bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural and thermal behavior of comb‐like polymer having n‐octadecyl side chains
Authors: Saikia Prakash J. , Baruah Shashi D.
Published: January 2007

The cocrystallization behavior of poly(n‐octadecyl methacrylate) (POMA) and its blends with corresponding fatty acid (n‐octadecanoic acid) (C18) was explored by differential scanning calorimetry (DSC) and X‐ray diffraction studies. The DSC curves for blended samples of POMA with C18 show the characteristic melting endotherms that correspond to the melting of the cystallites. The existence of hexagonally packed crystalline lattice is confirmed from the X‐ray diffraction studies. Thermal degradation of the polymer and its blend proceeds in a one‐step reaction. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 1226–1231, 2007
Collection and identification of organic materials accumulated on a rubber composite
Authors: Choi Sung‐Seen , Ha Sung‐Ho
Published: January 2007

Rubber composites are composed of rubber(s), reinforcing filler(s), crosslinking agents, antidegradants, and processing aids. Organic materials with low molecular weight can migrate to the surface of the rubber composite and get accumulated on the surface. The bloomed materials make the appearance worse and contaminate the surroundings. It is not easy to collect successfully the bloomed materials without damage to the sample. The collecting methods of scratching with a polished glass, heating with an iron, scrubbing with solvent‐soaked cellulose tissue, and scrubbing with solvent‐soaked melamine foam were compared. The collected materials were analyzed using gas chromatography/mass spectrometry (GC/MS). The scrubbing with solvent‐soaked melanine foam or with solvent‐soaked cellulose tissue was found to be recommendable. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 1260–1264, 2007
Arsenic detection by nanogold/conducting‐polymer‐modified glassy carbon electrodes
Authors: Chowdhury Al‐Nakib , Ferdousi Sara , Islam Md. Mominul , Okajima Takeyoshi , Ohsaka Takeo
Published: January 2007

This article discusses the results for the development of a nanogold‐particle/polyaniline‐modified glassy carbon electrode for the detection of arsenic(III) in water. A thin polyaniline film was electropolymerized onto a glassy carbon electrode. The gold nanoparticle was then deposited onto the polyaniline‐coated glassy carbon electrode via potential step electrolysis from 1.1 to 0 V versus Ag/AgCl/NaCl (saturated) for 45 s from a 0.5M H2SO4 solution containing 0.1 mM NaAuCl4 in the absence and presence of a 0.1 mM KI additive. The surface of the modified electrode was examined with scanning electron microscopy. Cyclic and anodic stripping voltammetry of arsenic(III) was performed on the modified electrode. The thus modified nanogold‐particle/polyaniline‐modified glassy carbon electrode prepared in the presence of the I− (KI) additive showed a high sensitivity in detecting arsenic(III) in water, and with stripping voltammetry, a limit of detection of 0.4 ppb arsenic was obtained, which is much lower than the arsenic guideline limit of the World Health Organization. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 1306–1311, 2007
Biobased thermosets from the free‐radical copolymerization of conjugated linseed oil
Authors: Henna Phillip H. , Andjelkovic Dejan D. , Kundu Petit P. , Larock Richard C.
Published: January 2007

New polymeric thermosets were prepared through the bulk free‐radical copolymerization of 100% conjugated linseed oil, acrylonitrile, and divinylbenzene. Under the appropriate reaction conditions and with the appropriate curing sequence, 61–96 wt % of the oil was incorporated into the crosslinked thermosets. The resulting yellow, transparent thermosets varied from being soft and flexible to being hard and brittle. Dynamic mechanical analysis and thermogravimetric analysis showed that these thermosets had good mechanical properties and thermal stability. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 979–985, 2007
Characterization of molecular orientation in injection–stretch–blow‐molded poly(ethylene terephthalate) bottles by means of external reflection infrared spectroscopy
Authors: Ben Daly H. , Cole K. C. , Nguyen K. T. , Sanschagrin B.
Published: January 2007

The molecular orientation at the outer surface of injection–stretch–blow‐molded bottles made from poly(ethylene terephthalate) was characterized and quantified by means of front‐surface reflection infrared spectroscopy based on a method developed previously. Results were obtained for two different bottle shapes (cylindrical and rectangular) molded at different injection mold temperatures (16, 38, and 60°C). For the cylindrical bottles, the preferred molecular chain orientation was found to be in the axial direction, with the Hermans orientation function near 0.3 for all three mold temperatures. For the less symmetrical rectangular bottles, a significant difference was observed between the large and small faces. For the large face, the orientation was mainly in the hoop direction; the Hermans orientation function was in the range of 0.3–0.5 and was essentially the same at all mold temperatures and positions along the bottle height. For the small face, on the other hand, the preferred orientation changed from the hoop direction near the bottom to the axial direction near the top, and the variation was more pronounced at lower mold temperatures. The utility of the front‐surface reflection technique was clearly demonstrated. It was also applied, with the use of an infrared microscope, to examine the orientation gradient across the wall thickness. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 1319–1327, 2007
Modification of isotactic polypropylene by the free‐radical grafting of 1,1,1‐trimethylolpropane trimethacrylate
Authors: Mousavi‐Saghandikolaei Seyyed Abbas , Frounchi Masoud , Dadbin Susan , Augier Sylvain , Passaglia Elisa , Ciardelli Francesco
Published: January 2007

The chemical modification of isotactic polypropylene was performed by the free‐radical‐promoted grafting of 1,1,1‐trimethylolpropane trimethacrylate (TMPTMA) in the presence of dicumyl peroxide (DCP) as the initiator. The reaction was carried out both in a batch internal mixer and in a corotating twin‐screw extruder; the effects of the peroxide and monomer concentrations on the extent of modification in terms of the grafting efficiency and polymer chain structure variations were investigated. The modified samples were characterized with Fourier transform infrared to determine the structure of the grafted groups and the degree of functionalization, with gel permeation chromatography and the melt flow index to evaluate changes in the molecular weight, and with differential scanning calorimetry, thermogravimetric analysis, and dynamic mechanical thermal analysis to measure the final thermal properties. In addition, solvent extraction with xylene was performed to highlight the presence of gel and its extent. The structure of the grafted groups was determined, and the number of grafted groups was quantitatively evaluated. The degree of functionalization increased with an increasing TMPTMA/DCP molar ratio. Thermal analysis results hinted at the presence of grafted chains with an increased percentage of TMPTMA. Although degradation reactions predominated at high amounts of peroxide, grafting and branching processes became competitive at high levels of TMPTMA. The balance between competing β‐scission and grafting/branching reactions could be adjusted on the basis of feed conditions. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 950–958, 2007
Oxygen and water vapor gas barrier poly(ethylene naphthalate) films by deposition of SiOx plasma polymers from mixture of tetramethoxysilane and oxygen
Authors: Inagaki N. , Cech V. , Narushima K. , Takechi Y.
Published: January 2007

SiOx films were deposited from a mixture of tetramethoxysilane (TMOS) and oxygen on poly(ethylene 2,6‐naphthalate) film using ion‐assisted plasma polymerization technique (Method II) and conventional plasma polymerization technique (Method I), and were compared in chemical composition and gas barrier properties. Methods I and II were different in electrical circuit between electrodes (anode and cathode) and electric power supply. In Method I, the anode electrode was grounded, and the cathode electrode was coupled to the discharge power supply. In Method II, the anode electrode was connected with the discharge power supply, and the cathode electrode was grounded. There was not large difference in SiOx deposition rate between the plasma polymerizations by Methods I and II. Plasma polymers deposited from TMOS/O2 mixtures by Method II possessed smaller C/Si and O/Si atomic ratios than those deposited by Method I and showed advantage in gas barrier properties. The oxygen and water vapor permeation rates were 0.08–0.13 cm3 m−2 day−1 atm−1 at 30°C at 90% RH and 0.244–0.276 g m−2 day−1 at 40°C at 90% RH, respectively. From these results, it can be concluded that the ion‐assisted plasma polymerization is a useful technique for deposition of gas barrier SiOx thin films. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 915–925, 2007
The preparation and characterization of high‐performance and thermally stable electroluminescent poly(p‐phenylene‐vinylene‐b‐oligoethylene oxide)
Authors: Zhu Lu , Tang Xiaozheng
Published: January 2007

Two luminescent block copolymers (PPVPEO200 and PPVPEO600), composed of poly(p‐phenylene‐vinylene) (PPV) segments with three phenylene vinylene units and poly(ethylene oxide) (PEO) segments with molecular weight of 200 and 600, respectively, have been successfully synthesized. The structures of the copolymers were verified using FTIR, 1H‐NMR, and elemental analysis. Single‐layer polymer light‐emitting electrochemical cells (LEC) devices fabricated on the bases of thin films of PPVPEO600 and on the bases of thin films of blends of PPVPEO200 with additional PEO both demonstrated good electroluminescent (EL) performance with the onset voltage of 2.6 V and EL efficiency of 0.64 cd/A and 0.68 cd/A at 3.2 V, respectively. Thermal analysis shows that the decomposition temperature of PPVPEO600 is about 305°C, which is higher than that of PPVPEO200 and PEO. AFM studies of PPVPEO600 thin films exhibits that the block copolymer self‐assembles to form nanoscale network structures with pseudo‐cross‐linking points, thus accounting for its high thermal stability and good EL performance. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 1118–1125, 2007
Novel application of partial carboxymethylation in the wet processing of linen fabric
Authors: Higazy A. , Ramadan M. A. , Hebeish A.
Published: January 2007

Scoured linen fabrics were treated with NaOH at different concentrations (1–7N). Unscoured (gray) linen fabrics were modified via partial carboxymethylation under different conditions, including monochloroacetic acid concentration (1–4N), sodium hydroxide concentration (0.5–3.5N), reaction time (30–180 min), and reaction temperature (30–90°C). Alkali treated and partially carboxymethylated linen fabrics were bleached using H2O2 (20 g/L), sodium silicate (3 g/L), and nonionic wetting agent (1 g/L) at pH 10 for 150 min at 95°C. The unbleached and bleached linen fabrics (alkali treated and partially carboxymethylated) were assessed for technical properties, namely, whiteness index (W.I.), loss in fabric weight, copper number, carboxyl content, and H2O2 decomposition percent. A comparison was made between the properties of the two substrates. It indicates that the properties of partially carboxymethylated linen fabric were comparable, if not superior, to alkali treated linen fabric. Hence it is advantageous to introduce partial carboxymethylation in the wet processing of linen fabrics since scouring and alkali treatment can be omitted. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 996–1001, 2007
Polymer modified grass fiber, part 1: Characterization of grass fiber and assessment of properties of polymer modified fiber
Authors: Debasish De  , Debapriya De  , Adhikari Basudam
Published: January 2007

Natural fibers are used for reinforcement of ecofriendly green composites. These grass fibers have wide range of applications for the preparation of various domestic goods and handicraft items. But the chemical composition of the grass fiber has not been reported; therefore composition analysis of grass fiber was carried out. Morphology of the dry grass was studied by using scanning electron microscopy. Since the grass fiber contains around 22% water‐soluble matters, we have studied its influence on the tensile strength and aging characteristics. The tensile strength of the grass fiber was measured before and after water leaching. This study has shown a definite scope for the suitability of grass fiber in composite applications. To improve the strength of grass fiber, modification with various polymers such as P‐F resin, polyurethane and acrylamide was carried out. Moisture absorption property of unleached, water‐leached and different polymer modified fiber was also evaluated. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 1095–1103, 2007
Characterizing composite of multiwalled carbon nanotubes and POE‐g‐AA prepared via melting method
Authors: Wu Chin‐San
Published: January 2007

Multiwalled carbon nanotubes (MWNTs) with acyl chloride functional groups and a metallocene polyethylene–octene elastomer (POE) or an acrylic acid‐grafted metallocene polyethylene–octene elastomer (POE‐g‐AA) were used to prepare hybrids (POE/MWNTs or POE‐g‐AA/MWNTs) using a melting method, with a view to identify a hybrid with improved thermal properties. Hybrids were characterized using Fourier transform infrared spectroscopy, 13C solid‐state nuclear magnetic resonance, X‐ray diffraction, thermogravimetry analysis, and scanning electron microscopy. MWNTs were purified using acid treatment, and results showed that COOH of MWNTs increased with acid treatment time and leveled off after 24‐h treatment. Much better dispersion and homogeneity of MWNTs was obtained with POE‐g‐AA in place of POE as the matrix. As a result, tensile strength at break of POE‐g‐AA/MWNTs was significantly improved even at 5 wt % MWNT content. Moreover, temperature of thermal decomposition for POE‐g‐AA/MWNTs was about 40–50°C higher than that for POE‐g‐AA, indicating higher thermal stability. This was because the carboxylic acid groups in POE‐g‐AA and the acyl chloride functional sites in MWNTs allow the formation of stronger chemical bonds. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 1328–1337, 2007
The effects of maleic anhydride terpolymer and its ester derivatives on tensile bond strength between the acrylic resin and resilient lining material
Authors: Dogan O. Murat , Bolayõõir Giray , Boztuğ Ali , Turgut Mehmet , Zengin H. Bayram
Published: January 2007

The present study investigated the effects on the bonding between the denture base acrylic resin and the soft silicon based lining material of maleic anhydride‐styrene‐vinyl acetate (MA‐St‐VA) terpolymer and some of its ester derivatives. These ester derivatives were n‐propylmaleate‐styrene‐vinyl acetate (n‐PrMA‐St‐VA), n‐buthylmaleate‐styrene‐vinyl acetate (n‐BuMA‐St‐VA) and n‐benzylmaleate‐styrene‐vinyl acetate (n‐BzMA‐St‐VA). Fourier Transform infrared spectroscopy method was used to determine interactions between terpolymers with the acrylic resin and soft lining material. The tensile bond strength of all the groups was compared and the obtained differences were statistically significant (P < 0.05). The highest value was found for the samples lined with n‐BuMA‐St‐VA (2.11 ± 0.21 MPa) and the samples lined with n‐BzMA‐St‐VA had the lowest bond strength (0.3 ± 0.12 MPa). © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 1338–1341, 2007
Effects of olefin‐based compatibilizers on the morphology, thermal and mechanical properties of ABS/polyamide‐6 blends
Authors: Ozkoc Guralp , Bayram Goknur , Bayramli Erdal
Published: January 2007

In this study, commercially available epoxidized and maleated olefinic copolymers, EMA‐GMA (ethylene‐methyl acrylate‐glycidyl methacrylate) and EnBACO‐MAH (ethylene‐n butyl acrylate‐carbon monoxide‐maleic anhydride), were used at 0, 5, and 10% by weight to compatibilize the blend composed of ABS (acrylonitrile‐butadiene‐styrene) terpolymer and PA6 (polyamide 6). Compatibilizing performance of these two olefinic polymers was investigated from blend morphologies, thermal and mechanical properties as a function of blend composition, and compatibilizer loading level. Scanning electron microscopy (SEM) studies showed that incorporation of compatibilizer resulted in a fine morphology with reduced dispersed particle diameter at the presence of 5% compatibilizer. The crystallization behavior of PA6 phase in the blends was explored for selected blend compositions by differential scanning calorimetry (DSC). At high compatibilizer level a decrease in the degree of crystallization was observed. In 10% compatibilizer containing blends, formation of γ‐crystals was observed contrary to other compatibilizer compositions. The behavior of the compatibilized blend system in tensile testing showed the negative effect of using excess compatibilizer. Different trends in yield strengths and strain at break values were observed depending on compatibilizer type, loading level, and blend composition. With 5% EnBACO‐MAH, the blend toughness was observed to be the highest at room temperature. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 926–935, 2007
Controlled‐release polymers for delivery of dipyridyls and tetraalkyl ammonium hydroxide
Authors: Carrington Nathan A. , Rodman D. Lynn , Goswami Kisholoy , Xue Zi‐Ling
Published: January 2007

A method to incorporate 2,2′‐(or 4,4′‐)dipyridyl and tetra‐n‐butylammonium hydroxide into poly(vinyl alcohol) (PVA) monoliths and the controlled‐release properties of these polymer monoliths for delivery of the reagents are reported. The monoliths were prepared by heating PVA beads until they formed a viscous liquid and then loading the molten polymers with the desired reagents. Several freeze‐thaw cycles were then carried out to provide the mechanically stable, reagent‐loaded monoliths. The release of the reagents from the PVA monoliths was monitored by UV–vis spectroscopy, and the release was found to proceed in a controlled manner, yielding consistent results among different reagent‐loaded PVA monoliths. In addition, the reagents underwent no chemical changes upon their release from the monoliths. Limitations of the use of the controlled‐released chemicals as replenished reagents in Fujiwara reactions for the continuous monitoring of halocarbons are discussed. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 1043–1048, 2007
Crystallization kinetics of iPP: Influence of operating conditions and molecular parameters
Authors: La Carrubba V. , Piccarolo S. , Brucato V.
Published: January 2007

An analysis of the crystallization kinetics of different grades of isotactic polypropylene (iPP) is here presented. To describe the crystallization kinetics as a function of molecular and operating parameters, the methodological path followed was the preparation of quenched samples of known cooling histories, calorimetric crystallization isotherms tests, differential scanning calorimetry cooling ramps, wide angle X‐ray diffraction (WAXD) measurements, and density determination. The WAXD analysis performed on the quenched iPP samples confirmed that during the fast cooling at least a crystalline structure and a mesomorphic one form. The diffractograms were analyzed by a deconvolution procedure, to identify the relationship between the cooling history and the distribution of the crystalline phases. The whole body of results (including calorimetric ones) provides a wide basis for the identification of a crystallization model suitable to describe solidification in polymer‐processing operations, based on the Kolmogoroff–Avrami–Evans nonisothermal approach. The kinetic parameters, determined for all the materials, are discussed, highlighting the effect of molecular parameters on the crystallization kinetics: molecular mass and distribution, tacticity, nucleating agents, and ethylene units content. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 1358–1367, 2007
Preparation of poly(divinylbenzene‐co‐N‐isopropylacrylamide) microspheres and their hydrogen‐bonding assembly behavior for raspberry‐like core‐corona polymer composite
Authors: Li Guoliang , Song Yanyan , Yang Xinlin , Huang Wenqiang
Published: January 2007

Narrowdisperse poly(divinylbenzene‐co‐N‐isopropylacrylamide) (poly(DVB‐co‐NIPAM)) functional microspheres with the diameter in the range of 630 nm and 2.58 μm were prepared by distillation–precipitation polymerization in neat acetonitrile in the absence of any stabilizer. The effect of N‐isopropylacrylamide (NIPAM) ratio in the comonomer feed on the morphology of the resultant polymer particles was investigated in detail with divinylbenzene (DVB) as crosslinker and 2,2′‐azobisisobutyronitrile (AIBN) as initiator. The monodisperse poly(DVB‐co‐NIPAM) microspheres with NIPAM fraction of 20 wt % were selected for the preparation of raspberry‐like core‐corona polymer composite by the hydrogen‐bonding self‐assembly heterocoagulation with poly(ethyleneglycol dimethacrylate‐co‐acrylic acid) [poly(EGDMA‐co‐AA)] nanospheres. Both of the functional poly(DVB‐co‐NIPAM) microspheres and the core‐corona particles were characterized with scanning electron microscopy (SEM), Fourier transform infrared spectra (FTIR), and elemental analysis (EA). © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 1350–1357, 2007
Production of yoghurt with mild taste by a Lactobacillus delbrueckii subsp. bulgaricus mutant with altered proteolytic properties
Authors: Möller Claudia , Bockelmann Wilhelm , Ammann Andreas , Heller Knut J.
Published: January 2007

In this communication, we describe the isolation of a Lactobacillus delbrueckii subsp. bulgaricus 92063 mutant strain named pH‐P11, which differed from the parent strain by low proteolytic activity and altered regulation of expression of lacZ in the presence of glucose or lactose. In the presence of lactose, β‐galactosidase activity was approximately twice as high in pH‐P11 than in the wild type. pH‐P11 exhibited protosymbiosis together with Streptococcus thermophilus. Yoghurt produced with pH‐P11 was characterized by low acidity and little post‐acidification during storage. The organoleptic properties (absence of bitterness and other off‐flavors, weak sourness, and clear yoghurt taste) were those of a typical “yoghurt mild”. This mild flavor was achieved at rather high cell counts of lactobacilli even at the end of shelf‐life. High cell counts in conjunction with high β‐galactosidase activity make pH‐P11 an interesting strain for application in yoghurt especially designed for consumers with lactose malabsorption. In contrast to “yoghurt mild”, which is predominantly produced with Lactobacillus acidophilus together with Streptococcus thermophilus, the product obtained by fermentation with pH‐P11 and Streptococcus thermophilus concurs with international standards for yoghurt. During frequent sub‐culturing, strain pH‐P11, which is supposed to differ from the wild type by one or a few so‐far‐not‐characterized mutations, showed sufficient stability for application in industrial production.
Growth of microbial populations. Mathematical modeling, laboratory exercises, and model‐based data analysis
Authors: Juška Alfonsas , Gedminienė Genovaitė , Ivanec Rūta
Published: January 2007

This paper has arisen as a result of teaching Models in Biology to undergraduates of Bioengineering at the Gediminas Technical University of Vilnius. The aim is to teach the students to use a fresh approach to the problems they are familiar with, to come up with an articulate verbal model after a mental effort, to express it in rigorous mathematical terms, to solve (with the aid of computers) corresponding equations, and finally, to analyze and interpret experimental data in terms of their (mathematical) models. Investigation of microbial growth provides excellent possibilities to combine laboratory exercises, mathematical modeling, and model‐based data analysis. Application of mathematics in this field proved to be very fruitful in getting deeper insight into the processes of microbial growth. The step‐by‐step modeling resulted in an extended model of the growth covering conventional “lag,” “exponential,” and “stationary” phases. In contrast to known models (differential equations that can be solved only numerically), the present model is expressed symbolically as a finite combination of elementary functions. The approach can be applied in other areas of modern biology, such as dynamics of various cellular processes, enzyme and receptor kinetics, and others.
Time, the forgotten dimension of ligand binding teaching
Authors: Corzo Javier
Published: January 2007

Ligand binding is generally explained in terms of the equilibrium constant Kd for the protein‐ligand complex dissociation. However, both theoretical considerations and experimental data point to the life span of the protein‐ligand complex as an important, but generally overlooked, aspect of ligand binding by macromolecules. Short‐lived protein‐ligand complexes may be unable to trigger further biological processes as signal transduction or internalization if such processes are relatively slow with respect to dissociation of the complex that initiated them. Protein‐ligand complex life span depends on the first‐order rate constant for the dissociation of the complex, Koff, but this constant and its implications are generally not treated in textbooks. This report presents a brief discussion and some examples useful for teaching the importance of time in ligand binding by macromolecules in the context of a general biochemistry course.
Databases of metabolic pathways
Authors: Likić Vladimir A.
Published: January 2007

Studies of metabolism usually evoke memories of densely written wall charts of metabolic pathways of enormous complexity, such as the IUBMB‐Nicholson metabolic pathways map or the Roche metabolic pathways wall chart. Advances in bioinformatics in the past decade have brought about a revolution in the way the information in metabolic pathways is viewed and managed. Today, metabolic pathways are stored in knowledge bases that can be queried, modified, copied, and extended with ease, precision, and speed. Moreover, the flexibility of the digital medium for the presentation of metabolic pathways surpasses the traditional printed form used in classical pathway maps. In digital presentations, the separation of the content from the visual presentation is the norm, implying that metabolic pathway maps can be generated dynamically from the information stored in the knowledge base. The most advanced metabolic pathways databases are freely available over the Internet, and this has important implications for modern studies of metabolic pathways in biochemistry and molecular biology. This study reviews two such databases: the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the BioCyc collection of pathway/genome databases. The background information and the structure of these databases are presented, with the emphasis on BioCyc, which represents a global multicollaborative effort to unify the representation of metabolic pathways.
Microarrays for undergraduate classes
Authors: Hancock Dale , Nguyen Lisa L. , Denyer Gareth S. , Johnston Jill M.
Published: January 2007

A microarray experiment is presented that, in six laboratory sessions, takes undergraduate students from the tissue sample right through to data analysis. The model chosen, the murine erythroleukemia cell line, can be easily cultured in sufficient quantities for class use. Large changes in gene expression can be induced in these cells by erythropoietic agents such as DMSO over a 72‐h time period. Students isolate total RNA from control (0 h) and 72‐h DMSO‐treated murine erythroleukemia cells. From this, they synthesize a cDNA copy incorporating amino‐allyl dUTP, which is then coupled to either a Cy5 or a Cy3 dye. Equal amounts of the two labeled cDNA samples are then applied to a standard cDNA microarray, which is then hybridized, washed, and scanned. Up‐ and down‐regulated genes are selected using an “in‐house” user‐friendly data base program. Quality control checks are included at various stages throughout the procedure and, as the process of erythropoiesis is well characterized, a number of erythroid sequences serve as internal controls on the validity of the array data. Through this experiment, students gain experience in a wide range of molecular biology techniques, the use of controls to check a multistep process, validation of results, and strategies to manage the large amount of data generated. Most importantly, it provides undergraduate students with an opportunity to carry out experiments using cutting edge techniques normally found only in research laboratories.
Exploring the ubiquitin‐proteasome protein degradation pathway in yeast
Authors: Will Tamara J. , McWatters Melissa K. , McQuade Kristi L.
Published: January 2007

This article describes an undergraduate biochemistry laboratory investigating the ubiquitin‐proteasome pathway in yeast. In this exercise, the enzyme β‐galactosidase (β‐gal) is expressed in yeast under the control of a stress response promoter. Following exposure to heat stress to induce β‐gal expression, cycloheximide is added to halt translation, and β‐gal degradation is monitored by measuring enzyme activity as a function of time. Students observe that an N‐Ile‐β‐gal variant with an N‐terminal isoleucine has a significantly lower stability than wild‐type β‐gal, whose N‐terminal residue is methionine. This strong dependence of protein stability on the N‐terminal residue is known as the “N‐end rule.” To corroborate the enzyme activity assay results, students perform denaturing protein electrophoresis and immunoblotting of lysates, observing that the time‐dependent loss of enzyme activity is coincident with the disappearance of the β‐gal protein.
Vectorial Transport in intestinal epithelial cells
Authors: Szeberenyi Jozsef
Published: January 2007

Terms to be familiar with before you start to solve the test: polarized cells, vectorial transport, apical and basolateral membrane, tight junction, occludin, transmembrane proteins, passive and active transport, glucose transporter, Na+/glucose symporter, Na+/K+ ATPase, uniporter, antiporter, facilitated diffusion, lateral diffusion.
Three New Triterpenoids from Potentilla multicaulis
Authors: Li Ping‐Lin , Lin Chang‐Jun , Zhang Zhan‐Xin , Jia Zhong‐Jian
Published: January 2007

Three new triterpenoids, 19‐hydroxy‐2,3‐secours‐12‐ene‐2,3,28‐trioic acid 3‐ methyl ester (1), 19‐hydroxy‐1‐oxo‐2‐nor‐2,3‐secours‐12‐ene‐3,28‐dioic acid (2), and (3β,18α,19α)‐3,28‐dihydroxy‐20,28‐epoxyursan‐24‐oic acid (3), were isolated from the roots of Potentilla multicaulis. Their structures were elucidated on the basis of spectroscopic methods (IR, HR‐ESI‐MS, and 1D‐ and 2D‐NMR). Compound 2b exhibited moderate cytotoxic activity against human promyelocytic leukemia (HL‐60) cells.
Isolation and Enzyme‐Inhibition Studies of the Chemical Constituents from Ajuga bracteosa
Authors: Riaz Naheed , Nawaz Sarfraz A. , Mukhtar Naveen , Malik Abdul , Afza Nighat , Ali Samar , Ullah Shafi , Muhammad Pir , Choudhary M. Iqbal
Published: January 2007

Bractin A (=(2S,3S,4R,5E)‐2‐{[(2R)‐2‐hydroxydodecanoyl]amino}triacont‐5‐ene‐1,3,4‐triol; 1) and bractin B (=(2S,3S,4R,5E,8E)‐2‐{[(2R)‐2‐hydroxyhexacosanoyl]amino}pentadeca‐5,8‐diene‐3,4,15‐triol 1‐O‐β‐D‐glucopyranoside; 2), new sphingolipids, and bractic acid (=(5Z,10Z,15Z)‐2‐decyl‐4,7,8,12,13,17,18‐heptahydroxy‐20,23‐dioxopentacosa‐5,10,15‐trienoic acid; 3), a long‐chain polyhydroxy acid, were isolated from the whole plant Ajuga bracteosa along with four known diterpenoids 4–7. Their structures were deduced by spectral studies including 1D‐ and 2D‐NMR spectroscopy. Compounds 1–3 displayed inhibitory potential against enzyme lipoxygenase, while compounds 4–7 inhibited cholinesterase enzymes in a concentration‐dependent manner with IC50 values in the range 10.0–33.0, 14.0–35.2, and 10.0–19.0 μM for lipoxygenase, acetylcholinesterase, and butyrylcholinesterase, respectively. Lineweaver–Burk, and Dixon plots, and their secondary replots indicated that all compounds exhibit non‐competitive type of inhibition with Ki values in the range of 9.5–35.2, 15.2–36.0, and 11.6–20.5 μM, for lipoxygenase, acetylcholinesterase, and butyrylcholinesterase, respectively.
A New Metabolite with a New Substitution Pattern from the Seeds of the Chinese Yew, Taxus mairei
Authors: Huo Chang‐Hong , Wang Yu‐Fang , Zhang Xi‐Ping , Li Cun‐Fang , Shi Qing‐Wen , Kiyota Hiromasa
Published: January 2007

A new taxoid metabolite with a new substitution pattern was isolated from the methanol extract of the seeds of Taxus mairei, and its structure was established as 5α,15‐dihydroxy‐7β,9α‐diacetoxy‐11(15→1)abeo‐taxa‐4(20),11‐dien‐13‐one (1) on the basis of spectral analysis including 1H‐ and 13C‐NMR, HMQC, HMBC, NOESY, and confirmed by HR‐FAB mass spectrometry.
Conjugate Additions of Cyclic Oxygen‐Bound Nickel Enolates to α,β‐Unsaturated Ketones
Authors: Maya Celia M. , Cámpora Juan , Carmona Ernesto , Matas Inmaculada , Palma Pilar , Gutiérrez‐Puebla Enrique , Monge Angeles
Published: January 2007

The reaction of nickel enolates displaying a metallacyclic structure with the α,β‐unsaturated ketones methyl vinyl ketone (MVK) or methyl propenyl ketone (MPK) takes place in two stages, affording initially bicyclic adducts, which subsequently isomerize to the corresponding open‐chain products. The former are generated with high stereoselectivity and can be considered as the products of the [2+4] cycloaddition of the enolate to the enone. The ring opening process involves a prototropic rearrangement that can be catalyzed by water. In the case of the reaction of the parent nickel enolate complex 1 (which displays an unsubstituted NiOC(R)CH2 arrangement) with MVK, a double‐addition process has been observed, consisting of two successive cycloaddition/isomerization reactions. The carbonylation of the different cyclic and noncyclic products affords the corresponding lactones that retain the stereochemistry of the organometallic precursors. This methodology allowed trapping the primary product of the reaction of 1 with MPK as the corresponding organic lactone, demonstrating that the cycloaddition process takes place with exo selectivity. DFT modeling of the latter reaction provides further support for a quasi‐concerted cycloaddition mechanism, displaying a nonsymmetric transition state in which the CC and the CO bond are formed in an asynchronous manner.
Molecular Aggregation within Self‐Ordered Monolayers
Authors: Gross Leo , Rieder Karl‐Heinz , Gourdon André , Joachim Christian , Moresco Francesca
Published: January 2007

The monolayer growth of pyrimido‐pentaphenylbenzene (NPB) on Cu(111) is investigated by means of low‐temperature scanning tunneling microscopy (LT‐STM). The pyrimidine side group gives rise to a pronounced resonant tunneling state and, furthermore, affects molecular self‐ordering. Different molecular aggregates are formed inside the hexagonal closed packed monolayer. A structure model for the monolayer is proposed and the temperature dependence of this self‐ordering process is investigated by varying the preparation temperature between 270 and 370 K. The intermolecular bonding of the aggregates is demonstrated by STM manipulation experiments. Moreover, different aggregations of the molecules induce characteristic energy shifts in the resonant tunneling state, as revealed by means of scanning tunneling spectroscopy.
Cover Picture: Magnetic Properties of a Ni2+ Kagome System (ChemPhysChem 2/2007)
Authors: Behera J. N. , Sundaresan A. , Pati Swapan K. , Rao C. N. R.
Published: January 2007

The cover picture shows the in‐plane segment of a Ni‐kagome layer, giving rise to magnetic polarization (see hysteresis) due to Ni spins lying above and below the kagome plane. The spin densities of a hexagon of this Ni‐kagome compound obtained through density functional theory shows that the spin‐polarized structure (shown) with canted moments due to Dzyaloshinsky–Moriya (DM) interactions is more stable compared to the spin‐zero structure. Find out more in the Communication article by Behera et al. on page 217.
Tubular sprouting as a mode of vascular formation in a colonial ascidian (tunicata)
Authors: Gasparini Fabio , Longo Fabrizio , Manni Lucia , Burighel Paolo , Zaniolo Giovanna
Published: January 2007

Although phylogenetically related to vertebrates, invertebrate chordate tunicates possess an open circulatory system, with blood flowing in lacunae among organs. However, the colonial circulatory system (CCS) of the ascidian Botryllus schlosseri runs in the common tunic and forms an anastomized network of vessels, defined by simple epithelium, connected to the open circulatory system of the zooids. The CCS originates from epidermal evagination, grows, and increases its network accompanying colony propagation. New vessels are formed by means of mechanisms of tubular sprouting which, in their morphogenesis and molecular regulation, are very similar to those occurring in other metazoans, particularly during vertebrate angiogenesis. From the apex of new vessels, epithelial cells detach and migrate into the tunic, while exploring filopodia extend toward the tunic and possibly guide vessel growth. Immunohistology showed that growth factors fibroblast growth factor‐2 and vascular endothelial growth factor and the receptor vascular endothelial growth factor receptor‐1 participate in sprouting, associated with cell proliferation. As in vertebrates, these factors may regulate cell migration, proliferation, sprouting, and tube formation. Our data indicate that similar, conserved signals were co‐opted in the sprouting processes of two nonhomologous circulatory systems, that of ascidian CCS, and vertebrate circulatory systems, by recruitment of the same signaling pathway. Developmental Dynamics 236:719–731, 2007. © 2007 Wiley‐Liss, Inc.
Aberrant Bmp signaling and notochord delamination in the pathogenesis of esophageal atresia
Authors: Li Yina , Litingtung Ying , Ten Dijke Peter , Chiang Chin
Published: January 2007

Human foregut malformation known as esophageal atresia with tracheoesophageal fistula (EA/TEF) occurs in 1 in 4,000 live births with unknown etiology. We found that mice lacking Noggin (Nog−/−) displayed Type C EA/TEF, the most common form in humans, and notochordal defects strikingly similar to the adriamycin‐induced rat EA/TEF model. In accord with esophageal atresia, Nog−/− embryos displayed reduction in the dorsal foregut endoderm, which was associated with reduced adhesion and disrupted basement membrane. However, significant apoptosis in the Nog−/− dorsal foregut was not observed. Instead, non‐notochordal, likely endodermal, cells were found in Nog−/− notochord, suggesting that Noggin function is required in the notochordal plate for its proper delamination from the dorsal foregut. Notably, ablating Bmp7 function in Nog−/− embryos rescued EA/TEF and notochord branching defects, establishing a critical role of Noggin‐mediated Bmp7 antagonism in EA/TEF pathogenesis. Developmental Dynamics 236:746–754, 2007. © 2007 Wiley‐Liss, Inc.
Murine liver plasmacytoid dendritic cells become potent immunostimulatory cells after Flt-3 ligand expansion
Authors: Kingham Peter T. , Chaudhry Umer I. , Plitas George , Katz Steven C. , Raab Jesse , DeMatteo Ronald P.
Published: January 2007

The liver has unique immunological properties. Although dendritic cells (DCs) are central mediators of immune regulation, little is known about liver DCs. Plasmacytoid DCs (pDCs) are a recently identified subtype of murine liver DC. We sought to define the function of freshly isolated murine liver pDCs. We found that normal liver pDCs were weak in stimulating T cells, yet they possessed a proinflammatory cytokine profile with high tumor necrosis factor-α and low IL-10 secretion. To facilitate the investigation of murine liver pDCs, we expanded them

in vivo

with fms-like tyrosine kinase 3 ligand (Flt3L). After Toll-like receptor-9 ligation, expanded liver pDCs secreted high levels of IFN-α and were able to stimulate NK cells, NKT cells, and antigen-specific CD8+ T cells

in vitro

. In addition, Flt3L expansion alone generated pDCs capable of activating antigen-specific CD8+ T cells

in vivo

.

Conclusion:

Unstimulated liver pDCs exist in a latent state with the potential to become potent activators of the innate and adaptive immune systems through their interactions with other immune effectors. Our findings have implications for understanding the role of the liver in tolerance and immunity.
Maid (GCIP) is involved in cell cycle control of hepatocytes
Authors: Sonnenberg-Riethmacher Eva , Wüstefeld Torsten , Miehe Michaela , Trautwein Christian , Riethmacher Dieter
Published: January 2007

The function of Maid (GCIP), a cyclinD-binding helix-loop-helix protein, was analyzed by targeted disruption in mice. We show that Maid function is not required for normal embryonic development. However, older Maid-deficient mice—in contrast to wild-type controls—develop hepatocellular carcinomas. Therefore, we studied the role of Maid during cell cycle progression after partial hepatectomy (PH). Lack of Maid expression after PH was associated with a delay in G1/S-phase progression as evidenced by delayed cyclinA expression and DNA replication in Maid-deficient mice. However, at later time points liver mass was restored normally.

Conclusion:

These results indicate that Maid is involved in G1/S-phase progression of hepatocytes, which in older animals is associated with the development of liver tumors.
Activation of LXRs prevents bile acid toxicity and cholestasis in female mice
Authors: Uppal Hirdesh , Saini Simrat P.S. , Moschetta Antonio , Mu Ying , Zhou Jie , Gong Haibiao , Zhai Yonggong , Ren Songrong , Michalopoulos George K. , Mangelsdorf David J. , Xie Wen
Published: January 2007

Liver X receptors (LXRs) have been identified as sterol sensors that regulate cholesterol and lipid homeostasis and macrophage functions. In this study, we found that LXRs also affect sensitivity to bile acid toxicity and cholestasis. Activation of LXRα in transgenic mice confers a female-specific resistance to lithocholic acid (LCA)–induced hepatotoxicity and bile duct ligation (BDL)–induced cholestasis. This resistance was also seen in wild-type female mice treated with the synthetic LXR ligand TO1317. In contrast, LXR double knockout (DKO) mice deficient in both the α and β isoforms exhibited heightened cholestatic sensitivity. LCA and BDL resistance in transgenic mice was associated with increased expression of bile acid–detoxifying sulfotransferase 2A (

Sult2a

) and selected bile acid transporters, whereas basal expression of these gene products was reduced in the LXR DKO mice. Promoter analysis showed that the mouse

Sult2a9

gene is a transcriptional target of LXRs. Activation of LXRs also suppresses expression of oxysterol 7α-hydroxylase (

Cyp7b1

), which may lead to increased levels of LXR-activating oxysterols.

Conclusion :

We propose that LXRs have evolved to have the dual functions of maintaining cholesterol and bile acid homeostasis by increasing cholesterol catabolism and, at the same time, preventing toxicity from bile acid accumulation.
IL-10, regulatory T cells, and Kupffer cells mediate tolerance in concanavalin A–induced liver injury in mice
Authors: Erhardt Annette , Biburger Markus , Papadopoulos Thomas , Tiegs Gisa
Published: January 2007

The liver appears to play an important role in immunological tolerance, for example, during allo-transplantation. We investigated tolerance mechanisms in the model of concanavalin A (ConA)-induced immune-mediated liver injury in mice. We found that a single injection of a sublethal ConA dose to C57BL/6 mice induced tolerance toward ConA-induced liver damage within 8 days. This tolerogenic state was characterized by suppression of the typical Th1 response in this model and increased IL-10 production. Tolerance induction was fully reversible in IL-10−/− mice and after blockade of IL-10 responses by anti-IL10R antibody. Co-cultures of CD4+CD25+ regulatory T cells (Tregs) and CD4+CD25− responder cells revealed Treg from ConA-tolerant mice being more effective in suppressing polyclonal T cell responses than Treg from control mice. Moreover, Treg from tolerant but not from control mice were able to augment in vitro IL-10 expression. Depletion by anti-CD25 monoclonal antibody (MAb) indicated a functional role of Tregs in ConA tolerance in vivo. Cell depletion studies revealed Tregs and Kupffer cells (KC) to be crucial for IL-10 expression in ConA tolerance. Studies with CD1d−/− mice lacking natural killer T (NKT) cells disclosed these cells as irrelevant for the tolerogenic effect. Finally, cellular immune therapy with CD4+CD25+ cells prevented ConA-induced liver injury, with higher protection by Treg from ConA-tolerized mice.

Conclusion :

The immunosuppressive cytokine IL-10 is crucial for tolerance induction in ConA hepatitis and is mainly expressed by CD4+CD25+ Treg and KC. Moreover, Tregs exhibit therapeutic potential against immune-mediated liver injury.
Vascular dysfunction in human and rat cirrhosis: Role of receptor-desensitizing and calcium-sensitizing proteins
Authors: Hennenberg Martin , Trebicka Jonel , Biecker Erwin , Schepke Michael , Sauerbruch Tilman , Heller Jörg
Published: January 2007

In cirrhosis, vascular hypocontractility leads to vasodilation and contributes to portal hypertension. Impaired activation of contractile pathways contributes to vascular hypocontractility. Angiotensin II type 1 receptors (AT1-Rs) are coupled to the contraction-mediating RhoA/Rho-kinase pathway and may be desensitized by phosphorylation through G-protein-coupled receptor kinases (GRKs) and binding of β-arrestin-2. In the present study, we analyzed vascular hypocontractility to angiotensin II in cirrhosis. Human hepatic arteries were obtained during liver transplantation. In rats, cirrhosis was induced by bile duct ligation (BDL). Contractility of rat aortic rings was measured myographically. Protein expression and phosphorylation were analyzed by Western blot analysis. Immunoprecipitation was performed with protein A–coupled Sepharose beads. Myosin light chain (MLC) phosphatase activity was assessed as dephosphorylation of MLCs. Aortas from BDL rats were hyporeactive to angiotensin II and extracellular Ca2+. Expression of AT1-R and Gαq/11,12,13 remained unchanged in hypocontractile rat and human vessels, whereas GRK-2 and β-arrestin-2 were up-regulated. The binding of β-arrestin-2 to the AT1-R was increased in hypocontractile rat and human vessels. Inhibition of angiotensin II–induced aortic contraction by the Rho-kinase inhibitor Y-27632 was pronounced in BDL rats. Basal phosphorylation of the ROK-2 substrate moesin was reduced in vessels from rats and patients with cirrhosis. Analysis of the expression and phosphorylation of Ca2+-sensitizing proteins (MYPT1 and CPI-17) in vessels from rats and patients with cirrhosis suggested decreased Ca2+ sensitivity. Angiotensin II–stimulated moesin phosphorylation was decreased in aortas from BDL rats. MLC phosphatase activity was elevated in aortas from BDL rats.

Conclusion :

Vascular hypocontractility to angiotensin II in cirrhosis does not result from changes in expression of AT1-Rs or G-proteins. Our data suggest that in cirrhosis-induced vasodilation, the AT1-R is desensitized by GRK-2 and β-arrestin-2 and that changed patterns of phosphorylated Ca2+-sensitizing proteins decrease Ca2+ sensitivity.