is a very arduous and challenging subject for the students to comprehend. In teaching laboratories, experiments are also difficult to perform because mitochondrial isolation as well as oxygen consumption determinations require expensive equipment, rarely present in Mexican teaching laboratories. For this purpose, we adapted the 1‐(4,5‐dimethylthiazol‐2‐yl)‐3,5‐diphenyltetrazolium bromide (MTT) assay, usually done with cell lines, to corroborate mitochondrial respiration in yeast. We used the reduction of the MTT to learn and distinguish the respiratory yield between different substrates as well as the effects of respiratory inhibitors. This is an economical, easily done laboratory experiment that quantifies mitochondrial functionality and provides a good idea of the respiratory process.
“Mini‐array” transcriptional analysis of the Listeria monocytogenes lecithinase operon as a class project: A student investigative molecular biology laboratory experience*
Authors: Christensen Douglas , Jovic Marko 
Published: February 2007

AbstractThis report describes a molecular biotechnology‐based laboratory curriculum developed to accompany an undergraduate genetics course. During the course of a semester, students researched the pathogen, developed a research question, designed experiments, and performed transcriptional analysis of a set of genes that confer virulence to the food‐borne pathogen, Listeria monocytogenes. Gene fragments were amplified via PCR and utilized in “mini‐arrays,” a dot‐blot‐based format suitable for the simultaneous transcriptional analysis of multiple genes. The project provides exposure to a wide range of molecular techniques and can be easily modified for variations in class size. Data are generated at various steps of the process, allowing for student interpretation, troubleshooting, and assessment opportunities.
Fluorescence analysis of sulfonamide binding to carbonic anhydrase
Authors: Wang Sheila C. , Zamble Deborah B. 
Published: February 2007

AbstractA practical laboratory experiment is described that illustrates the application of fluorescence resonance energy transfer to the study of protein‐ligand binding. The affinities of wild‐type and mutant human carbonic anhydrase II for dansylamide were determined by monitoring the increase in ligand fluorescence that occurs due to energy transfer from tryptophan residues near the enzyme active site. In a subsequent experiment, the binding constant of azetazolamide, a weaker fluorophore but a stronger ligand, is measured by competition with dansylamide. This simple experiment introduces students to the widely used technique of fluorescence spectroscopy and to the determination of protein‐ligand binding constants.
Helping parents to manage infant crying and sleeping: a review of the evidence and its implications for services
Authors: James‐Roberts Ian St 
Published: February 2007

AbstractInfant crying and night waking are common concerns for parents, costly problems for health services and may trigger infant abuse or lead to serious child disturbances. Parents are given contradictory advice on how to manage infant crying and sleeping, indicating the need for evidence‐based guidance. This review of recent research draws distinctions between infant crying and sleeping problems, between the problem identified by parents and the infant behaviour underlying the problem, between different types of crying behaviour and their causes, and between the types of cases which present at different ages. It proposes that the two main approaches to parenting advocated by baby‐care experts, ‘infant‐demand’ and ‘structured’ parenting, have different benefits, and costs. Comparative studies have found that infant‐demand parenting is associated with low amounts of fussing and crying in the first three months of age, but with night waking which continues beyond three months. Randomised controlled trials have provided evidence that structured parenting leads to more overall fussing and crying during the first three months, but reduced night waking and crying after that. The findings are translated into recommendations for preventing and treating infant crying and sleeping problems, for policy debate, and for further research. Copyright © 2007 John Wiley & Sons, Ltd.
Theoretical Evaluation of the Substrate‐Assisted Catalysis Mechanism for the Hydrolysis of Phosphate Monoester Dianions
Authors: Iché‐Tarrat Nathalie , Ruiz‐Lopez Manuel , Barthelat Jean‐Claude , Vigroux Alain 
Published: February 2007

AbstractQuantum chemistry methods coupled with a continuum solvation model have been applied to evaluate the substrate‐assisted catalysis (SAC) mechanism recently proposed for the hydrolysis of phosphate monoester dianions. The SAC mechanism, in which a proton from the nucleophile is transferred to a nonbridging phosphoryl oxygen atom of the substrate prior to attack, has been proposed in opposition to the widely accepted mechanism of direct nucleophilic reaction. We have assessed the SAC proposal for the hydrolysis of three representative phosphate monoester dianions (2,4‐dinitrophenyl phosphate, phenyl phosphate, and methyl phosphate) by considering the reactivity of the hydroxide ion toward the phosphorus center of the corresponding singly protonated monoesters. The reliability of the calculations was verified by comparing the calculated and the observed values of the activation free energies for the analogous SN2(P) reactions of F− with the monoanion of the monoester 2,4‐dinitrophenyl phosphate and its diester analogue, methyl 2,4‐dinitrophenyl phosphate. It was found that the orientation of the phosphate hydrogen atom has important implications with regard to the nature of the transition state. Hard nucleophiles such as OH− and F− can attack the phosphorus atom of a singly protonated phosphate monoester only if the phosphate hydrogen atom is oriented toward the leaving‐group oxygen atom. As a result of this proton orientation, the SAC mechanism in solution is characterized by a small Brønsted coefficient value (βlg=−0.25). This mechanism is unlikely to apply to aryl phosphates, but becomes a likely possibility for alkyl phosphate esters. If oxyanionic nucleophiles of pKa<11 are involved, as in alkaline phosphatase, then the SN2(P) reaction may proceed with the phosphate hydrogen atom oriented toward the nucleophile. In this situation, a large negative value of βlg (−0.95) is predicted for the substrate‐assisted catalysis mechanism.
N‐Octylquinolinium Tribromide: A Task Specific Quinoline Based Ionic Liquid as a New Brominating Agent.
Authors: Kaushik M. P. , Polshettiwar Vivek 
Published: February 2007

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Adenylate kinase in sea urchin embryonic cilia
Authors: Kinukawa Masashi , Vacquier Victor D. 
Published: February 2007

AbstractSea urchin embryos swim by ciliary movement. Hypertonic shock causes deciliation and loss of motility. Within 2–4 h, cilia regenerate and the embryos swim again. Regeneration of cilia occurs multiple times. The adenylate kinase (AK) activity of isolated cilia was studied. A 130‐kDa Sp‐AK isozyme, present in sperm flagella, is also present in embryonic cilia. AK activity is responsible for ∼93% of nonmitochondrial ATP regeneration from ADP in embryonic cilia. This is unlike sea urchin sperm flagella, where ∼31% of the nonmitochondrial ATP regeneration is from the 130‐kDa Sp‐AK isozyme and ∼69% from the flagellar creatine kinase (Sp‐CK). Embryos were deciliated 1–3 times and after a 2‐h period of regeneration the major ciliary axonemal proteins such as the tubulins appeared constant in amount. However, a moderate decrease in ATPase activity, and a large decrease of total AK activity, were measured. The decrease in AK activity paralleled the decrease in embryo swimming velocity. Embryos were deciliated once and cilia regeneration followed for 4 h. ATPase activity recovered to control levels by 3 h, but AK activity and swimming velocity remained lower than in controls. Detergent solubility data and kinetic experiments indicate that, in addition to the 130‐kDa Sp‐AK, there is at least one additional AK isozyme in embryonic cilia. Analysis of the S. purpuratus genome indicates five AK isozymes in addition to the 130‐kDa Sp‐AK isozyme. Decreased swimming velocity of embryos with regenerated cilia suggests that regenerated cilia are not as functionally perfect as naturally grown cilia. Cell Motil. Cytoskeleton 2007. © 2007 Wiley‐Liss, Inc.
Effects of cross‐fostering on cocaine‐induced conditioned taste aversions in Fischer and Lewis rats
Authors: Roma Peter G. , Davis Catherine M. , Riley Anthony L. 
Published: February 2007

AbstractThe systematic comparison between Fischer and Lewis rats is a popular animal model of genetic factors in drug abuse. Although genetic and environmental factors interact to affect drug abuse in humans, analogous effects have not yet been reported within the Fischer–Lewis model. In order to assess the contributions and interaction of genotype and early maternal environment on responses to a drug of abuse, the present study employed a cross‐fostering design, where male and female Fischer and Lewis pups were reared by unrelated dams of their own strain (in‐fostered) or of the other strain (cross‐fostered). As adults, rats from both strains were tested for their ability to acquire a conditioned taste aversion to a novel saccharin solution that had been repeatedly paired with an injection of cocaine (32 mg/kg, subcutaneous). In‐fostered Fischer females acquired significantly weaker aversions than in‐fostered Lewis females across the multiple saccharin‐cocaine pairings. However, cross‐fostered Fischer females exhibited aversions that were not only significantly stronger than their in‐fostered Fischer counterparts, but identical to all groups of the Lewis genotype. No strain differences or cross‐fostering effects were observed in the males. The data with the female subjects cannot be accounted for simply by the genetic strain of the subjects and demonstrate a clear gene‐environment interaction effect on responses to the aversive effects of cocaine in Fischer and Lewis rats. Implications for studying maternal behavior as a source of epigenetic modulation of drug abuse vulnerability were discussed. © 2007 Wiley Periodicals, Inc. Dev Psychobiol 49: 172–179, 2007.
Children's skin conductance level and reactivity: Are these measures stable over time and across tasks?
Authors: El‐Sheikh Mona 
Published: February 2007

AbstractThe stability of children's skin conductance level during baselines (SCL‐B) and SCL reactivity (SCL‐R) were examined longitudinally. During two laboratory sessions (T1 and T2), 2 years apart, children participated in procedures during which they were exposed to two stressors namely exposure to an audiotaped conflict between two adults, and a problem solving task. Children ranged in age between 6 and 13 years at T1. Measures of SCL‐B and SCL‐R during the two stressors were obtained. Findings illustrated the temporal stability of SCL‐B and SCL‐R to the star‐tracing task over 2 years. Results also indicated stability in SCL‐R to the two stressors (argument and problem‐solving) examined within the same session at either T1 or T2. These results support the proposition that SCL‐B and SCL‐R constitute stable individual differences at the ages examined, and build on the scant longitudinal literature on psychophysiological development in children. © 2007 Wiley Periodicals, Inc. Dev Psychobiol 49: 180–186, 2007.
Cyanido‐Bridged Dimetallic Complexes Derived from Manganese(III) Schiff Bases and Pentacyanidonitrosylchromate(I): Synthesis, Crystal Structure and Magnetic Properties
Authors: Ni Zhong‐Hai , Zheng Lei , Zhang Li‐Fang , Cui Ai‐Li , Ni Wei‐Wei , Zhao Chong‐Chao , Kou Hui‐Zhong 
Published: February 2007

AbstractFour cyanido‐bridged MnIII–CrI heterodimetallic complexes have been synthesized by the reactions of MnIII Schiff‐base complexes with the [Cr(CN)5(NO)]3– building block. X‐ray diffraction analysis reveals that [Mn(5‐Cl‐salen)(H2O)2][Mn2(5‐Cl‐salen)2(H2O)1.5Cr(CN)5(NO)] (1) has a trinuclear structure, and [Mn3(salen)3(H2O)(CH3CN)Cr(CN)5(NO)]·0.5CH3CN·0.5MeOH·2H2O (2) and [Mn(5‐Br‐salen)(H2O)(CH3OH)][Mn2(5‐Br‐salen)2(CH3OH)Cr(CN)5(NO)]·2H2O (3) have novel 1D chain topological structures, whereas [{Mn(saltmen)}4Cr(CN)5(NO)]ClO4·3H2O (4) displays a 2D layered network structure. Magnetic measurements show that the magnetic interaction between the MnIII and CrI ions bridged by a cyanido group is antiferromagnetic for complexes 1–4. The magnetic fitting for the trinuclear complex 1 gives the magnetic coupling constant J = –10.4(1) cm–1 and J′ = –1.29(2) cm–1 based on the isotropic Hamiltonian Ĥ = –2JŜCr[ŜMn(1) + ŜMn(2)] – 2J′ŜMn(1)ŜMn(2). Complex 2 exhibits 3D antiferromagnetic ordering (TN = 3.5 K) with a metamagnetic character below TN. Complex 3 exhibits an obvious frequency‐dependent AC magnetic susceptibility below 4.0 K, which is due to the spin‐glass behavior. The layered complex 4 displays 3D ferromagnetic ordering with Tc = 6.4 K due to the ferromagnetic interaction between the ferrimagnetic layers. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)
A Two‐Dimensional, Hydrogen‐Bond‐Cross‐Linked Molybdenum(VI) Network Polymer with Catalytic Activity
Authors: Luan Yi , Wang Ge , Luck Rudy L. , Yang Mu 
Published: February 2007

AbstractThe new hybrid inorganic–organic polymer [MoO2Cl2(H2O)2]·(H2dipy‐pra)Cl2 (1), where dipy‐pra = 1,3‐bis(4‐pyridyl)propane, has been synthesized and crystallographically characterized. MoO2Cl2(H2O)2 and the [H2dipy‐pra]2+ cation are cross‐linked by Mo–H2O···Cl and H2dipy‐pra···Cl hydrogen bonds to form a two‐dimensional layer structure. Complex 1 is an efficient catalyst, with H2O2 as the oxygen‐source oxidant and NaHCO3 as the cocatalyst, in the epoxidation of olefinic compounds under ambient conditions.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)
Bioinspired Metal‐Catalysed Doebner–Knoevenagel Condensations between Malonic Acid Half Thioesters and Aldehydes
Authors: Berrué Fabrice , Antoniotti Sylvain , Thomas Olivier P. , Amade Philippe 
Published: February 2007

AbstractInspired by polyketide biosynthesis, unprecedented metal‐catalysed Doebner–Knoevenagel condensations between Malonic Acid Half Thioesters (MAHTs) and various aldehydes have been achieved through the use of Yb(OTf)3 as catalyst, mimicking a five‐domain polyketide synthase module for the first time. In the presence of 5‐methoxybenzimidazole, stereo‐ and regiocontrol of the reaction proved to be high. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)