bluuebunny/crossref_metadata_2025 huggingface dataset:
Developmental expression of the G protein-coupled receptor 54 and three GnRH mRNAs in the teleost fish cobia
Authors: Mohamed J Shaik , Benninghoff Abby D , Holt G Joan , Khan Izhar A
Published: February 2007

The cDNAs of the G protein-coupled receptor 54 (GPR54) and three prepro-gonadotropin-releasing hormones, GnRH-I (seabream GnRH), GnRH-II (chicken GnRH-II), and GnRH-III (salmon GnRH) were isolated and cloned from the brain of the teleost fish cobia, Rachycentron canadum. The cobia GPR54 cDNA was 95 and 51–56% identical to those of tilapia and mammalian models respectively. The GnRH cDNA sequences of cobia showed strong identities to those of tilapia, Atlantic croaker, red drum, and the seabass and seabream species. The real-time quantitative RT-PCR methods allowed detection of all three GnRH mRNAs on the first day after hatching (DAH). The GnRH-I mRNA levels, which were the lowest among the three GnRHs, increased gradually with two distinct peaks in larvae at 3 and 4 DAH. On the other hand, GnRH-II and GnRH-III mRNAs were significantly higher in larvae at 2 and 6 DAH compared with those on the preceding days. In addition, significant peaks of all the three GnRH mRNAs were observed in the brains of 26-day-old fish. The finding of higher GnRH-I and GnRH-II mRNAs in males than females at 153 DAH may be related to early puberty observed during the first year in laboratory-reared male cobia. Moreover, this study demonstrates for the first time the expression of GPR54 mRNA during larval development in a vertebrate species. The concomitant expression patterns of GPR54 and GnRH mRNAs during different stages of larval and juvenile developments, and during early puberty in male cobia suggest a potential relationship between GPR54 and multiple GnRHs during these stages of development consistent with the role of GPR54 in controlling GnRH release in mammals. The increase in GPR54 and GnRH mRNAs observed during early puberty in cobia is consistent with a similar change reported in pubertal rats. This finding together with the localization of GPR54 mRNAs on GnRH neurons in fish and mammals suggests that the GPR54–GnRH interactions may be conserved in different vertebrate groups.
Organically Doped Metals—A New Approach to Metal Catalysis: Enhanced Ag‐Catalyzed Oxidation of Methanol
Authors: Shter G. E. , Behar‐Levy H. , Gelman V. , Grader G. S. , Avnir D.
Published: February 2007

We report here a new approach for the modification of the performance of metal catalysts: organic doping of the metal. Specifically, we report that the doping of Ag with Congo Red (CR@Ag) significantly improves the performance of Ag as a catalyst for methanol oxidation to formaldehyde, outperforming both pure Ag and CR‐coated Ag (CR/Ag) in terms of lowering the temperature needed for maximal conversion by 100 °C, lowering the temperature by 200 °C to reach the maximal selectivity (aldehyde formation), and increasing the maximal space velocity by a factor of two. We were led to this discovery by a detailed investigation of the thermal behavior (thermogravimetric and differential thermal analysis and mass spectroscopy) of CR@Ag under an oxidative atmosphere, which has indicated that the metal is strongly catalyzing the CR oxidation, and which pointed to the relevant temperature for activation of the catalyst.
Cover Picture: Bright White‐Light Emission from Semiconductor Nanocrystals: by Chance and by Design (Adv. Mater. 4/2007)
Authors: Sapra S. , Mayilo S. , Klar T. A. , Rogach A. L. , Feldmann J.
Published: February 2007

Onionlike core/shell/shell (CdSe/ZnS/CdSe) nanocrystals are designed to emit in the yellow–orange regime from the CdSe core and in the blue regime from the CdSe shell. By changing the synthesis parameters, the intensity of emission from the shell can be varied, thereby tuning the shade of the emitted light, as reported Sameer Sapra and co‐workers on p. 569.
Acoustic features contributing to the individuality of wild agile gibbon (Hylobates agilis agilis) songs
Authors: Oyakawa Chisako , Koda Hiroki , Sugiura Hideki
Published: February 2007

We examined acoustic individuality in wild agile gibbon Hylobates agilis agilis and determined the acoustic variables that contribute to individual discrimination using multivariate analyses. We recorded 125 female‐specific songs (great calls) from six groups in west Sumatra and measured 58 acoustic variables for each great call. We performed principal component analysis to summarize the 58 variables into six acoustic principal components (PCs). Generally, each PC corresponded to a part of the great call. Significant individual differences were found across six individual gibbons in each of the six PCs. Moreover, strong acoustic individuality was found in the introductory and climax parts of the great call. In contrast, the terminal part contributed little to individual identification. Discriminant analysis showed that these PCs contributed to individual discrimination with high repeatability. Although we cannot conclude that agile gibbon use these acoustic components for individual discrimination, they are potential candidates for individual recognition. Am. J. Primatol. 69:777–790, 2007. © 2007 Wiley‐Liss, Inc.
Characteristics and regulation of the ovarian cycle in vervet monkeys (Chlorocebus aethiops)
Authors: Molskness Theodore A. , Hess David L. , Maginnis Gwen M. , Wright Jay W. , Fanton John W. , Stouffer Richard L.
Published: February 2007

This study was designed to evaluate the timecourse of ovarian and pituitary endocrine events throughout the menstrual cycle in the vervet monkey, and whether circulating luteinizing hormone (LH) or the uterus regulates the functional lifespan of the vervet corpus luteum. Daily saphenous blood samples were collected from adult females (1) during spontaneous menstrual cycles (n= 7), and (2) during cycles in which a gonadotropin‐releasing hormone antagonist (acyline) was administered for 3 days at midluteal phase (n= 3), and (3) for 30 days following recovery from hysterectomy (n= 4). Estradiol (E) and progesterone (P) levels were assayed using electrochemoluminescent assays. Gonadotropin levels were measured by radioimmunoassay using reagents developed for the assay of follicle‐stimulating hormone and LH in macaques. Spontaneous cycles exhibited a midcycleErise (476±49 pg/ml), engendering an LH surge, 12±1 days after onset of menses, followed by a luteal phase with peakPlevels of 4.7±0.9 ng/ml. Histologic evaluation of the ovaries at late follicular phase or early luteal phase revealed the presence of a single, large Graafian follicle or developing corpus luteum, respectively. Acyline treatment caused a significant (P<0.05) decline inPlevels (2.9±0.5 vs 0.5±0.3 ng/ml, 0 vs 48 h post‐treatment) and premature menstruation compared with untreated controls (P<0.05). Hysterectomy had no apparent effect on the monthly pattern or levels of circulatingEorP. Thus, the characteristics and regulation of the ovarian cycle in vervets appear similar to those in women and macaques, with cyclicity dependent on pituitary gonadotropin hormones and independent of a uterine luteolytic factor. Am. J. Primatol. 69:890–900, 2007. © 2007 Wiley‐Liss, Inc.
Behavioral thermoregulation of wild Japanese macaques: comparisons between two subpopulations
Authors: Hanya Goro , Kiyono Mieko , Hayaishi Shuhei
Published: February 2007

We studied the behavioral thermoregulation of Japanese macaques in two troops that live in the coniferous (1,000–1,200 m in elevation) and coastal forests (0–200 m in elevation) of Yakushima. Frequency of sunbathing, huddling, and microhabitat selection during inactivity was compared. The difference in mean annual air temperature between the forests was more than 7°C. In both forests, when the weather was clear, macaques spent more time being inactive in the sunshine in winter than in autumn. In winter, they huddled more often when it was clear than when cloudy. Microhabitat selection to stay in the sunshine during winter differed between the two forests. In winter, macaques spent more time inactive in open habitats in the coniferous forest and in the trees in the coastal forest than in autumn, respectively. This difference is related to the lower crown height in the coastal forest and the large open habitats (logged area) available only in the coniferous forest. In winter, skin temperature measured by temperature‐sensitive transmitters was 1.32–1.71°C higher when sunbathing, and 0.83–4.75°C higher when huddling than staying in the shade without huddling. In winter, the proportion with which they stayed in the sunshine or huddled in winter did not differ between the two forests, in spite of the difference in air temperature. This suggests that Japanese macaques respond to seasonal changes in air temperature, not the absolute temperature, and that they acclimatize themselves to thermal conditions that require behavioral thermoregulation only during the season when thermoregulation is most costly. Am. J. Primatol. 69:802–815, 2007. © 2007 Wiley‐Liss, Inc.
Socio‐sexual behavior of female northern muriquis (Brachyteles hypoxanthus)
Authors: Possamai Carla B. , Young Robert J. , Mendes Sergio L. , Strier Karen B.
Published: February 2007

Female northern muriquis (Brachyteles hypoxanthus) are known to engage in frequent copulations with multiple partners, a pattern that in other primates has been attributed to various functions such as confusing paternity, reducing male aggression, or ensuring fertilization. However, in some female primates, promiscuity is restricted to times when conceptions are unlikely. We investigated whether female northern muriquis might exhibit a similarly mixed strategy by examining their mating, social, and activity patterns during their conception cycles versus other times. Systematic behavioral data were collected during an 18‐month period between August 2001 and February 2003 on 13 adult females in a well‐studied group at the RPPN‐Feliciano Miguel Abdala, Minas Gerais, Brazil. Females mated on an average of 12.5±7.9 days during the study period, and spent significantly less time resting and engaging in non‐sexual social behaviors, and significantly more time in sexual behaviors on days that they copulated than on days they did not. Three of the eight females for which sufficient data were available copulated significantly more often with their spatially closest non‐kin associates, and four of five females that could be analyzed copulated significantly more often with their most frequent non‐kin embrace partners. Comparisons between conception and non‐conception periods revealed no differences in female activity budgets or in either the number of copulations or the number of different mating partners per female. Our results suggest that some females mate preferentially with close associates and social partners, but there is no indication that females alter their behavior during the cycles in which they conceive. Am. J. Primatol. 69:766–776, 2007. © 2007 Wiley‐Liss, Inc.
Hematological changes in vervet monkeys (Chlorocebus aethiops) during eight months' adaptation to captivity
Authors: Kagira J.M. , Ngotho M. , Thuita J.K. , Maina N.W. , Hau J.
Published: February 2007

This study investigated fluctuations in hematological values of 50 wild‐caught vervet monkeys (African green monkeys, grivets, Chlorocebus aethiops) during habituation to captivity. The monkeys were categorized into four groups according to age and sex viz adult males, adult females, juvenile males, and juvenile females. The erythrocyte values were significantly higher (P<0.05) in the adult males than in the other animals. There was an increase in most of the erythrocyte parameters studied during the monitoring period with the most significant being hemoglobin, hematocrit, and mean corpuscular volume. However, the red cell distribution widths, which were higher in adult females, declined. The total white blood cell (WBC) counts, which were higher in adult females than in the other animals, were closely correlated with granulocytes counts. The WBC levels decreased in all the animals throughout the 8 months study, indicating gradually decreasing stress, but they were relatively stable in males. The platelet counts declined significantly (P<0.05) and at 8 months post capture the counts were higher in females than in males. The juvenile female platelet counts were relatively stable during the monitoring period. The maintenance of the monkeys on an improved stable diet and in environment‐controlled housing combined with progressing psycho‐physiological adaptation may be important factors for the gradual improvements of the hematological values recorded. There were wide variations in these between individual animals emphasizing the need for long adaptation combined with establishment of individual baseline values before experimental studies. Am. J. Primatol. 69:1053–1063, 2007. © 2007 Wiley‐Liss, Inc.
The Woodward–Doering/Rabe–Kindler Total Synthesis of Quinine: Setting the Record Straight
Authors: Seeman Jeffrey I.
Published: February 2007

In 1918, Paul Rabe and Karl Kindler reported the three‐step conversion of d‐quinotoxine into quinine. In 1944 Robert B. Woodward and William von Eggers Doering reported the total synthesis of homomeroquinene and d‐quinotoxine from 7‐hydroxyisoquinoline. Based on the transformations by Rabe and Kindler, Woodward and Doering asserted the “Total Synthesis of Quinine” (the title of their 1944 and 1945 papers). In 2000 and 2001, Gilbert Stork concluded that the claim by Woodward and Doering is a “myth” because they had synthesized only homomeroquinene and d‐quinotoxine; no synthetic quinine had been made in Cambridge. In fact, Rabe and Kindler never published the experimental details of their conversion of d‐quinotoxine into quinine. This Review presents the results of a detailed examination of the synthesis of cinchona alkaloids, and previously unpublished material combined with unpublished material and numerous interviews give insight into the lives of the personalities in this nearly 100‐year saga.
Cinnoline Derivatives with Biological Activity
Authors: Lewgowd Wieslawa , Stanczak Andrzej
Published: February 2007

Although cinnoline belongs to a family of fairly well known heterocycles, the interest in the study of its derivatives continues. Cinnoline compounds demonstrate interesting bioactivity and many research papers have discussed the biological property, structure‐activity relationship, and applications in medicinal science. Attention has been paid to the synthesis of heterocyclic compounds bearing a cinnoline moiety, mainly because of the interest in their broad spectrum of pharmacological activities. This chronological work summarizes almost all synthetic papers and patents concerning the biological properties of 107 cinnoline derivatives published over the last 50 years with 117 references.
Synthesis, Antiviral, Antituberculostic, and Antibacterial Activities of Some Novel, 4‐(4‐substituted phenyl)‐6‐(4‐nitrophenyl)‐2‐(substituted imino)pyrimidines
Authors: Siddiqui Anees A. , Rajesh Ramadoss , Mojahid‐Ul‐Islam  , Alagarsamy Veerachamy , De Clercq Erick
Published: February 2007

A variety of novel 4‐(4‐substituted phenyl)‐6‐(4‐nitrophenyl)‐2‐substituted imino) pyrimidines were synthesized by reacting 4‐(4‐substituted phenyl)‐6‐(4‐nitrophenyl)‐2‐amino pyrimidines with different substituted aromatic aldehydes, coumarin chloroisatin. The 4‐(4‐substituted phenyl)‐6‐(4‐nitrophenyl)‐2‐amino pyrimidines were synthesized by reacting 3‐(4′‐substituted phenyl)‐1‐(4‐nitrophenyl)‐2‐propen‐1‐ones with guanine hydrochloride. 3‐(4‐Substituted phenyl)‐1‐(4‐nitrophenyl)‐2‐propen‐1‐ones were synthesized by reacting 4‐nitroacetophenone with different para‐substituted aromatic aldehydes. Spectral data (IR, NMR, and mass spectra) confirmed the structures of the synthesized compounds. The synthesized compounds were investigated for their antiviral, antituberculostic, and antibacterial activities. The results of antiviral, antituberculostic, and antibacterial activities indicated that the synthesized compounds exhibited mild to potent activities compared to the respective reference standards.
Synthesis and Evaluation of Some Gastrointestinal Sparing Anti‐Inflammatory Aminoethyl Ester Derivatives of Naphthalene‐Based NSAIDs
Authors: Halen Parmeshwari K. , Raval Manisha K. , Chagti Kewal K. , Giridhar Rajani , Yadav Mange R.
Published: February 2007

To overcome the local gastric toxicity associated with use of common non‐steroidal anti‐inflammatory drugs (NSAIDs), some aminoalcohol esters of NSAIDs bearing structural resemblance to the aminoalcohol ester class of anticholinergics were specially designed and synthesized. Besides blocking the acidic carboxyl group to overcome the local gastric irritation, the anticholinergic activity was incorporated with the expected advantage of reducing the gastric toxicity by decreasing gastric acid secretions and motility. Derivatives of naproxen and 6‐methoxy‐2‐napthylacetic acid (6‐MNA) were synthesized. The hydrolysis studies in buffers revealed the majority of the compounds to be sufficiently stable with a high enzymatic susceptibility in 80% human serum. Most of the derivatives exhibited a fairly good anticholinergic action against acetylcholine with a significant reduction in ulcerogenicity while retaining the anti‐inflammatory potency of the parent drug. The combination of anti‐inflammatory and anticholinergic activities, with a simultaneous reduction of the acidic character, may lead to development of therapeutically better compounds than the parent NSAIDs for long‐term oral anti‐inflammatory therapy.
Differential metabolism of benzo[α]pyrene in vitro by human placental tissues exposed to active maternal cigarette smoke
Authors: Sanyal Mrinal K. , Li You Lan
Published: February 2007

OBJECTIVES: Generation of different metabolites and DNA‐adduct(s) of metabolites of benzo[α]pyrene (B[α]P) in vitro by placental tissues (microsomes) of mothers who actively smoked cigarettes (tobacco) and those who did not smoke were analyzed to determine the variability in metabolism of the B[α]P substrate among individual placental samples. METHODS: Overall B[α]P metabolism was assayed by alkaline aqueous extraction of metabolites, and reactive metabolites by DNA adducts of B[α]P‐metabolites produced by salmon sperm DNA added to the incubation mixtures of the substrate and microsomes of exposed‐ and unexposed‐placentas to maternal cigarette smoke. Array of B[α]P‐metabolites produced by the same incubations were identified by high pressure liquid chromatography of the aqueous extracts. RESULTS: Subsets of smoke‐exposed placentas assessed by cluster analysis had augmented metabolic activity, others did not respond to smoke exposure. CYP1A1 expression in trophoblast cells analyzed by immunohistochemistry did not correlate with smoke exposure. The DNA‐adducts generated was variable, regardless of verbally reported levels of maternal exposure. The amounts of different B[α]P‐metabolites produced by individual samples matched for similar levels of exposure during pregnancy by self‐reported smoking (1 pack/day) were also not comparable. Metabolism of B[α]P into different metabolites, and production of toxic DNA adducts from metabolites in vitro by human placenta were variable and unrelated to the extent of smoke exposure. CONCLUSIONS: The metabolic characteristic of human placenta for xenobiotic exposure substrates is based on the expression and function of diverse enzymes, and such metabolism exhibited inter‐individual variation for toxic metabolite production or detoxification of the substrates in response to maternal smoke exposure. Birth Defects Res (Part B) 80:49–56, 2007. © 2007 Wiley‐Liss, Inc.
An optimized ATP/PPi‐exchange assay in 96‐well format for screening of adenylation domains for applications in combinatorial biosynthesis
Authors: Otten Linda G. , Schaffer Michelle L. , Villiers Benoit R.M. , Stachelhaus Torsten , Hollfelder Florian
Published: February 2007

We report a new format for measuring ATP/[32P]pyrophosphate exchange in a higher throughput assay of adenylation domains (A‐domains) of non‐ribosomal peptide synthetases. These enzymes are key specificity determinants in the assembly line biosynthesis of non‐ribosomal peptides, an important class of natural products with an activity spectrum ranging from antibiotic to antitumor activities. Our assay in 96‐well format allows the rapid measurement of approximately 1000 data points per week as a basis for precise assessment of the kinetics of A‐domains. The assay also allows quantitative high‐throughput screening of the substrate specificity of A‐domains identifying alternative, promiscuous substrates. We show that our assay is able to give high quality data for the T278A mutant of the A‐domain of the tyrocidine synthetase module TycA with a 330‐fold lower kcat/KM. The large dynamic range of this assay will be useful for the screening of libraries of mutant A‐domains. Finally we describe and evaluate a procedure for the high‐throughput purification of A‐domains in 96‐well format for the latter purpose. Our approach will be of utility for mechanistic analysis, substrate profiling and directed evolution of the A‐domains, to ultimately enable the combinatorial biosynthesis of non‐natural analogues of non‐ribosomal peptides that may have potential as alternative drug candidates.
Updating the metagenomics toolbox
Authors: Gabor Esther , Liebeton Klaus , Niehaus Frank , Eck Juergen , Lorenz Patrick
Published: February 2007

Metagenomics – the application of the genomics suit of technologies to uncultivated microorganisms – is coming of age. Sophisticated technologies are being developed and adapted to this promising genetic resource to make increasing use of the seemingly boundless molecular and functional diversity. Particular progress has been made in the areas of randomly proliferating limited‐source DNA, massively parallel sequencing without cloning, isolating specific target sequences from highly complex template mixtures, high‐throughput assay systems targeting metabolic pathways, artificial transcriptional regulators activating reporter genes to indicate enzymatic substrate conversion and cDNA cloning from extracted mRNA to directly clone actively expressed genes from a microbial consortium. However, challenges still lie ahead. Most prominently, the efficient heterologous expression of a plethora of potentially interesting enzymes from unknown source organisms is not readily achieved.
The most proficient enzyme as the central theme in an integrated, research‐based biochemistry laboratory course
Authors: Smiley Jeffrey A.
Published: February 2007

The enzyme orotidine‐5′‐monophosphate decarboxylase is an attractive choice for the central theme of an integrated, research‐based biochemistry laboratory course. A series of laboratory exercises common to most instructional laboratories, including enzyme assays, protein purification, enzymatic characterization, elementary kinetics, and recombinant DNA methods, has been devised. The series of exercises requires biochemical instrumentation common to most laboratories and some specialized materials available from the author's institution to laboratory instructors.
Nitrophorins: Lipocalin‐based heme proteins transporting nitric oxide
Authors: Ascenzi Paolo , Nardini Marco , Bolognesi Martino , Montfort William R.
Published: February 2007

Nitrophorins 1–4 (NPs; NP1 to NP4) are salivary heme proteins secreted from the blood‐sucking insect Rhodnius prolixus. NPs transfer nitric oxide (NO) to the victim, resulting in vasodilatation, sequester histamine, reducing host inflammation and immune response, and inhibit blood coagulation. The NP fold is based on an eight‐stranded antiparallel β‐barrel, typically observed in the lipocalin homology family, which hosts a heme group. Although NPs use the ferric heme to bind NO and histamine, they are unrelated to the six/eight α‐helix (non)vertebrate hemoglobins, which bind NO preferentially to the ferrous heme, but do not bind histamine. Therefore, NPs and hemoglobins can be considered as an evolutionary experiment, where the heme group has been adapted to structurally different protein families to achieve similar function(s).
Detection of legume protease inhibitors by the Gel‐X‐ray film contact print technique
Authors: Mulimani Veerappa H. , Sudheendra Kulkarni , Giri Ashok P.
Published: February 2007

Redgram (Cajanus cajan L.) extracts have been analyzed for the protease inhibitors using a new, sensitive, simple, and rapid method for detection of electrophoretically separated protease inhibitors. The detection involves equilibrating the gel successively in the protease assay buffer and protease solution, rinsing the gel in assay buffer, and later exposing it to an unprocessed x‐ray film. Gelatin on the film in places corresponding to the inhibitor bands remains unhydrolyzed. A simple and inexpensive laboratory experiment to detect protease inhibitors of legume seeds by the gel‐x‐r ay film contact print technique is described.
Introducing students to DNA: Identifying nutritional plants in a simple tried and tested laboratory experiment
Authors: Streicher Hansjörg , Brodte Annette
Published: February 2007

In this paper we report on a practical experiment, containing isolation, purification, and characterization of plant DNA, which is designed to give students unexperienced in DNA handling and molecular biology a glimpse of the field. Based on well established procedures, genomic DNA of a nutritional crop is isolated, and a non‐coding region of chloroplast DNA is amplified by use of PCR with universal primers. The origin of the sample is revealed by the size of the amplified fragment and in case of indistinguishable fragment sizes of wheat and barley by selective digestion with a suitable restriction endonuclease.
Vitamin requirements: Relationship to basal metabolic need and functions
Authors: Rucker Robert B. , Steinberg Francene M.
Published: February 2007

The dietary requirements for most water‐soluble vitamins in homeothermic animals, particularly vitamins utilized in energy‐related pathways, are related directly to metabolic rate. As a consequence, vitamin requirements are similar when expressed relative to empirical functions of metabolic body size, e.g. (Wtkg)3/4 or body surface area. The vitamin requirements for a range of animals are expressed relative to their corresponding rates of basal metabolism. Data for the rates of ascorbic acid production and turnover in animals that produce ascorbic acid are also compared with the ascorbic acid requirements and turnover in humans and guinea pigs, species that require ascorbic acid as a dietary essential. Factors that are most important in dictating the relative need for a given vitamin from a chemical perspective include chemical stability, the relative number of catalytic events that are involved in the process, the nature of the interactions with associated enzymes, and the presence or absence of pathways for partial synthesis or regeneration of the given vitamin. Vitamins that are required daily in millimolar amounts are usually less stable chemically, are involved in numerous reactions, and often exist in tissues as dissociable cofactors. In contrast, vitamins that are required daily in micromolar amounts are involved in fewer reactions and are often covalently bound to the proteins or enzymes for which they serve as cofactors. Development of the preceding concepts allows linkages of relative vitamin requirements to energy utilization and related biochemical and oxidative processes, which can aid in developing a better understanding of the integrative nature of nutritional and biochemical relationships.
Nitrate reductase: A model system for the investigation of enzyme induction in eukaryotes
Authors: Pike Carl S. , Cohen William S. , Monroe Jonathan D.
Published: February 2007

Plant nitrate reductase is an easily studied enzyme whose induction by various signals can be explored in inquiry‐based undergraduate laboratories. Barley, mustard, and radish seedlings are grown for 3–7 days with different light conditions and nitrogen nutrition. The enzyme activity of crude extracts is assayed in a colorimetric procedure. The protocols can be used in student independent research projects.
Liposomes as tools to study drug diffusion and toxin‐induced leaks
Authors: Levillain Florence , Lanéelle Gilbert
Published: February 2007

Multilayered vesicles made of egg‐phosphatidylcholine and of phosphatidic acid were used to teach in a 4‐h session of practical work with a low cost spectrophotometer how to determine osmolarity inside multilayered vesicles and to show, by using two anti‐tuberculous drugs (isonicotinic acid hydrazide, p‐aminosalicylate), that a small and non‐ionized molecule diffused freely through phospholipid vesicles, whereas a charged one did not. In addition, the permeabilizing effect of melittin, a membrane‐targeted bee‐venom toxin, was tested.
Assessment of the purification of a protein by ion exchange and gel permeation chromatography
Authors: Pugh Michael Eugene , Schultz Emeric
Published: February 2007

A 3‐week group laboratory project experiment that involves the partial purification of myoglobin (Mb) from bovine hamburger is described. The experiment compares alternate purification methods (gel filtration and ion exchange chromatography) as to both overall yield and enhancement in relative purity. The purity and molecular weight of purified Mb is established by SDS‐PAGE. Group reports are directed toward having students put together all the information that is collected in the experiment. We discuss what we have learned and continue to learn from experiments done in the cooperative learning mode.
Dealing with the challenges of teaching molecular biophysics to biochemistry majors through an heuristics‐based approach
Authors: Castanho Miguel A. R. B.
Published: February 2007

The main distinction between the overlapping fields of molecular biophysics and biochemistry resides in their different approaches to the same problems. Molecular biophysics makes more use of physical techniques and focuses on quantitative data. This difference encounters two difficult pedagogical challenges when teaching molecular biophysics to biochemistry majors; an aversion to math, “Mathematophobia,” combined with little appreciation for the importance of models in scientific progress. To overcome these problems, I have used an heuristic approach to student learning. Although inspired by problem‐based learning, it has a lesser demand for material resources and can be managed by a single teacher in small classes. This approach is especially suited for elective courses in the final years of a program of study. It consists of teaching/touching the art of discovery by turning laboratories into original research projects and lectures into seminars.
Protein tryptophan accessibility studied by fluorescence quenching
Authors: Möller Matías , Denicola Ana
Published: February 2007

A laboratory class is described to introduce the biochemistry major students to the basic concepts and various applications of fluorescence spectroscopy. Through simple and inexpensive experiments the students learn how to record excitation and emission spectra and measure intrinsic protein fluorescence and its quenching to elucidate the local tryptophan environment. Free tryptophan, ovalbumin, and bovine serum albumin are used for the experiments. The structural information that can be retrieved from emission spectra, as well as from quenching data, is discussed.
The adaptive response to ambient pH in Neurospora crassa: Contribution of a model organism to the elucidation of gene expression in eukaryotes
Authors: Nozawa Sérgio R. , Thedei Geraldo , Ciancaglini Pietro , Rossi Antonio
Published: February 2007

The main objective of this class experiment is to show that the extracellular levels of inorganic phosphate and the pH of the growth medium affect the synthesis and secretion of alkaline phosphatase in the filamentous mold Neurospora crassa. This type of study integrates knowledge of biochemistry and genetics through the regulation of gene expression and shows that the secretion of alkaline phosphatase is responsive to extracellular Pi levels and ambient pH. However, because N. crassa is a eukaryotic organism, other factors have to be considered, like the post‐translational modifications necessary for the movement of secreted enzymes through the secretory pathway, which may alter their catalytic properties. Thus, the enzymatic activity data, although useful, should not be analyzed alone but should be considered as just one of the tools needed to understand the biological phenomena involved in the gene expression of adaptivity in eukaryotic organisms.
Using computers to teach biochemistry
Authors: Whitehead Joyce P. , Pence Harry E.
Published: February 2007

This paper describes a symposium entitled “Using Computers to Teach Biochemistry,” which was presented at the fall, 2001 National Meeting of the American Chemical Society in Chicago, IL. The use of computers has increased in all areas of chemical education; however, the visualization capabilities needed to convey some aspects of biochemistry are quite complex, so the upward trend in the use of computers for this purpose has been especially significant. The various speakers in this symposium discussed the use of a wide range of instructional technologies, including presentation software, Chime, online data exercises, interactive visualization tools, self‐designed tutorial programs, and bioinformatics.
Restriction mapping
Authors: Szeberényi József
Published: February 2007

Terms to be familiar with before you start to solve the test: restriction endonucleases, DNA polymerase, exonucleases, agarose gel electrophoresis, autoradiography, DNA synthesis.
Strategies for introducing computer technologies into a biology laboratory program
Authors: Tillotson Joanne Kivela
Published: February 2007

Computers have been installed in the General Biology laboratory at Purchase College and incorporated into the laboratory curriculum for all biology majors at the introductory level. The goal is to ensure that all students become familiar with general computer applications in the biological sciences and are comfortable enough to use them regularly. Thus, students will be prepared for later courses involving use of computer applications in bioinformatics or other technologically advanced subjects.
Incorporation of bioinformatics exercises into the undergraduate biochemistry curriculum
Authors: Feig Andrew L. , Jabri Evelyn
Published: February 2007

The field of bioinformatics is developing faster than most biochemistry textbooks can adapt. Supplementing the undergraduate biochemistry curriculum with data‐mining exercises is an ideal way to expose the students to the common databases and tools that take advantage of this vast repository of biochemical information. An integrated collection of exercises based on pet proteins has been assembled. The exercises described are applicable to either a lecture or laboratory format and require only basic desktop computers, an Internet connection, a current web browser, and the free Chime plug‐in module. In an open‐ended, inquiry‐based format, the assignments ask students to explore concepts such as the relative information content of the different biopolymers, the relationship between primary sequence and tertiary structure, and how sequence conservation can be used to find an enzyme active site.
Study of protein‐ligand binding by fluorescence
Authors: Möller Matías , Denicola Ana
Published: February 2007

A practical class experiment is described to show the students an application of fluorescence spectroscopy in the study of protein‐ligand binding. This class is part of an undergraduate physical biochemistry course for life science students. The major aim is to introduce the students to the basic concepts of fluorescence emission (intrinsic and extrinsic), the effect of environment on fluorescence parameters, and how this could be applied to the study of ligand binding to proteins. In particular, binding of the fluorescent probe 1‐anilinonaphthalene‐8‐sulfonate to albumin (native and oxidized) is described. From the obtained results, the stoichiometry of complex formation, the binding equilibrium constants, and alterations of the environment of the binding sites are determined and discussed with the students.
Insulin signaling
Authors: Szeberényi József
Published: February 2007

Terms to be familiar with before you start to solve the test: Signal transduction, insulin, insulin receptor, insulin receptor substrate 1 (IRS‐1), adaptor proteins, Western blotting, immunoprecipitation, tyrosine protein kinases, tyrosine phosphorylation, SH2 and SH3 domains.
Hemopexin: The primary specific carrier of plasma heme*
Authors: Mattu Marco , Fasano Mauro , Spallarossa Andrea , Bolognesi Martino , Ascenzi Paolo
Published: February 2007

Hemopexin (HPX) is the primary specific carrier of plasma heme and participates in its clearance by transport to the liver. After delivering the heme intracellularly, HPX is released intact into the bloodstream. HPX is formed by two four‐bladed β‐propeller domains, resembling two thick disks that lock together at a 90° angle; the face of the N‐terminal β‐propeller domain packs against one edge of the C‐terminal domain. Each propeller blade comprises a four‐stranded antiparallel β‐sheet, with the first and the fourth blades tied together by disulfide bridges. The heme ligand is bound between the two four‐bladed β‐propeller domains in a pocket formed by the interdomain linker peptide. Residues His‐213 and His‐266 coordinate the heme iron atom giving a stable bis‐histidyl Fe(III) complex. Heme release results from opening of the heme binding pocket, through movement of the two β‐propeller domains and/or the interdomain linker peptide.
Building a foundation for bioenergetics
Authors: Hamori Eugene
Published: February 2007

To give students a lasting comprehension of bioenergetics, first such basics as heat, work, equilibrium, entropy, free energy, closed versus open systems, steady state, and reversibility should be explained to them in a meticulous manner, albeit with a minimal use of mathematical formulae. The unique feature of thermodynamics, that it does not require any structural, mechanistic, and kinetic assumptions and models about the microscopic nature of the matter, should be exploited. Its laws could be considered as given, reflecting simply empirical observations that science has found unassailable so far. The familiarization of the students with the basic concepts should rely more on problem solving exercises than on the molecular mechanistic explanations. Only at a later phase should structural molecular inferences be made and (if justified) more rigorous mathematical derivations given. When the students are later confronted with the seemingly complex energetics of biological processes the idea of a steady‐state reaction should be stressed. Even without nonequilibrium thermodynamics a wealth of useful information can be deduced from this simple model of metabolic reactions. Because biological processes are typically homeostatic and progress at de facto constant temperature and pressure, using the steady‐state assumption, their thermodynamic treatment can be surprisingly straight forward. Thus the conceptual role of the steady‐state model in bioenergetics might be viewed as similar in pedagogical significance to the ideal gas model of basic chemistry.
Lactose operon mutants
Authors: Szeberényi József
Published: February 2007

Terms to be familiar with before you start to solve the test: Lactose operon, operator, electrophoretic mobility shift assay, repressor, catabolite activator protein, RNA polymerase, σ‐factor, gel filtration, exclusion limit, void volume (V0), elution volume (Ve), expression plasmid.
Using the human genome: A case study in education*
Authors: Boyle John A.
Published: February 2007

The working drafts of the human genome, announced in February 2001, have clearly provided a breakthrough in biochemistry and molecular biology research. The scientific data also provide an opportunity to vary a typical approach to teaching. Advanced graduate students at our university can elect to take a course in molecular genetics. The human genome drafts and the initial publications generated by the drafts were used as the framework for a variation of this course in the fall of 2001. Instead of a traditional, linear lecture‐driven course, this approach provided a more methods‐driven focus to the topics considered. It also required the introduction of some recent historical facts to put the material into proper context. The bulk of the topics normally taught remained unchanged; however, their order of appearance was greatly modified. Nevertheless, the material remained coherent because of the constant tie‐in with the genome data. Evaluation of student performance was challenging because of the variety of material presented. Web‐based assignments proved useful as mechanisms to probe the level of student understanding as well as providing another means of imparting information.
Thermostable glucoamylase‐type enzyme from Bacillus acidocaldarius RP1*
Authors: Natalia Dessy , Yuliani Yuyu , Ermayadhie Yusdiana , Putra Redha , Sindumarta Muliawati
Published: February 2007

We present an experiment that enables student to understand the properties of thermostable glucoamylase‐type enzyme produced by thermophilic Bacillus acidocaldarius RP1 isolated from Cimanggu Hot Spring, West Java, Indonesia. In addition, the students also gain experience working with a thermostable microorganism and some techniques frequently used in biochemistry, e.g. ultrasonication, ammonium sulfate fractionation, and spectrophotometric analysis. The glucoamylase‐type enzyme activities were detected both as cell‐associated and in the culture supernatant. The 20–40% saturated ammonium sulfate fraction of glucoamylase‐type enzyme exhibited an optimum temperature of 65 °C and an optimum pH of 4.5. The enzyme showed a Vmax of 600 milliunits/mg and Km of 11.7 mg/ml.
Kinetic studies with alkaline phosphatase in the presence and absence of inhibitors and divalent cations
Authors: Dean Rob L.
Published: February 2007

A very robust and inexpensive kinetic assay for determining rates of hydrolysis of p‐nitrophenyl phosphate by the enzyme alkaline phosphatase is presented. The reaction increases in rate with increase in pH. The enzyme is competitively inhibited by the reaction products, uncompetitively inhibited by L‐phenylalanine, and responds to the presence of two cofactors, magnesium and zinc ions. The reaction rate increases as Mg2+ concentration is increased from 1–5 mM. With increasing Zn2+ concentration, the reaction rate is stimulated and then depressed. Experimental work on the interaction between Mg2+ and Zn2+ in the reaction is suggested for more capable students.
A collaborative, investigative recombinant DNA technology course with laboratory*
Authors: Pezzementi Leo , Johnson Joy F.
Published: February 2007

A recombinant DNA technology course was designed to promote contextual, collaborative, inquiry‐based learning of science where students learn from one another and have a sense of ownership of their education. The class stressed group presentations and critical reading and discussion of scientific articles. The laboratory consisted of two research projects: random cDNA cloning and in vitro expression and site‐directed mutagenesis of cholinesterase. Students prepared a poster and wrote a scientific paper peer‐reviewed by scientists at a nearby university. Multiple methods were used to evaluate the course. Evaluation data were consistent and positive. Students learned to read, present, and discuss scientific articles in depth, work collaboratively in small teams, and perform genetic engineering experiments. The students also outperformed all biology majors on the molecular biology/genetics subtest of the Major Field Achievement Test. The course has an extensive website at http://panther.bsc.edu/∼lepezzem/bi405_html/bi405.html.
Comparison of the interaction of cobalt bovine carbonic anhydrase II with acetazolamide and methazolamide and the reaction of apoenzyme with cobalt(II) complexes of acetazolamide and methazolamide: Spectrophotometric study
Authors: Rubio Silvia , Borrás Consuelo , Alzuet Gloria , Borrás Joaquin
Published: February 2007

The metalloenzyme carbonic anhydrase (CA) is an attractive choice for a research‐based bioinorganic laboratory course. In this project the interaction of cobalt bovine carbonic anhydrase II (CoBCAII) with acetazolamide and methazolamide and the reaction of apoenzyme with cobalt(II) complexes of acetazolamide and methazolamide is studied by UV‐visible spectroscopy. Prior to this spectroscopic study students are given native BCAII, and they prepare apoBCAII and CoBCAII. A major aim is to provide experience in handling metalloproteins and in the study of metal complexes‐protein interactions.
Assessment of verbal communication in science education: A comparison of small and large classes*
Authors: Haworth Ian S. , Garrill Ashley
Published: February 2007

Clear verbal communication is a key skill for the modern scientist. In this article we describe two model science courses, one given to a small class and the other to a large class, in which verbal communication is emphasized as a key learning objective. Both courses use a form of problem‐based learning (PBL) with an end point that involves students communicating their results and ideas verbally. Hence, assessment of verbal communication is necessary. We describe several different approaches to this challenge and highlight their applicability to small and large class sizes. We then show that, with careful application of these methods, a good relationship can be obtained between scores on verbal assessment exercises and scores on written examinations. On this basis, we argue that the verbal assessment can give an accurate reflection of the student's ability and can therefore be used as a method of formative evaluation in addition to being a component of the overall grade.
Crime scene investigation: An exercise in generating and analyzing DNA evidence*
Authors: Lounsbury Karen M.
Published: February 2007

The goal of this project is to introduce students to molecular biology techniques using an experimental setting that inspires both scientific and personal interest. The project is designed as a small group apprenticeship for gifted high school juniors or seniors who can spend full time in a sponsor's laboratory for at least 1 week. The students begin by examining evidence from a mock crime scene that consists of hair samples from the crime scene and from five potential suspects. Students extract DNA from the hair samples and amplify a hypervariable region within the mitochondrial genome using the polymerase chain reaction. Amplified products are then sequenced and compared with the crime scene sequence using DNA alignment software. In consecutive projects, students from four different schools successfully identified the suspect who matched the crime scene evidence. This project is a valuable learning tool not only due to the comprehensive introduction to molecular biology techniques but also because it helps the students to connect scientific exploration with well publicized media events and provides a window into potential career opportunities in the field of molecular biology.
Concepts and skills in the biochemistry/molecular biology lab
Authors: Boyer Rodney
Published: February 2007

Most colleges and universities throughout the world now offer a Biochemistry/Molecular Biology (BMB) lab course that is designed for undergraduate students in the molecular life sciences, chemistry, and related fields. To best serve our students, we must introduce them to the most current concepts, skills, and methods available. Suggestions for teaching a modern BMB lab are given here.