http://www.mdpi.com/journal/ijms Latest open access articles published in Int. J. Mol. Sci. at http://www.mdpi.com/journal/ijms/ http://www.mdpi.com/1422-0067/11/3/1141/ A shortcoming of most correlation distance methods based on the composition vectors without alignment developed for phylogenetic analysis using complete genomes is that the “distances” are not proper distance metrics in the strict mathematical sense. In this paper we propose two new correlation-related distance metrics to replace the old one in our dynamical language approach. Four genome datasets are employed to evaluate the effects of this replacement from a biological point of view. We find that the two proper distance metrics yield trees with the same or similar topologies as/to those using the old “distance” and agree with the tree of life based on 16S rRNA in a majority of the basic branches. Hence the two proper correlation-related distance metrics proposed here improve our dynamical language approach for phylogenetic analysis. http://www.mdpi.com/1422-0067/11/3/1141/ Thu, 18 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-18 11 3 Article 1141 1154 1422-0067 Proper Distance Metrics for Phylogenetic Analysis Using Complete Genomes without Sequence Alignment 2010-03-18 doi: 10.3390/ijms11031141 Yu Zhan Han Wang Anh Chu http://www.mdpi.com/1422-0067/11/3/1114/ Changes in the laser induced molecular dissociation of 1,1,1-trichloroethane (TCE) were studied using a range of intensities and standard laser wavelengths with nanosecond and femtosecond pulse durations. TCE contains C-H, C-C and C-Cl bonds and selective bond breakage of one or more of these bonds is of scientific interest. Using laser ionization time of flight mass spectrometry, it was found that considerable variation of fragment ion peak heights as well as changes in relative peak ratios is possible by varying the laser intensity (by attenuation), wavelength and pulse duration using standard laser sources. The nanosecond laser dissociation seems to occur via C-Cl bond breakage, with significant fragmentation and only a few large mass ion peaks observed. In contrast, femtosecond laser dissociative ionization results in many large mass ion peaks. Evidence is found for various competing dissociation and ionization pathways. Variation of the nanosecond laser intensity does not change the fragmentation pattern, while at high femtosecond intensities large changes are observed in relative ion peak sizes. The total ionization yield and fragmentation ratios are presented for a range of wavelengths and intensities, and compared to the changes observed due to a linear chirp variation. http://www.mdpi.com/1422-0067/11/3/1114/ Wed, 17 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-17 11 3 Article 1114 1140 1422-0067 Comparative Study of the Dissociative Ionization of 1,1,1 Trichloroethane Using Nanosecond and Femtosecond Laser Pulses 2010-03-17 doi: 10.3390/ijms11031114 du Plessis Strydom Botha http://www.mdpi.com/1422-0067/11/3/1103/ Dye sensitized solar cell (DSSC) is the only solar cell that can offer both the flexibility and transparency. Its efficiency is comparable to amorphous silicon solar cells but with a much lower cost. This review not only covers the fundamentals of DSSC but also the related cutting-edge research and its development for industrial applications. Most recent research topics on DSSC, for example, applications of nanostructured TiO2, ZnO electrodes, ionic liquid electrolytes, carbon nanotubes, graphene and solid state DSSC have all been included and discussed. http://www.mdpi.com/1422-0067/11/3/1103/ Tue, 16 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-16 11 3 Review 1103 1113 1422-0067 Dye Sensitized Solar Cells 2010-03-16 doi: 10.3390/ijms11031103 Wei http://www.mdpi.com/1422-0067/11/3/1090/ Catostomid fishes (suckers) have duplicate copies of the growth hormone gene and other nuclear genes, due to a genome duplication event early in the group’s history. Yet, paralogs of GH in suckers are more than 90% conserved in nucleotide (nt) and amino acid (aa) sequence. Within paralogs across species, variation in nt and aa sequence averages 3.33% and 4.46% for GHI, and 3.22% and 2.43% for GHII, respectively. Selection tests suggest that the two GH paralogs are under strong purifying selection. Consensus trees from phylogenetic analysis of GH coding region data for 23 species of suckers, other cypriniform fishes and outgroups resolved cypriniform relationships and relationships among GHI sequences of suckers more or less consistently with analyses based on other molecular data. However, the analysis failed to resolve all sucker GHI and GHII sequences as monophyletic sister groups. This unexpected topology did not differ significantly from topologies constrained to make all GH sequences monophyletic. We attribute this result either to limitations in our GHII data set or convergent adaptive changes in GHII of tribe Catostomini. http://www.mdpi.com/1422-0067/11/3/1090/ Tue, 16 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-16 11 3 Article 1090 1102 1422-0067 Evolutionary Divergence of Duplicate Copies of the Growth Hormone Gene in Suckers (Actinopterygii: Catostomidae) 2010-03-16 doi: 10.3390/ijms11031090 Bart Jr. Reneau Doosey Bell http://www.mdpi.com/1422-0067/11/3/1082/ Oxidized metabolites of dopamine known as dopamine quinone derivatives are thought to play a pivotal role in the degeneration of nigrostriatal dopaminergic neurons in Parkinson’s disease. Although such quinone derivatives are usually produced via the autoxidation of catecholamines, tyrosinase, which is a key enzyme in melanin biosynthesis via the production of DOPA and subsequent molecules, can potentially accelerate the induction of catecholamine quinone derivatives by its oxidase activity. We have developed neuronal cell lines in which the expression of human tyrosinase was inducible. Overexpression of tyrosinase resulted in increased intracellular dopamine content in association with the formation of melanin pigments in neuronal somata, which eventually causes apoptotic cell death. This cellular model will provide a useful tool for detailed analyses of the neurotoxicity of oxidized catechol metabolites. http://www.mdpi.com/1422-0067/11/3/1082/ Fri, 12 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-12 11 3 Review 1082 1089 1422-0067 Tyrosinase-Expressing Neuronal Cell Line as in Vitro Model of Parkinson’s Disease 2010-03-12 doi: 10.3390/ijms11031082 Hasegawa http://www.mdpi.com/1422-0067/11/3/1070/ Advances in stem cell research have provided important understanding of the cell biology and offered great promise for developing new strategies for tissue regeneration. The beneficial effects of stem cell therapy depend also by the development of new approachs for the track of stem cells in living subjects over time after transplantation. Recent developments in the use of nanotechnologies have contributed to advance of the high-resolution in vivo imaging methods, including positron emission tomography (PET), single-photon emission tomography (SPECT), magnetic resonance (MR) imaging, and X-Ray computed microtomography (microCT). This review examines the use of nanotechnologies for stem cell tracking. http://www.mdpi.com/1422-0067/11/3/1070/ Fri, 12 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-12 11 3 Review 1070 1081 1422-0067 Stem Cell Tracking by Nanotechnologies 2010-03-12 doi: 10.3390/ijms11031070 Villa Erratico Razini Fiori Rustichelli Torrente Belicchi http://www.mdpi.com/1422-0067/11/3/1057/ This study aims to elucidate the effects of chrysin on human ER-negative breast cancer cell line, MDA-MB-231. The study demonstrated that treatment of MDA-MB-231 cells with 20 µM chysin for 48 h significantly inhibited the growth of MDA-MB-231 cells and induced cytoplasmic lipid accumulation in the cells, but that the observed of cell death was not caused by apoptosis. The expression of PPARalpha mRNA in chrysin-treated MDA-MB-231 cells was significantly increased, which was likely associated to the proliferation of the cells post chrysin treatment. http://www.mdpi.com/1422-0067/11/3/1057/ Thu, 11 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-11 11 3 Article 1057 1069 1422-0067 Potential Effects of Chrysin on MDA-MB-231 Cells 2010-03-11 doi: 10.3390/ijms11031057 Teh Ban Hong Anizah Rahumatullah Thaneswary Yogarajah Maimunah Ahmad Khoo Boon Yin http://www.mdpi.com/1422-0067/11/3/1048/ The present study was undertaken to evaluate the effects of soybean varieties on content of anti-nutritional factors, growth, and nutrient digestibility in rat. For this purpose, the content of trypsin inhibitor and lectin was firstly measured in five soybean varieties. Then sixty male Wistar rats were randomly divided into six groups and fed on different diets as follows: groups 1 to 5 were fed on treatment diets containing five different varieties of soybean flour; group 6 was fed on a control diet containing casein. All animals were fed for four weeks. During this period, faeces and urine were collected to determine the nutritional efficiency of diets and body weight were measured weekly on ten rats from each group. The results showed that trypsin inhibitor and lectin content of Jilin45 was the highest, and those of Jinong7 were the lowest of the soybean varieties. In comparison, all measured parameters, that is including gain in body weight, feed utilization efficiency, nutrient digestibility, nitrogen balance and nitrogen retention, were markedly different among the five groups of animals, but were significantly lower than the control group. These findings show that soybean varieties could significantly affect trypsin inhibitor and lectin content in soybean. http://www.mdpi.com/1422-0067/11/3/1048/ Tue, 09 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-09 11 3 Article 1048 1056 1422-0067 Effect of Soybean Variety on Anti-Nutritional Factors Content, and Growth Performance and Nutrients Metabolism in Rat 2010-03-09 doi: 10.3390/ijms11031048 Chunmei Gu Hongbin Pan Zewei Sun Guixin Qin http://www.mdpi.com/1422-0067/11/3/1020/ This paper presents a review on recent progress in quantitative structure-property relationship (QSPR) studies of surfactants and applications of various molecular descriptors. QSPR studies on critical micelle concentration (cmc) and surface tension (γ) of surfactants are introduced. Studies on charge distribution in ionic surfactants by quantum chemical calculations and its effects on the structures and properties of the colloids of surfactants are also reviewed. The trends of QSPR studies on cloud point (for nonionic surfactants), biodegradation potential and some other properties of surfactants are evaluated . http://www.mdpi.com/1422-0067/11/3/1020/ Mon, 08 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-08 11 3 Review 1020 1047 1422-0067 A Review on Progress in QSPR Studies for Surfactants 2010-03-08 doi: 10.3390/ijms11031020 Jiwei Hu Xiaoyi Zhang Zhengwu Wang http://www.mdpi.com/1422-0067/11/3/982/ The mechanisms of regulation of respiration and energy fluxes in the cells are analyzed based on the concepts of systems biology, non-equilibrium steady state kinetics and applications of Wiener’s cybernetic principles of feedback regulation. Under physiological conditions cardiac function is governed by the Frank-Starling law and the main metabolic characteristic of cardiac muscle cells is metabolic homeostasis, when both workload and respiration rate can be changed manifold at constant intracellular level of phosphocreatine and ATP in the cells. This is not observed in skeletal muscles. Controversies in theoretical explanations of these observations are analyzed. Experimental studies of permeabilized fibers from human skeletal muscle vastus lateralis and adult rat cardiomyocytes showed that the respiration rate is always an apparent hyperbolic but not a sigmoid function of ADP concentration. It is our conclusion that realistic explanations of regulation of energy fluxes in muscle cells require systemic approaches including application of the feedback theory of Wiener’s cybernetics in combination with detailed experimental research. Such an analysis reveals the importance of limited permeability of mitochondrial outer membrane for ADP due to interactions of mitochondria with cytoskeleton resulting in quasi-linear dependence of respiration rate on amplitude of cyclic changes in cytoplasmic ADP concentrations. The system of compartmentalized creatine kinase (CK) isoenzymes functionally coupled to ANT and ATPases, and mitochondrial-cytoskeletal interactions separate energy fluxes (mass and energy transfer) from signalling (information transfer) within dissipative metabolic structures – intracellular energetic units (ICEU). Due to the non-equilibrium state of CK reactions, intracellular ATP utilization and mitochondrial ATP regeneration are interconnected by the PCr flux from mitochondria. The feedback regulation of respiration occurring via cyclic fluctuations of cytosolic ADP, Pi and Cr/PCr ensures metabolic stability necessary for normal function of cardiac cells. http://www.mdpi.com/1422-0067/11/3/982/ Mon, 08 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-08 11 3 Review 982 1019 1422-0067 Application of the Principles of Systems Biology and Wiener's Cybernetics for Analysis of Regulation of Energy Fluxes in Muscle Cells in Vivo 2010-03-08 doi: 10.3390/ijms11030982 Rita Guzun Valdur Saks http://www.mdpi.com/1422-0067/11/3/967/ Magnetic nanoparticles (MNPs) are important contrast agents used to monitor a range of neuropathological processes; microglial cells significantly contribute to MNP uptake in sites of pathology. Microglial activation occurs following most CNS pathologies but it is not known if such activation alters MNP uptake, intracellular processing and toxicity. We assessed these parameters in microglial cultures with and without experimental ‘activation’. Microglia showed rapid and extensive MNP uptake under basal conditions with no changes found following activation; significant microglial toxicity was observed at higher particle concentrations. Based on our findings, we suggest that avid MNP uptake by endogenous CNS microglia could significantly limit uptake by other cellular subtypes in mixed neural cell populations. http://www.mdpi.com/1422-0067/11/3/967/ Mon, 08 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-08 11 3 Communication 967 981 1422-0067 Robust Uptake of Magnetic Nanoparticles (MNPs) by Central Nervous System (CNS) Microglia: Implications for Particle Uptake in Mixed Neural Cell Populations 2010-03-08 doi: 10.3390/ijms11030967 Mark R. Pickard Divya M. Chari http://www.mdpi.com/1422-0067/11/3/956/ A test system for cell viability based on colony formation has been established and applied to high resolution fluorescence microscopy and single molecule detection. Living cells were irradiated either by epi-illumination or by total internal reflection (TIR) of a laser beam, and light doses where at least 90% of irradiated cells survived were determined. These light doses were in the range of a few J/cm2 up to about 200 J/cm2 depending on the wavelength of illumination as well as on the presence or absence of a fluorescent dye (e.g., the membrane marker laurdan). In general, cells were less sensitive to TIR than to epi-illumination. However, comparably high light doses needed for repetitive excitation of single molecules limit the application of super-resolution microscopy to living cells. http://www.mdpi.com/1422-0067/11/3/956/ Mon, 08 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-08 11 3 Article 956 966 1422-0067 Light Dose is a Limiting Factor to Maintain Cell Viability in Fluorescence Microscopy and Single Molecule Detection 2010-03-08 doi: 10.3390/ijms11030956 Michael Wagner Petra Weber Thomas Bruns Wolfgang S. L. Strauss Rainer Wittig Herbert Schneckenburger http://www.mdpi.com/1422-0067/11/3/943/ The stacking of discotic molecules (hexakis(alkoxy)diquinoxalino[2,3-a:2’,3’-c]phenazines) in the columnar phase sandwiched between two flat glass substrates has been studied. The surface free energy of the substrates, measured by means of sessile drop technique, is found to have significant influence on the way that the discotic molecules anchor on the surface, and a steady thermal state of the system is crucial for a homogenous orientation of the discotic columns. On a surface of high free energy, the discotic molecules anchor with their disc-face toward the surface. A decrease in the surface free energy of the substrate causes the discotic columns to tilt away from the normal of the substrate. http://www.mdpi.com/1422-0067/11/3/943/ Mon, 08 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-08 11 3 Article 943 955 1422-0067 Orientational Packing of a Confined Discotic Mesogen in the Columnar Phase 2010-03-08 doi: 10.3390/ijms11030943 Wenjun Zheng Ya-Ting Hu Cheng-Yan Chiang Chi Wi Ong http://www.mdpi.com/1422-0067/11/3/927/ Activated carbons were characterized texturally and chemically before and after treatment, using surface area determination in the BET model, Boehm titration, TPR, DRX and immersion calorimetry. The adsorption capacity and the kinetics of sulphur compound removal were determined by gas chromatography. It was established that the propanethiol retention capacity is dependent on the number of oxygenated groups generated on the activated carbon surface and that activated carbon modified with CuO at 0.25 M shows the highest retention of propanethiol. Additionally is proposed a mechanism of decomposition of propenothiol with carbon-copper system. http://www.mdpi.com/1422-0067/11/3/927/ Thu, 04 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-04 11 3 Article 927 942 1422-0067 Activated Carbon Modified with Copper for Adsorption of Propanethiol 2010-03-04 doi: 10.3390/ijms11030927 Juan Carlos Moreno-Piraján Joaquín Tirano Brisa Salamanca Liliana Giraldo http://www.mdpi.com/1422-0067/11/3/912/ The catalytic properties of bulky water-soluble salen complexes in the oxidation of isoeugenol(2-methoxy-4-(1-propenyl) phenol) have been investigated in aqueous ethanol solutions in order to obtain a mixture of polymeric compounds through dehydrogenative polymerization. The average molecular weight of dehydrogenated polymers (DHPs) was monitored by GPC and correlated to reaction conditions such as time, concentration of substrate, concentration of catalyst, type of oxidation agent, etc. The DHP synthesized by adopting the best reaction conditions was characterized by different analytical techniques (GPC, 13C-NMR, 31P-NMR and LC-MS) to elucidate its structure. The lignin-like polymer resulting from isoeugenol radical coupling possesses valuable biological activity and finds applications in a variety of fields, such as packaging industry and cultural heritage conservation. http://www.mdpi.com/1422-0067/11/3/912/ Thu, 04 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-04 11 3 Article 912 926 1422-0067 Oxidation of Isoeugenol by Salen Complexes with Bulky Substituents 2010-03-04 doi: 10.3390/ijms11030912 Anika Salanti Marco Orlandi Eeva-Liisa Tolppa Luca Zoia http://www.mdpi.com/1422-0067/11/3/896/ A bacterial strain EMS with the capability of degrading microcystins (MCs) was isolated from Lake Taihu, China. The bacterium was tentatively identified as a Stenotrophomonas sp. The bacterium could completely consume MC-LR and MC-RR within 24 hours at a concentration of 0.7 µg/mL and 1.7 µg/mL, respectively. The degradation of MC-LR and MC-RR by EMS occurred preferentially in an alkaline environment. In addition, mlrA gene involved in the degradation of MC-LR and MC-RR was detected in EMS. Due to the limited literature this gene has rare homologues. Sequencing analysis of the translated protein from mlrA suggested that MlrA might be a transmembrane protein, which suggests a possible new protease family having unique function. http://www.mdpi.com/1422-0067/11/3/896/ Tue, 02 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-02 11 3 Article 896 911 1422-0067 Degradation of Microcystin-LR and RR by a Stenotrophomonas sp. Strain EMS Isolated from Lake Taihu, China 2010-03-02 doi: 10.3390/ijms11030896 Jian Chen Liang Bin Hu Wei Zhou Shao Hua Yan Jing Dong Yang Yan Feng Xue Zhi Qi Shi http://www.mdpi.com/1422-0067/11/3/880/ Andrographolide derivatives were shown to inhibit α-glucosidase. To investigate the relationship between activities and structures of andrographolide derivatives, a training set was chosen from 25 andrographolide derivatives by the principal component analysis (PCA) method, and a quantitative structure-activity relationship (QSAR) was established by 2D and 3D QSAR methods. The cross-validation r2 (0.731) and standard error (0.225) illustrated that the 2D-QSAR model was able to identify the important molecular fragments and the cross-validation r2 (0.794) and standard error (0.127) demonstrated that the 3D-QSAR model was capable of exploring the spatial distribution of important fragments. The obtained results suggested that proposed combination of 2D and 3D QSAR models could be useful in predicting the α-glucosidase inhibiting activity of andrographolide derivatives. http://www.mdpi.com/1422-0067/11/3/880/ Tue, 02 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-02 11 3 Article 880 895 1422-0067 QSAR Studies on Andrographolide Derivatives as α-Glucosidase Inhibitors 2010-03-02 doi: 10.3390/ijms11030880 Jun Xu Sichao Huang Haibin Luo Guoji Li Jiaolin Bao Shaohui Cai Yuqiang Wang http://www.mdpi.com/1422-0067/11/3/858/ The use of biocatalysts for the production of both consumer goods and building blocks for chemical synthesis is consistently gaining relevance. A significant contribution for recent advances towards further implementation of enzymes and whole cells is related to the developments in miniature reactor technology and insights into flow behavior. Due to the high level of parallelization and reduced requirements of chemicals, intensive screening of biocatalysts and process variables has become more feasible and reproducibility of the bioconversion processes has been substantially improved. The present work aims to provide an overview of the applications of miniaturized reactors in bioconversion processes, considering multi-well plates and microfluidic devices, update information on the engineering characterization of the hardware used, and present perspective developments in this area of research. http://www.mdpi.com/1422-0067/11/3/858/ Tue, 02 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-02 11 3 Review 858 879 1422-0067 Miniaturization in Biocatalysis 2010-03-02 doi: 10.3390/ijms11030858 Pedro Fernandes http://www.mdpi.com/1422-0067/11/3/807/ Two main fields of interest form the background of actual demand for optimized levels of phenolic compounds in crop plants. These are human health and plant resistance to pathogens and to biotic and abiotic stress factors. A survey of agricultural technologies influencing the biosynthesis and accumulation of phenolic compounds in crop plants is presented, including observations on the effects of light, temperature, mineral nutrition, water management, grafting, elevated atmospheric CO2, growth and differentiation of the plant and application of elicitors, stimulating agents and plant activators. The underlying mechanisms are discussed with respect to carbohydrate availability, trade-offs to competing demands as well as to regulatory elements. Outlines are given for genetic engineering and plant breeding. Constraints and possible physiological feedbacks are considered for successful and sustainable application of agricultural techniques with respect to management of plant phenol profiles and concentrations. http://www.mdpi.com/1422-0067/11/3/807/ Tue, 02 Mar 2010 00:00:00 CET International Journal of Molecular Sciences 2010-03-02 11 3 Review 807 857 1422-0067 Managing Phenol Contents in Crop Plants by Phytochemical Farming and Breeding—Visions and Constraints 2010-03-02 doi: 10.3390/ijms11030807 Dieter Treutter http://www.mdpi.com/1422-0067/11/3/789/ Interleukin 12 (termed IL-12p70 and commonly designated IL-12) is an important immunoregulatory cytokine that is produced mainly by antigen-presenting cells. The expression of IL-12 during infection regulates innate responses and determines the type of adaptive immune responses. IL-12 induces interferon-γ (IFN-γ) production and triggers CD4+ T cells to differentiate into type 1 T helper (Th1) cells. Studies have suggested that IL-12 could play a vital role in treating many diseases, such as viral and bacterial infections and cancers. The unique heterodimeric structure, which IL-12 shares with its family members including IL-23, IL-27, and IL-35, has recently brought more attention to understanding the mechanisms that regulate the functions of IL-12. This article describes the structure and biological activities of IL-12 in both the innate and adaptive arms of the immune system, and discusses the applications of IL-12 in treating and preventing infections. http://www.mdpi.com/1422-0067/11/3/789/ Fri, 26 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-26 11 3 Review 789 806 1422-0067 Interleukin 12 a Key Immunoregulatory Cytokine in Infection Applications 2010-02-26 doi: 10.3390/ijms11030789 Therwa Hamza John B. Barnett Bingyun Li http://www.mdpi.com/1422-0067/11/2/779/ A series of phthalimide derivatives planned as drugs candidates to treat the symptoms of sickle cell anemia were evaluated in a mutagenicity test using strains of Salmonella typhimurium TA100 and TA102, without and with addition of S9 mixture, with the aim to identify the best structural requirements for a drug candidate without genotoxic activity. The compounds (1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl nitrate (1); (1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)ethyl nitrate (2); 3-(1,3-dioxo-1,3-dihydro-2H-iso-indol-2-yl)benzyl nitrate (3); 4-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)-N-hydroxy-benzenesulfonamide (4); 4-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)benzyl nitrate (5) and 2-[4-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)phenyl]ethyl nitrate (6) presented mutagenic potency ranging between 0-4,803 revertants/μmol. These results allowed us to propose that a methyl spacer linked to a nitrate ester subunit associated to meta aromatic substitution decreases mutagenicity. http://www.mdpi.com/1422-0067/11/2/779/ Thu, 25 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-25 11 2 Communication 779 788 1422-0067 Mutagenicity of New Lead Compounds to Treat Sickle Cell Disease Symptoms in a Salmonella/Microsome Assay 2010-02-25 doi: 10.3390/ijms11020779 Jean Leandro dos Santos Eliana A. Varanda Lídia Moreira Lima Chung Man Chin http://www.mdpi.com/1422-0067/11/2/762/ Functionalization of porous solids plays an important role in many areas, including heterogeneous catalysis and enzyme immobilization. In this study, large-pore ordered mesoporous SBA-15 molecular sieves were synthesized with tetraethyl orthosilicate (TEOS) in the presence of the non-ionic triblock co-polymer Pluronic P123 under acidic conditions. These materials were grafted with 3 aminopropyltrimethoxysilane (ATS), 3-glycidoxypropyltrimethoxysilane (GTS) and with 3 aminopropyltrimethoxysilane and glutaraldehyde (GA-ATS) in order to provide covalent anchoring points for enzymes. The samples were characterized by nitrogen adsorption, powder X-ray diffraction, solid-state NMR spectroscopy, elemental analysis, diffuse reflectance fourier transform infrared spectroscopy and diffuse reflectance UV/Vis spectroscopy. The obtained grafted materials were then used for the immobilization of chloroperoxidase (CPO) and glucose oxidase (GOx) and the resulting biocatalysts were tested in the oxidation of indole. It is found that enzymes anchored to the mesoporous host by the organic moieties can be stored for weeks without losing their activity. Furthermore, the covalently linked enzymes are shown to be less prone to leaching than the physically adsorbed enzymes, as tested in a fixed-bed reactor under continuous operation conditions. http://www.mdpi.com/1422-0067/11/2/762/ Wed, 24 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-24 11 2 Article 762 778 1422-0067 Covalent Anchoring of Chloroperoxidase and Glucose Oxidase on the Mesoporous Molecular Sieve SBA-15 2010-02-24 doi: 10.3390/ijms11020762 Dirk Jung Carsten Streb Martin Hartmann http://www.mdpi.com/1422-0067/11/2/754/ Lipid bilayer fusion is a complex process requiring several intermediate steps. Initially, the two bilayers are brought into close contact following removal of intervening water layers and overcoming electrostatic repulsions between opposing bilayer head groups. In this study we monitor by light scattering the reversible aggregation of phosphatidylcholine single shell vesicles during which adhesion occurs but stops prior to a fusion process. Light scattering measurements of dimyristoyl-sn-glycero-3-phosphocholine (DMPC), dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) in water show that lowering the temperature of about 0.14 micron single shell vesicles of DPPC (from 20 °C to 5 °C) and about 2 micron vesicles of DSPC (from 20 °C to 15 °C), but not of 1 micron vesicles of DMPC, results in extensive aggregation within 24 hours that is reversible by an increase in temperature. Aggregation of DSPC vesicles was confirmed by direct visual observation. Orientation of lipid head groups parallel to the plane of the bilayer and consequent reduction of the negative surface charge can account for the ability of DPPC and DSPC vesicles to aggregate. Retention of negatively charged phosphates on the surface and the burial of positively charged cholines within the bilayer offer an explanation for the failure of DMPC vesicles to aggregate. Lowering the temperature of 1,2-dipalmitoyl-sn-glycero-3-phosphoserine (DPPS) vesicles from 20 °C to 5 °C failed to increase aggregation within 24 hours at Mg++/DPPS ratios that begin to initiate aggregation and fusion. http://www.mdpi.com/1422-0067/11/2/754/ Sun, 21 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-21 11 2 Article 754 761 1422-0067 Lipid Vesicle Aggregation Induced by Cooling 2010-02-21 doi: 10.3390/ijms11020754 Frank B. Howard Ira W. Levin http://www.mdpi.com/1422-0067/11/2/745/ RNA interference (RNAi) is a post-transcriptional gene-silencing process that occurs in many eukaryotic organisms upon intracellular exposure to double-stranded RNA. Argonaute 2 (Ago2) protein is the catalytic engine of mammalian RNAi. It contains a PIWI domain that is structurally related to RNases H and possibly shares with them a two-metal-ion catalysis mechanism. Here we describe the expression in E. coli of mouse Ago2 and testing of its enzymatic activity in a RISC assay, i.e., for the ability to cleave a target RNA in a single position specified by a complementary small interfering RNA (siRNA). The results show that the enzyme can load the siRNA and cleave the complementary RNA in absence of other cellular factors, as described for human Ago2. It was also found that mutation of Arg669, a residue previously proposed to be involved in substrate and/or B metal ion binding, doesn’t affect the enzymatic activity, suggesting that this residue doesn’t belong to the active site. http://www.mdpi.com/1422-0067/11/2/745/ Fri, 12 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-12 11 2 Article 745 753 1422-0067 Bacterial Expression of Mouse Argonaute 2 for Functional and Mutational Studies 2010-02-12 doi: 10.3390/ijms11020745 Vincenzo Salvatore Nicoletta Potenza Umberto Papa Valentina Nobile Aniello Russo http://www.mdpi.com/1422-0067/11/2/731/ 2-Bromopropane (2-BP), an alternative to ozone-depleting solvents, is used as a cleaning solvent. Here, we examined the cytotoxic effects of 2-bromopropane (2-BP) on mouse embryos at the blastocyst stage, subsequent embryonic attachment and outgrowth in vitro, and in vivo implantation via embryo transfer. Mouse blastocysts were incubated in medium with or without 2-BP (2.5, 5 or 10 μM) for 24 h. Cell proliferation and growth were investigated with dual differential staining, apoptosis was analyzed by terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) analysis, and implantation and post-implantation development of embryos were assessed using in vitro development analysis and in vivo embryo transfer, respectively. Blastocysts treated with 5 or 10 μM 2-BP displayed significantly increased apoptosis, and decreased inner cell mass (ICM) and trophectoderm (TE) cell number. Additionally, the implantation success rates of 2-BP-pretreated blastocysts were lower than those of untreated controls. In vitro treatment with 5 or 10 μM 2-BP was associated with increased resorption of postimplantation embryos, and decreased placental and fetal weights. Our results collectively indicate that in vitro exposure to 2-BP induces apoptosis, suppresses implantation rates after transfer to host mice, and retards early postimplantation development. http://www.mdpi.com/1422-0067/11/2/731/ Thu, 11 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-11 11 2 Article 731 744 1422-0067 Cytotoxic Effects of 2-Bromopropane on Embryonic Development in Mouse Blastocysts 2010-02-11 doi: 10.3390/ijms11020731 Wen-Hsiung Chan http://www.mdpi.com/1422-0067/11/2/719/ The implantation process is complex, requiring reciprocal interactions between implantation-competent blastocysts and the receptive uterus. There were reports to show that some microRNAs (miRNAs) may play a key role during embryo implantation in mouse. However, the miR-320 expression profiles in the rat uterus during peri-implantation are unknown. In the present study, we found that the expression level of miR-320 was lower on day 5 of gestation (g.d. 5) in rats than g.d.3 and g.d.4 and restored gradually from g.d.6. MiR-320 was specifically localized in glandular and luminal epithelia and decidua. The expression of miR-320 was not significantly different in the pseudopregnant uterus and decreased in the uteri of rats subjected to activation of delayed implantation. Artificial decidualization and treatment with progesterone increased the miR-320 expression. Thus, miR-320 was differentially expressed in the rat uterus during implantation. The expression level was affected by active blastocysts and decidualization during the window of implantation. Steroid hormones, progesterone stimulated miR-320 expression. http://www.mdpi.com/1422-0067/11/2/719/ Thu, 11 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-11 11 2 Article 719 730 1422-0067 Temporal and Spatial Regulation of miR-320 in the Uterus during Embryo Implantation in the Rat 2010-02-11 doi: 10.3390/ijms11020719 Hong-Fei Xia Xiao-Hua Jin Pei-Pei Song Yi Cui Chun-Mei Liu Xu Ma http://www.mdpi.com/1422-0067/11/2/704/ If we could realize an autonomous polymer system driven under biological conditions by a tailor-made molecular design, human beings could create unprecedented biomimetic functions and materials such as heartbeats, autonomous peristaltic pumps, etc. In order to achieve this objective, we have investigated the molecular design of such a polymer system. As a result, we were the first to demonstrate a self-oscillating polymer system driven in a solution where only malonic acid existed, which could convert the chemical energy of the Belousov-Zhabotinsky (BZ) reaction into a change in the conformation of the polymer chain. To cause the self-oscillation in solution, we have attempted to construct a built-in system where the required BZ system substrates other than the organic acid are incorporated into the polymer itself. That is, the novel polymer chain incorporated the metal catalyst of the BZ reaction, a pH-control site and an oxidant supply site at the same time. As a result of introducing the pH control and oxidant supply sites into the conventional-type self-oscillating polymer chain, the novel polymer chain caused aggregation-disaggregation self-oscillations in the solution. We clarified that the period of the self-oscillation of the novel self-oscillating polymer chain was proportional to the concentration of the malonic acid. Therefore, the concentration of the malonic acid can be determined by measuring the period of the novel self-oscillating polymer solution. In this review, we introduce the detailed molecular design of the novel self-oscillating polymer chain and its self-oscillating behavior. Moreover, we report an autonomous self-oscillating polymer gel actuator that causes a bending-stretching motion under the constant conditions. http://www.mdpi.com/1422-0067/11/2/704/ Wed, 10 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-10 11 2 Review 704 718 1422-0067 Molecular Design and Functional Control of Novel Self-Oscillating Polymers 2010-02-10 doi: 10.3390/ijms11020704 Yusuke Hara Shingo Maeda Shuji Hashimoto Ryo Yoshida http://www.mdpi.com/1422-0067/11/2/691/ Phenolic esters have attracted considerable interest due to the potential they offer for peroxidase catalysed cross-linking of cell wall polysaccharides. Particularly, feruloyl residues undergo radical coupling reactions that result in cross-linking (intra-/intermolecular) between polysaccharides, between polysaccharides and lignin and, between polysaccharides and proteins. This review addresses for the first time different studies in which it is established that cross-linking by dehydrodiferulates contributes to maize’s defences to pests and diseases. Dehydrodiferulate cross-links are involved in maize defence mechanisms against insects such as the European, Mediterranean, and tropical corn borers and, storage pest as the maize weevil. In addition, cross-links are also discussed to be involved in genetic resistance of maize to fungus diseases as Gibberella ear and stalk rot. Resistance against insects and fungus attending dehydrodiferulates could go hand in hand. Quantitative trait loci mapping for these cell wall components could be a useful tool for enhancing resistance to pest and diseases in future breeding programs. http://www.mdpi.com/1422-0067/11/2/691/ Tue, 09 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-09 11 2 Review 691 703 1422-0067 Role of Dehydrodiferulates in Maize Resistance to Pests and Diseases 2010-02-09 doi: 10.3390/ijms11020691 Rogelio Santiago Rosa A. Malvar http://www.mdpi.com/1422-0067/11/2/672/ Separation of polyphenolic phytochemical compounds from their mixtures with sugars is necessary to produce an added-value sugar-reduced extract with high biological activity from fruit juice processing industry waste streams. The separation characteristics of a binary mixture of rutin and glucose using a Pellicon-2 regenerated cellulose ultrafiltration membrane with an area of 0.1 m2 having nominal MWCO of 1,000 Da were investigated, to demonstrate the separation of phenolic compounds from sugars. The effects of the operating variables–transmembrane pressure, feed solution temperature and pH, initial feed concentration and feed flow rate–on the permeate flux and enrichment of rutin, were determined. The permeate flux increased with the increase in transmembrane pressure up to a certain limit and after that the flux remained more or less constant. The optimum transmembrane pressure was within 4–5 bar. The flux increased with the increase in feed solution temperature because of reduced feed viscosity, and better solubility. The concentration of rutin was optimum at lower temperature (30ºC), with an enrichment factor of 1.3. The effect of pH on permeate flux was less obvious. Lowering the feed solution pH increased the retention of rutin and the optimum separation was obtained within pH 3–4. The permeate flux decreased with the increase in feed concentration of rutin (concentration range 0.1–0.5 g/L). The enrichment of rutin was significant in the glucose concentration range 0.35–0.5 g/L. The feed flow rate had a significant effect on the flux and separation characteristics. Higher cross-flow through the membrane reduced the fouling by providing a shear force to sweep away deposited materials from the membrane surface. At high feed flow rate, more rutin was retained by the membrane with less sugar permeating through. The optimum feed flow rate was 1.5 L/min. For the separation of rutin (in the retentate) and glucose (in the permeate), the best results were obtained at rutin enrichment of 2.9 and recovery 72.5%, respectively. The performance of this system was further improved by operating it in a diafiltration mode, in which only approx. 11% of glucose remained in the retentate. http://www.mdpi.com/1422-0067/11/2/672/ Tue, 09 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-09 11 2 Article 672 690 1422-0067 Concentration of Rutin Model Solutions from Their Mixtures with Glucose Using Ultrafiltration 2010-02-09 doi: 10.3390/ijms11020672 Swallow Wei Md. M. Hossain Zaid S. Saleh http://www.mdpi.com/1422-0067/11/2/656/ Functionalizing of single molecules on surfaces has manifested great potential for bottom-up construction of complex devices on a molecular scale. We discuss the growth mechanism for the initial layers of polycyclic aromatic hydrocarbons on metal surfaces and we review our recent progress on molecular machines, and present a molecular rotor with a fixed off-center axis formed by chemical bonding. These results represent important advances in molecular-based nanotechnology. http://www.mdpi.com/1422-0067/11/2/656/ Tue, 09 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-09 11 2 Review 656 671 1422-0067 Anchoring of a Single Molecular Rotor and Its Array on Metal Surfaces using Molecular Design and Self-Assembly 2010-02-09 doi: 10.3390/ijms11020656 Li Gao Shi-Xuan Du Hong-Jun Gao http://www.mdpi.com/1422-0067/11/2/647/ Drywall from China has been reported to release sulfur producing products which are corrosive to metals, result in noxious odors, and represent a significant health risk. It has been reported that these emissions produce medical symptoms such as respiratory or asthma type problems, sinusitis, gastrointestinal disorders, and vision problems in home owners and their household pets. We report here a method of identifying a causative agent for these emissions by sampling affected gypsum wallboard and subjecting those samples to Real Time Polymerase Chain Reaction [RT-PCR] studies. Specific DNA probes and primers have been designed and patented that detect a specific iron and sulfur reducing bacterium (i.e., Thiobacillus ferrooxidans). One hundred percent of affected drywall samples obtained from homes located in the southeastern United States tested positive for the presence of T. ferrooxidans. All negative controls consisting of unaffected wallboard and internal controls, Geotrichum sp., tested negative within our limits of detection. http://www.mdpi.com/1422-0067/11/2/647/ Fri, 05 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-05 11 2 Article 647 655 1422-0067 Isolation of Sulfur Reducing and Oxidizing Bacteria Found in Contaminated Drywall 2010-02-05 doi: 10.3390/ijms11020647 Dennis G. Hooper John Shane David C. Straus Kaye H. Kilburn Vincent Bolton John S. Sutton Frederick T. Guilford http://www.mdpi.com/1422-0067/11/2/622/ The dietary consumption of grape and its products is associated with a lower incidence of degenerative diseases such as cardiovascular disease and certain types of cancers. Most recent interest has focused on the bioactive phenolic compounds in grape. Anthocyanins, flavanols, flavonols and resveratrol are the most important grape polyphenols because they possess many biological activities, such as antioxidant, cardioprotective, anticancer, anti-inflammation, antiaging and antimicrobial properties. This review summarizes current knowledge on the bioactivities of grape phenolics. The extraction, isolation and identification methods of polyphenols from grape as well as their bioavailability and potential toxicity also are included. http://www.mdpi.com/1422-0067/11/2/622/ Thu, 04 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-04 11 2 Review 622 646 1422-0067 Biological Activities of Polyphenols from Grapes 2010-02-04 doi: 10.3390/ijms11020622 En-Qin Xia Gui-Fang Deng Ya-Jun Guo Hua-Bin Li http://www.mdpi.com/1422-0067/11/2/595/ Flavonoids and biochemically-related chalcones are important secondary metabolites, which are ubiquitously present in plants and therefore also in human food. They fulfill a broad range of physiological functions in planta and there are numerous reports about their physiological relevance for humans. Flavonoids have in common a basic C6-C3-C6 skeleton structure consisting of two aromatic rings (A and B) and a heterocyclic ring (C) containing one oxygen atom, whereas chalcones, as the intermediates in the formation of flavonoids, have not yet established the heterocyclic C-ring. Flavonoids are grouped into eight different classes, according to the oxidative status of the C-ring. The large number of divergent chalcones and flavonoid structures is from the extensive modification of the basic molecules. The hydroxylation pattern influences physiological properties such as light absorption and antioxidative activity, which is the base for many beneficial health effects of flavonoids. In some cases antiinfective properties are also effected. http://www.mdpi.com/1422-0067/11/2/595/ Thu, 04 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-04 11 2 Review 595 621 1422-0067 The Creation and Physiological Relevance of Divergent Hydroxylation Patterns in the Flavonoid Pathway 2010-02-04 doi: 10.3390/ijms11020595 Heidi Halbwirth http://www.mdpi.com/1422-0067/11/2/562/ 70 years have passed since the first isolation of the naphthodianthrones hypericin and pseudohypericin from Hypericum perforatum L. Today, they continue to be one of the most promising group of polyphenols, as they fascinate with their physical, chemical and important biological properties which derive from their unique chemical structure. Hypericins and their derivatives have been extensively studied mainly for their antitumor, antiviral and antidepressant properties. Notably, hypericin is one of the most potent naturally occurring photodynamic agents. It is able to generate the superoxide anion and a high quantum yield of singlet oxygen that are considered to be primarily responsible for its biological effects. The prooxidant photodynamic properties of hypericin have been exploited for the photodynamic therapy of cancer (PDT), as hypericin, in combination with light, very effectively induces apoptosis and/or necrosis of cancer cells. The mechanism by which these activities are expressed continues to be a main topic of discussion, but according to scientific data, different modes of action (generation of ROS & singlet oxygen species, antiangiogenesis, immune responces) and multiple molecular pathways (intrinsic/extrinsic apoptotic pathway, ERK inhibition) possibly interrelating are implicated. The aim of this review is to analyse the most recent advances (from 2005 and thereof) in the chemistry and biological activities (in vitro and in vivo) of the pure naphthodianthrones, hypericin and pseudohypericin from H. perforatum. Extracts from H. perforatum were not considered, nor pharmakokinetic or clinical data. Computerised literature searches were performed using the Medline (PubMed), ChemSciFinder and Scirus Library databases. No language restrictions were imposed. http://www.mdpi.com/1422-0067/11/2/562/ Thu, 04 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-04 11 2 Review 562 594 1422-0067 Hypericins as Potential Leads for New Therapeutics 2010-02-04 doi: 10.3390/ijms11020562 Anastasia Karioti Anna Rita Bilia http://www.mdpi.com/1422-0067/11/2/544/ Retinal ischemia can be effectively modeled by permanent bilateral common carotid artery occlusion, which leads to chronic hypoperfusion-induced degeneration in the entire rat retina. The complex pathways leading to retinal cell death offer a complex approach of neuroprotective strategies. In the present review we summarize recent findings with different neuroprotective candidate molecules. We describe the protective effects of intravitreal treatment with: (i) urocortin 2; (ii) a mitochondrial ATP-sensitive K+ channel opener, diazoxide; (iii) a neurotrophic factor, pituitary adenylate cyclase activating polypeptide; and (iv) a novel poly(ADP-ribose) polymerase inhibitor (HO3089). The retinoprotective effects are demonstrated with morphological description and effects on apoptotic pathways using molecular biological techniques. http://www.mdpi.com/1422-0067/11/2/544/ Wed, 03 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-03 11 2 Review 544 561 1422-0067 Novel Neuroprotective Strategies in Ischemic Retinal Lesions 2010-02-03 doi: 10.3390/ijms11020544 Krisztina Szabadfi Laszlo Mester Dora Reglodi Peter Kiss Norbert Babai Boglarka Racz Krisztina Kovacs Aliz Szabo Andrea Tamas Robert Gabriel Tamas Atlasz http://www.mdpi.com/1422-0067/11/2/532/ The amorphous polymer film swelling in a liquid solvent below the glass transition temperature was characterized by a few kinetic parameters (especially the mutual diffusion coefficient of swelling and its mean value) obtained by interference of monochromatic light in the wedge arrangement. This interferometric method allows one to determine the concentration field in the swollen surface layer and consequently to compute the concentration-dependent diffusion coefficient. A software system developed at the Department of Physics and Material Engineering at TBU in Zlin has been used for the evaluation of the main kinetic parameters of the swelling process. The software can be used for the on-line analyses of interferograms during the swelling process. The main application outputs are the computation of the concentration profile, the concentration gradient, the mutual diffusion coefficient of the swelling by the solvent and its mean value. http://www.mdpi.com/1422-0067/11/2/532/ Wed, 03 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-03 11 2 Article 532 543 1422-0067 The Measurement of Polymer Swelling Processes by an Interferometric Method and Evaluation of Diffusion Coefficients 2010-02-03 doi: 10.3390/ijms11020532 Aleš Mráček http://www.mdpi.com/1422-0067/11/2/521/ The nuclear factor kappa B is widely expressed in the distinct subpopulations of chorionic villi and deciduas of first-trimester pregnancies. We examined the cellular distribution and expression of nuclear factor kappa B in the human first-trimester chorionic villi and deciduas of women with early spontaneous miscarriage and viable pregnancy by confocal laser scanning microscope and immunohistochemistry. There is a greater nuclear translocation of nuclear factor kappa B is restricted to villous stromal cells, decidual stromal cells, glandular epithelial cells and vessel endothelial cells in early spontaneous miscarriage than in viable pregnancies. Collectively these observations suggest that over-activation of nuclear factor kappa B has a relationship with early spontaneous miscarriages. http://www.mdpi.com/1422-0067/11/2/521/ Wed, 03 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-03 11 2 Article 521 531 1422-0067 Nuclear Translocation of Nuclear Factor Kappa B in First Trimester Deciduas and Chorionic Villi in Early Spontaneous Miscarriage Women 2010-02-03 doi: 10.3390/ijms11020521 Li-qin Wang Xue-wen Yu Chun-fang Yan Xiang Wang http://www.mdpi.com/1422-0067/11/2/507/ A Gram-positive, facultatively anaerobic, endospore-forming and rod-shaped bacterium was isolated from soil samples and designated strain LQQ. This organism strongly quenches the acylhomoserine lactone quorum-sensing signal. The LQQ strain exhibits phenotypic characteristics consistent with its classification in the genus Bacillus. It is positive in catalase and no special growth factor is needed. It uses glucose as sole carbon source. The DNA G + C content is 39.8 mol %. The closest relatives based on the 16S rRNA gene sequence are Bacillus anthracis, Bacillus thuringiensis, and Brevibacillus brevis (syn. Bacillus brevis) with the similarity of 96.5%. The DNA–DNA hybridization data indicates a low level of genomic relatedness with the relative type strains of Bacillus thuringiensis (6.1%), Bacillus anthracis (10.5%) and Brevibacillus brevis (8.7%). On the basis of the phenotypic and phylogenetic data together with the genomic distinctiveness, the LQQ strain represents a novel species of the genus Bacillus, for which the name Bacillus marcorestinctum sp. nov. is proposed. The type strain is LQQT. http://www.mdpi.com/1422-0067/11/2/507/ Wed, 03 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-03 11 2 Article 507 520 1422-0067 Bacillus marcorestinctum sp. nov., a Novel Soil Acylhomoserine Lactone Quorum-Sensing Signal Quenching Bacterium 2010-02-03 doi: 10.3390/ijms11020507 Yan Han Fang Chen Nuo Li Bo Zhu Xianzhen Li http://www.mdpi.com/1422-0067/11/2/492/ Species delimitation has long been a difficult and controversial process, and different operational criteria often lead to different results. In particular, investigators using phenotypic vs. molecular data to delineate species may recognize different boundaries, especially if morphologically or ecologically differentiated populations have only recently diverged. Here we examine the genetic relationship between the widespread sunflower species Helianthus petiolaris and its narrowly distributed sand dune endemic sister species H. neglectus using sequence data from nine nuclear loci. The two species were initially described as distinct based on a number of minor morphological differences, somewhat different ecological tolerances, and at least one chromosomal rearrangement distinguishing them; but detailed molecular data has not been available until now. We find that, consistent with previous work, H. petiolaris is exceptionally genetically diverse. Surprisingly, H. neglectus harbors very similar levels of genetic diversity (average diversity across loci is actually slightly higher in H. neglectus). It is extremely unlikely that such a geographically restricted species could maintain these levels of genetic variation in isolation. In addition, the two species show very little evidence of any genetic divergence, and estimates of interspecific gene flow are comparable to gene flow estimates among regions within H. petiolaris. These results indicate that H. petiolaris and H. neglectus likely do not represent two distinct, isolated gene pools; H. neglectus is probably more accurately thought of as a geographically restricted, morphologically and ecologically distinct subspecies of H. petiolaris rather than a separate species. http://www.mdpi.com/1422-0067/11/2/492/ Tue, 02 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-02 11 2 Article 492 506 1422-0067 Effective Population Size, Gene Flow, and Species Status in a Narrow Endemic Sunflower, Helianthus neglectus, Compared to Its Widespread Sister Species, H. petiolaris 2010-02-02 doi: 10.3390/ijms11020492 Andrew R. Raduski Loren H. Rieseberg Jared L. Strasburg http://www.mdpi.com/1422-0067/11/2/458/ The Mediterranean diet is associated with a lower incidence of atherosclerosis, cardiovascular disease, neurodegenerative diseases and certain types of cancer. The apparent health benefits have been partially ascribed to the dietary consumption of virgin olive oil by Mediterranean populations. Much research has focused on the biologically active phenolic compounds naturally present in virgin olive oils to aid in explaining reduced mortality and morbidity experienced by people consuming a traditional Mediterranean diet. Studies (human, animal, in vivo and in vitro) have demonstrated that olive oil phenolic compounds have positive effects on certain physiological parameters, such as plasma lipoproteins, oxidative damage, inflammatory markers, platelet and cellular function, antimicrobial activity and bone health. This paper summarizes current knowledge on the bioavailability and biological activities of olive oil phenolic compounds. http://www.mdpi.com/1422-0067/11/2/458/ Tue, 02 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-02 11 2 Review 458 479 1422-0067 Biological Activities of Phenolic Compounds Present in Virgin Olive Oil 2010-02-02 doi: 10.3390/ijms11020458 Sara Cicerale Lisa Lucas Russell Keast http://www.mdpi.com/1422-0067/11/2/480/ The increase of human life span will have profound implications in Public Health in decades to come. By 2030, there will be an estimated 1.2 billion women in post-menopause. Hormone Replacement Therapy with synthetic hormones is still full of risks and according to the latest developments, should be used for the shortest time possible. Searching for alternative drugs is inevitable in this scenario and science must provide physicians with other substances that can be used to treat the same symptoms with less side effects. Systematic research carried out on this field of study is focusing now on isoflavones but the randomised controlled trials and reviews of meta-analysis concerning post-menopause therapy, that could have an important impact on human health, are very controversial. The aim of the present work was to establish a theoretical calculation suitable for use as a way to estimate the “Theoretical Efficacy (TE)” of a mixture with different bioactive compounds as a way to obtain a “Theoretical Efficacy Related to Estradiol (TERE)”. The theoretical calculation that we propose in this paper integrates different knowledge about this subject and sets methodological boundaries that can be used to analyse already published data. The outcome should set some consensus for new clinical trials using isoflavones (isolated or included in mixtures) that will be evaluated to assess their therapeutically activity. This theoretical method for evaluation of a possible efficacy could probably also be applied to other herbal drug extracts when a synergistic or contradictory bio-effect is not verified. In this way, it we may contribute to enlighten and to the development of new therapeutic approaches. http://www.mdpi.com/1422-0067/11/2/480/ Tue, 02 Feb 2010 00:00:00 CET International Journal of Molecular Sciences 2010-02-02 11 2 Article 480 491 1422-0067 Bioactivity of Isoflavones: Assessment through a Theoretical Model as a Way to Obtain a “Theoretical Efficacy Related to Estradiol (TERE)” 2010-02-02 doi: 10.3390/ijms11020480 Maria da Graça R. Campos Miguel Pires Matos http://www.mdpi.com/1422-0067/11/2/427/ Fluorescence correlation spectroscopy (FCS) is a single molecule technique used mainly for determination of mobility and local concentration of molecules. This review describes the specific problems of FCS in planar systems and reviews the state of the art experimental approaches such as 2-focus, Z-scan or scanning FCS, which overcome most of the artefacts and limitations of standard FCS. We focus on diffusion measurements of lipids and proteins in planar lipid membranes and review the contributions of FCS to elucidating membrane dynamics and the factors influencing it, such as membrane composition, ionic strength, presence of membrane proteins or frictional coupling with solid support. http://www.mdpi.com/1422-0067/11/2/427/ Thu, 28 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-28 11 2 Review 427 457 1422-0067 Recent Developments in Fluorescence Correlation Spectroscopy for Diffusion Measurements in Planar Lipid Membranes 2010-01-28 doi: 10.3390/ijms11020427 Radek Macháň Martin Hof http://www.mdpi.com/1422-0067/11/2/407/ Collagens, or more precisely collagen-based extracellular matrices, are often considered as a metazoan hallmark. Among the collagens, fibrillar collagens are present from sponges to humans, and are involved in the formation of the well-known striated fibrils. In this review we discuss the different steps in the evolution of this protein family, from the formation of an ancestral fibrillar collagen gene to the formation of different clades. Genomic data from the choanoflagellate (sister group of Metazoa) Monosiga brevicollis, and from diploblast animals, have suggested that the formation of an ancestral α chain occurred before the metazoan radiation. Phylogenetic studies have suggested an early emergence of the three clades that were first described in mammals. Hence the duplication events leading to the formation of the A, B and C clades occurred before the eumetazoan radiation. Another important event has been the two rounds of “whole genome duplication” leading to the amplification of fibrillar collagen gene numbers, and the importance of this diversification in developmental processes. We will also discuss some other aspects of fibrillar collagen evolution such as the development of the molecular mechanisms involved in the formation of procollagen molecules and of striated fibrils. http://www.mdpi.com/1422-0067/11/2/407/ Thu, 28 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-28 11 2 Review 407 426 1422-0067 The Fibrillar Collagen Family 2010-01-28 doi: 10.3390/ijms11020407 Jean-Yves Exposito Ulrich Valcourt Caroline Cluzel Claire Lethias http://www.mdpi.com/1422-0067/11/2/386/ Electrostatic interactions between dielectric surfaces and different fluorophores used in ultrasensitive fluorescence microscopy are investigated using objective-based Total Internal Reflection Fluorescence Correlation Spectroscopy (TIR-FCS). The interfacial dynamics of cationic rhodamine 123 and rhodamine 6G, anionic/dianionic fluorescein, zwitterionic rhodamine 110 and neutral ATTO 488 are monitored at various ionic strengths at physiological pH. As analyzed by means of the amplitude and time-evolution of the autocorrelation function, the fluorescent molecules experience electrostatic attraction or repulsion at the glass surface depending on their charges. Influences of the electrostatic interactions are also monitored through the triplet-state population and triplet relaxation time, including the amount of detected fluorescence or the count-rate-per-molecule parameter. These TIR-FCS results provide an increased understanding of how fluorophores are influenced by the microenvironment of a glass surface, and show a promising approach for characterizing electrostatic interactions at interfaces. http://www.mdpi.com/1422-0067/11/2/386/ Thu, 28 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-28 11 2 Article 386 406 1422-0067 Electrostatic Interactions of Fluorescent Molecules with Dielectric Interfaces Studied by Total Internal Reflection Fluorescence Correlation Spectroscopy 2010-01-28 doi: 10.3390/ijms11020386 Hans Blom Kai Hassler Andriy Chmyrov Jerker Widengren http://www.mdpi.com/1422-0067/11/1/370/ Genotype/phenotype association analyses (Treescan) with plasma lipid levels and functional site prediction methods (TreeSAAP and PolyPhen) were performed using sequence data for ANGPTL4 from 3,551 patients in the Dallas Heart Study. Biological assays of rare variants in phenotypic tails and results from a Treescan analysis were used as “known” variants to assess the site prediction abilities of PolyPhen and TreeSAAP. The E40K variant in European Americans and the R278Q variant in African Americans were significantly associated with multiple lipid phenotypes. Combining TreeSAAP and PolyPhen performed well to predict “known” functional variants while reducing noise from false positives. http://www.mdpi.com/1422-0067/11/1/370/ Mon, 25 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-25 11 1 Article 370 385 1422-0067 Phylogenetics Applied to Genotype/Phenotype Association and Selection Analyses with Sequence Data from Angptl4 in Humans 2010-01-25 doi: 10.3390/ijms11010370 Taylor J. Maxwell Matthew L. Bendall Jeffrey Staples Todd Jarvis Keith A. Crandall http://www.mdpi.com/1422-0067/11/1/354/ Bone adaptation or integration of an implant is characterized by a series of biological reactions that start with bone turnover at the interface (a process of localized necrosis), followed by rapid repair. The wound healing response is guided by a complex activation of macrophages leading to tissue turnover and new osteoblast differentiation on the implant surface. The complex role of implant surface topography and impact on healing response plays a role in biological criteria that can guide the design and development of future tissue-implant surface interfaces. http://www.mdpi.com/1422-0067/11/1/354/ Mon, 25 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-25 11 1 Review 354 369 1422-0067 Surface Modification of Biomedical and Dental Implants and the Processes of Inflammation, Wound Healing and Bone Formation 2010-01-25 doi: 10.3390/ijms11010354 Clark M. Stanford http://www.mdpi.com/1422-0067/11/1/329/ New organic dyes comprising carbazole, iminodibenzyl, or phenothiazine moieties, respectively, as the electron donors, and cyanoacetic acid or acrylic acid moieties as the electron acceptors/anchoring groups were synthesized and characterized. The influence of heteroatoms on carbazole, iminodibenzyl and phenothiazine donors, and cyano-substitution on the acid acceptor is evidenced by spectral, electrochemical, photovoltaic experiments, and density functional theory calculations. The phenothiazine dyes show solar-energy-to-electricity conversion efficiency (η) of 3.46–5.53%, whereas carbazole andiminodibenzyl dyesshow η of 2.43% and 3.49%, respectively. http://www.mdpi.com/1422-0067/11/1/329/ Fri, 22 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-22 11 1 Article 329 353 1422-0067 Synthesis and Characterization of Organic Dyes Containing Various Donors and Acceptors 2010-01-22 doi: 10.3390/ijms11010329 Tzi-Yi Wu Ming-Hsiu Tsao Fu-Lin Chen Shyh-Gang Su Cheng-Wen Chang Hong-Paul Wang Yuan-Chung Lin Wen-Chung Ou-Yang I-Wen Sun http://www.mdpi.com/1422-0067/11/1/304/ Single molecule techniques improve our understanding of the photon and light. If the single photon double slit experiment is performed at the “single photon limit” of a multi-atom light source, faint light pulses with more than one photon hamper the interpretation. Single molecules, quantum dots or defect centres in crystals should be used as light source. “Single photon detectors” do not meet their promise―only “photon number resolving single photon detectors” do so. Particularly, the accumulation time argument, the only safe basis for the postulate of a strictly particle like photon, has so far not yet been verified. http://www.mdpi.com/1422-0067/11/1/304/ Thu, 21 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-21 11 1 Article 304 311 1422-0067 Single Molecule Experiments Challenge the Strict Wave-Particle Dualism of Light 2010-01-21 doi: 10.3390/ijms11010304 Karl Otto Greulich http://www.mdpi.com/1422-0067/11/1/312/ Since biological membranes are composed of lipids and proteins we tested the in vitro antioxidant properties of several indoleamines from the tryptophan metabolic pathway in the pineal gland against oxidative damage to lipids and proteins of synaptosomes isolated from the rat brain. Free radicals were generated by incubation with 0.1 mM FeCl3, and 0.1 mM ascorbic acid. Levels of malondialdehyde (MDA) plus 4-hydroxyalkenal (4-HDA), and carbonyl content in the proteins were measured as indices of oxidative damage to lipids and proteins, respectively. Pinoline was the most powerful antioxidant evaluated, with melatonin, N-acetylserotonin, 5-hydroxytryptophan, 5-methoxytryptamine, 5-methoxytryptophol, and tryptoline also acting as antioxidants. http://www.mdpi.com/1422-0067/11/1/312/ Thu, 21 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-21 11 1 Article 312 328 1422-0067 Melatonin and Structurally-Related Compounds Protect Synaptosomal Membranes from Free Radical Damage 2010-01-21 doi: 10.3390/ijms11010312 Sergio Millán-Plano Eduardo Piedrafita Francisco J. Miana-Mena Lorena Fuentes-Broto Enrique Martínez-Ballarín Laura López-Pingarrón María A. Sáenz Joaquín J. García http://www.mdpi.com/1422-0067/11/1/288/ We report self-assembly and phase transition behavior of lower diamondoid molecules and their primary derivatives using molecular dynamics (MD) simulation and density functional theory (DFT) calculations. Two lower diamondoids (adamantane and diamantane), three adamantane derivatives (amantadine, memantine and rimantadine) and two artificial molecules (ADM•Na and DIM•Na) are studied separately in 125-molecule simulation systems. We performed DFT calculations to optimize their molecular geometries and obtained atomic electronic charges for the corresponding MD simulation, by which we predicted self-assembly structures and simulation trajectories for the seven different diamondoids and derivatives. Our radial distribution function and structure factor studies showed clear phase transitions and self-assemblies for the seven diamondoids and derivatives. http://www.mdpi.com/1422-0067/11/1/288/ Thu, 21 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-21 11 1 Article 288 303 1422-0067 Self-Assembly of Diamondoid Molecules and Derivatives (MD Simulations and DFT Calculations) 2010-01-21 doi: 10.3390/ijms11010288 Yong Xue G. Ali Mansoori http://www.mdpi.com/1422-0067/11/1/268/ Microcystins (MC) are potent hepatotoxins produced by the cyanobacteria of the genera Planktothrix, Microcystis, Aphanizomenon, Nostoc and Anabaena. These cyclic heptapeptides have strong affinity to serine/threonine protein phosphatases (PPs) thereby acting as an inhibitor of this group of enzymes. Through this interaction a cascade of events responsible for the MC cytotoxic and genotoxic effects in animal cells may take place. Moreover MC induces oxidative stress in animal cells and together with the inhibition of PPs, this pathway is considered to be one of the main mechanisms of MC toxicity. In recent years new insights on the key enzymes involved in the signal-transduction and toxicity have been reported demonstrating the complexity of the interaction of these toxins with animal cells. Key proteins involved in MC up-take, biotransformation and excretion have been identified, demonstrating the ability of aquatic animals to metabolize and excrete the toxin. MC have shown to interact with the mitochondria. The consequences are the dysfunction of the organelle, induction of reactive oxygen species (ROS) and cell apoptosis. MC activity leads to the differential expression/activity of transcriptional factors and protein kinases involved in the pathways of cellular differentiation, proliferation and tumor promotion activity. This activity may result from the direct inhibition of the protein phosphatases PP1 and PP2A. This review aims to summarize the increasing data regarding the molecular mechanisms of MC toxicity in animal systems, reporting for direct MC interacting proteins and key enzymes in the process of toxicity biotransformation/excretion of these cyclic peptides. http://www.mdpi.com/1422-0067/11/1/268/ Thu, 21 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-21 11 1 Review 268 287 1422-0067 Molecular Mechanisms of Microcystin Toxicity in Animal Cells 2010-01-21 doi: 10.3390/ijms11010268 Alexandre Campos Vitor Vasconcelos http://www.mdpi.com/1422-0067/11/1/254/ Dye-sensitized solar cells (DSSCs) were assembled by using the bougainvillea flowers, red turnip and the purple wild Sicilian prickly pear fruit juice extracts as natural sensitizers of TiO2 films. The yellow orange indicaxanthin and the red purple betacyanins are the main components in the cocktail of natural dyes obtained from these natural products. The best overall solar energy conversion efficiency of 1.7% was obtained, under AM 1.5 irradiation, with the red turnip extract, that showed a remarkable current density (Jsc = 9.5 mA/cm2) and a high IPCE value (65% at λ = 470 nm). Also the purple extract of the wild Sicilian prickly pear fruit showed interesting performances, with a Jsc of 9.4 mA/cm2, corresponding to a solar to electrical power conversion of 1.26%. http://www.mdpi.com/1422-0067/11/1/254/ Wed, 20 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-20 11 1 Article 254 267 1422-0067 Efficient Dye-Sensitized Solar Cells Using Red Turnip and Purple Wild Sicilian Prickly Pear Fruits 2010-01-20 doi: 10.3390/ijms11010254 Giuseppe Calogero Gaetano Di Marco Silvia Cazzanti Stefano Caramori Roberto Argazzi Aldo Di Carlo Carlo Alberto Bignozzi http://www.mdpi.com/1422-0067/11/1/233/ Different types of enzymes such as lipases, several phosphatases, dehydrogenases, oxidases, amylases and others are well suited for the reactions in SC-CO2. The stability and the activity of enzymes exposed to carbon dioxide under high pressure depend on enzyme species, water content in the solution and on the pressure and temperature of the reaction system. The three-dimensional structure of enzymes may be significantly altered under extreme conditions, causing their denaturation and consequent loss of activity. If the conditions are less adverse, the protein structure may be largely retained. Minor structural changes may induce an alternative active protein state with altered enzyme activity, specificity and stability. http://www.mdpi.com/1422-0067/11/1/233/ Tue, 19 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-19 11 1 Review 233 253 1422-0067 A Review on the Effects of Supercritical Carbon Dioxide on Enzyme Activity 2010-01-19 doi: 10.3390/ijms11010233 Zdenĕk Wimmer Marie Zarevúcka http://www.mdpi.com/1422-0067/11/1/222/ The extracellular signal-regulated kinase (ERK) pathway is a member of the mitogen-activated protein kinase (MAPK) superfamily, which is an important, highly conserved family of enzymes associated with cell membrane receptors and regulative targets. In the central nervous system, there is almost no mature neuronal proliferation and differentiation, but the regulation of MAPK and its upstream and downstream molecular pathways is still widespread, with the ERK signaling pathway being one of the most actively studied signal transduction pathways. It is activated by a variety of cell growth factors and substances which promote mitotic activity, and transmits extracellular signals from the cell surface to the nucleus, which transmission plays an important role in the process of cell proliferation and differentiation. In recent years, accumulating evidence has shown that the ERK signaling pathway has an important link with the higher functions of learning and memory. http://www.mdpi.com/1422-0067/11/1/222/ Wed, 13 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-13 11 1 Review 222 232 1422-0067 ERK in Learning and Memory: A Review of Recent Research 2010-01-13 doi: 10.3390/ijms11010222 Sheng Peng Yan Zhang Jiannan Zhang Hua Wang Bingxu Ren http://www.mdpi.com/1422-0067/11/1/206/ Recent advances in nanophotonics open the way for promising applications towards efficient single molecule fluorescence analysis. In this review, we discuss how photonic methods bring innovative solutions for two essential questions: how to detect a single molecule in a highly concentrated solution, and how to enhance the faint optical signal emitted per molecule? The focus is set primarily on the widely used technique of fluorescence correlation spectroscopy (FCS), yet the discussion can be extended to other single molecule detection methods. http://www.mdpi.com/1422-0067/11/1/206/ Wed, 13 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-13 11 1 Review 206 221 1422-0067 Photonic Methods to Enhance Fluorescence Correlation Spectroscopy and Single Molecule Fluorescence Detection 2010-01-13 doi: 10.3390/ijms11010206 Jérome Wenger Hervé Rigneault http://www.mdpi.com/1422-0067/11/1/164/ A novel type of high-pressure membrane reactor has been developed for hydrogenation in supercritical carbon dioxide (scCO2). The main objectives of the design of the reactor are the separate feeding of hydrogen and substrate in scCO2 for safe reactions in a continuous flow process, and to reduce the reaction time. By using this new reactor, hydrogenation of cinnamaldehyde into hydrocinnamaldehyde has been successfully carried out with 100% selectivity at 50 °C in 10 MPa (H2: 1 MPa, CO2: 9 MPa) with a flow rate of substrate ranging from 0.05 to 1.0 mL/min. http://www.mdpi.com/1422-0067/11/1/164/ Wed, 13 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-13 11 1 Communication 164 172 1422-0067 Development of a Novel Catalytic Membrane Reactor for Heterogeneous Catalysis in Supercritical CO2 2010-01-13 doi: 10.3390/ijms11010164 Nazrul M. Islam Maya Chatterjee Yutaka Ikushima Toshiro Yokoyama Hajime Kawanami http://www.mdpi.com/1422-0067/11/1/189/ Aqueous solutions of ethoxylated alcohols which form lyotropic liquid crystals at high concentrations (40–80%) were selected as model lubricating substances. Microscopic studies under polarized light and viscosity measurements were carried out in order to confirm the presence of liquid crystalline structures in the case of alcohol solutions with ethoxylation degrees of 3, 5, 7 and 10. Microscopic images and viscosity coefficient values characteristic of various mesophases were obtained. As expected, the viscosity of LLCs decreases considerably with an increase in shearing rate which is characteristic of liquid crystals being non-Newtonian liquids. Antiseizure properties were determined by means of a four-ball machine (T-02 Tester) and characterized by scuffing load (Pt), seizure load (Poz) and limiting pressure of seizure (poz). Alcohol ethoxylates forming mesophases in aqueous solutions have the strongest effect on the Pt values which are several times higher than those measured in the presence of water. Ethoxylates with higher degrees of ethoxylation exhibit higher values of scuffing load. Those changes have been interpreted as a result of higher cloud points at which those compounds lose their amphiphilic properties. In general, the presence of mesophases in the bulk phase and particularly in the surface phase may lead to the formation of a lubricant film which separates the frictionally cooperating elements of a friction pair. The antiseizure efficiency of alcohol solutions is highest up to the load value which does not exceed the scuffing load value. http://www.mdpi.com/1422-0067/11/1/189/ Tue, 12 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-12 11 1 Article 189 205 1422-0067 The Effect of Liquid Crystalline Structures on Antiseizure Properties of Aqueous Solutions of Ethoxylated Alcohols 2010-01-12 doi: 10.3390/ijms11010189 Marian Wlodzimierz Sulek Anna Bak http://www.mdpi.com/1422-0067/11/1/173/ The host-guest complexation between an Alexa 488 labelled adamantane derivative and β-cyclodextrin is studied by Fluorescence Correlation Spectroscopy (FCS). A 1:1 complex stoichiometry and a high association equilibrium constant of K = 5.2 × 104 M-1 are obtained in aqueous solution at 25 °C and pH = 6. The necessary experimental conditions are discussed. FCS proves to be an excellent method for the determination of stoichiometry and association equilibrium constant of this type of complexes, where both host and guest are nonfluorescent and which are therefore not easily amenable to standard fluorescence spectroscopic methods. http://www.mdpi.com/1422-0067/11/1/173/ Tue, 12 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-12 11 1 Article 173 188 1422-0067 Host-Guest Complexation Studied by Fluorescence Correlation Spectroscopy: Adamantane–Cyclodextrin Inclusion 2010-01-12 doi: 10.3390/ijms11010173 Daniel Granadero Jorge Bordello Maria Jesus Pérez-Alvite Mercedes Novo Wajih Al-Soufi http://www.mdpi.com/1422-0067/11/1/154/ Imagine devices or particles so small that they are invisible to the naked eye. Imagine that such entities could be used to patrol our bodies and autonomously augment endogenous defense and repair mechanisms. Imagine the defeat of illness at a fraction of the current costs. Bionanotechnology is the field of science that deals with just that: the development of imaging, tracking, targeting, sensing, diagnostic, and eventually therapeutic capabilities based on particles in the nanometer range, i.e., “nanoparticles”. Within the extensive group of nanoparticles, semiconducting quantum dots play a central and prominent role. Quantum dots excel at a myriad of physical properties, most notably their fluorescent properties, such as high quantum yield, photo-stability, broad absorption spectra, and their remarkable size-dependent emission-tunability. http://www.mdpi.com/1422-0067/11/1/154/ Tue, 12 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-12 11 1 Editorial 154 163 1422-0067 Quantum Dots—From Synthesis to Applications in Biomedicine and Life Sciences 2010-01-12 doi: 10.3390/ijms11010154 Gregor P.C. Drummen http://www.mdpi.com/1422-0067/11/1/140/ Transient forebrain or global ischemia induces cell death in vulnerable CA1 pyramidal neurons. A brief period of ischemia, i.e., ischemic preconditioning, affords CA1 neurons robust protection against a subsequent, more prolonged ischemic challenge. Using the four-vessel occlusion model, we established an ischemic preconditioning model in which rodents were subjected to 3 min of sublethal ischemia 48 h before a 15 min lethal ischemia. We showed that preconditioning attenuated the ischemia-induced neural cell death and DNA fragmentation in the hippocampal CA1 region. RT-PCR and western blot analysis showed that preconditioning prior to an ischemic insult significantly increased ASIC 2a mRNA and protein expression in comparison to the ischemic insult alone (p < 0.01). These findings implicate a new role of ASIC 2a on endogenous neuroprotection from ischemic insult. http://www.mdpi.com/1422-0067/11/1/140/ Tue, 12 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-12 11 1 Article 140 153 1422-0067 Neuroprotective Effects of Ischemic Preconditioning on Global Brain Ischemia through Up-Regulation of Acid-Sensing Ion Channel 2a 2010-01-12 doi: 10.3390/ijms11010140 Yifeng Miao Weiqiao Zhang Yuchang Lin Xiaojie Lu Yongming Qiu http://www.mdpi.com/1422-0067/11/1/124/ The genetic variation found in small regions of the genomes of many species can be arranged into haplotype trees that reflect the evolutionary genealogy of the DNA lineages found in that region and the accumulation of mutations on those lineages. This review demonstrates some of the many ways in which clades (branches) of haplotype trees have been applied in recent years, including the study of genotype/phenotype associations at candidate loci and in genome-wide association studies, the phylogeographic history of species, human evolution, the conservation of endangered species, and the identification of species. http://www.mdpi.com/1422-0067/11/1/124/ Fri, 08 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-08 11 1 Review 124 139 1422-0067 The Diverse Applications of Cladistic Analysis of Molecular Evolution, with Special Reference to Nested Clade Analysis 2010-01-08 doi: 10.3390/ijms11010124 Alan R. Templeton http://www.mdpi.com/1422-0067/11/1/107/ Standardized extract from the leaves of the Ginkgo biloba tree, labeled EGb761, is one of the most popular herbal supplements. Numerous preclinical studies have shown the neuroprotective effects of EGb761 and support the notion that it may be effective in the treatment and prevention of neurodegenerative disorders such as Alzheimer’s disease (AD). Despite the preclinical promise, the clinical efficacy of this drug remains elusive. In this review, possible mechanisms underlying neuroprotective actions of EGb761 are described in detail, together with a brief discussion of the problem of studying this herb clinically to verify its efficacy in the treatment and prevention of AD. Moreover, various parameters e.g., the dosage and the permeability of the blood brain barrier (BBB), impacting the outcome of the clinical effectiveness of the extract are also discussed. Overall, the findings summarized in this review suggest that, a better understanding of the neuroprotective mechanisms of EGb761 may contribute to better understanding of the effectiveness and complexity of this herb and may also be helpful for design of therapeutic strategies in future clinical practice. Therefore, in future clinical studies, different factors that could interfere with the effect of EGb761 should be considered. http://www.mdpi.com/1422-0067/11/1/107/ Fri, 08 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-08 11 1 Review 107 123 1422-0067 Ginkgo biloba Extract in Alzheimer’s Disease: From Action Mechanisms to Medical Practice 2010-01-08 doi: 10.3390/ijms11010107 Chun Shi Jun Liu Fengming Wu David T. Yew http://www.mdpi.com/1422-0067/11/1/79/ Plant tannins, including hydrolysable and condensed varieties, are well known antioxidants in medicinal plants, foods, and edible fruits. Their diverse biological properties and potential for disease prevention have been demonstrated by various in vitro and in vivo assays. A number of ellagitannins, the largest group of hydrolysable tannins, have been isolated from dicotyledoneous angiosperms and characterized. This diverse class of tannins is sub-grouped into simple ellagitannins, C-glycosidic ellagitannins, complex tannins (condensates of C-glycosidic tannins with flavan-3-ol), and oligomers up to pentamers. This review outlines and describes the chemotaxonomic significance of structural features in various types of ellagitannins found in plants belonging to the Myrtaceae, Onagraceae, and Melastomataceae families, which are all included in the order Myrtales. Any biological activities that have been reported, including antitumor and antibacterial effects as well as enzyme inhibition, are also reviewed. http://www.mdpi.com/1422-0067/11/1/79/ Wed, 06 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-06 11 1 Review 79 106 1422-0067 Structural Features and Biological Properties of Ellagitannins in Some Plant Families of the Order Myrtales 2010-01-06 doi: 10.3390/ijms11010079 Takashi Yoshida Yoshiaki Amakura Morio Yoshimura http://www.mdpi.com/1422-0067/11/1/67/ Dandelion (Taraxacum officinale), an oriental herbal medicine, has been shown to favorably affect choleretic, antirheumatic and diuretin properties. Recent reports have indicated that excessive oxidative stress contributes to the development of atherosclerosislinked metabolic syndrome. The objective of this current study was to investigate the possible hypolipidemic and antioxidative effects of dandelion root and leaf in rabbits fed with a high-cholesterol diet. A group of twenty eight male rabbits was divided into four subgroups; a normal diet group, a high-cholesterol diet group, a high-cholesterol diet with 1% (w/w) dandelion leaf group, and a high-cholesterol diet with 1% (w/w) dandelion root group. After the treatment period, the plasma antioxidant enzymes and lipid profiles were determined. Our results show that treatment with dandelion root and leaf positively changed plasma antioxidant enzyme activities and lipid profiles in cholesterol-fed rabbits, and thus may have potential hypolipidemic and antioxidant effects. Dandelion root and leaf could protect against oxidative stress linked atherosclerosis and decrease the atherogenic index. http://www.mdpi.com/1422-0067/11/1/67/ Wed, 06 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-06 11 1 Article 67 78 1422-0067 Hypolipidemic and Antioxidant Effects of Dandelion (Taraxacum officinale) Root and Leaf on Cholesterol-Fed Rabbits 2010-01-06 doi: 10.3390/ijms11010067 Ung-Kyu Choi Ok-Hwan Lee Joo Hyuk Yim Chang-Won Cho Young Kyung Rhee Seong-Il Lim Young-Chan Kim http://www.mdpi.com/1422-0067/11/1/52/ Many kinds of stimuli-responsive polymer and gels have been developed and applied to biomimetic actuators or artificial muscles. Electroactive polymers that change shape when stimulated electrically seem to be particularly promising. In all cases, however, the mechanical motion is driven by external stimuli, for example, reversing the direction of electric field. On the other hand, many living organisms can generate an autonomous motion without external driving stimuli like self-beating of heart muscles. Here we show a novel biomimetic gel actuator that can walk spontaneously with a wormlike motion without switching of external stimuli. The self-oscillating motion is produced by dissipating chemical energy of oscillating reaction. Although the gel is completely composed of synthetic polymer, it shows autonomous motion as if it were alive. http://www.mdpi.com/1422-0067/11/1/52/ Tue, 05 Jan 2010 00:00:00 CET International Journal of Molecular Sciences 2010-01-05 11 1 Review 52 66 1422-0067 Active Polymer Gel Actuators 2010-01-05 doi: 10.3390/ijms11010052 Shingo Maeda Yusuke Hara Ryo Yoshida Shuji Hashimoto http://www.mdpi.com/1422-0067/11/1/41/ Different concentrations of asafoetida extract were added to the medium of Pleurotus ferulic and the effects of the extract on growth of P. ferulic mycelium and fruiting bodies was observed. As the amount of asafoetida extract additive was increased, the growth of Pleurotus mycelium was faster, the time formation of buds was shorter and that yield of fruiting bodies was stimulated. However, overdosing of asafoetida extract hampered the growth of Pleurotus ferulic. The amino acid composition and volatile components in three kinds of pleurotus’ were contrasted, including wild pleurotus (WP), cultivated pleurotus with asafoetida extract (CPAE) and cultivated pleurotus without asafoetida extract (CP). CPAE with 2.3 g/100 g asafoetida extract addition had the highest content of total amino acids, as well as essential amino acids. WP had a higher content of total amino acids and essential amino acids than CP. In addition, CPAE with 2.3 g/100 g had the highest score of protein content of pleurotus fruiting bodies, while WP had a higher score than CP. In the score of essential amino acid components of pleurotus fruiting bodies, CP had the highest score, while CPAE was higher than WP. Asafoetida extract influenced the volatile components of Pleurotus ferulic greatly, making the volatile components of cultivated pleurotus more similar to those of wild pleurotus (WP). http://www.mdpi.com/1422-0067/11/1/41/ Tue, 29 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-29 11 1 Article 41 51 1422-0067 Effect of Asafoetida Extract on Growth and Quality of Pleurotus ferulic 2009-12-29 doi: 10.3390/ijms11010041 Zuoshan Feng Yujia Bai Fanglin Lu Wenshu Huang Xinmin Li Xiaosong Hu http://www.mdpi.com/1422-0067/11/1/14/ This review will discuss recent progress in the chemistry of secondary polyphenols produced during food processing. The production mechanism of the secondary polyphenols in black tea, whisky, cinnamon, and persimmon fruits will be introduced. In the process of black tea production, tea leaf catechins are enzymatically oxidized to yield a complex mixture of oxidation products, including theaflavins and thearubigins. Despite the importance of the beverage, most of the chemical constituents have not yet been confirmed due to the complexity of the mixture. However, the reaction mechanisms at the initial stages of catechin oxidation are explained by simple quinone–phenol coupling reactions. In vitro model experiments indicated the presence of interesting regio- and stereoselective reactions. Recent results on the reaction mechanisms will be introduced. During the aging of whisky in oak wood barrels, ellagitannins originating from oak wood are oxidized and react with ethanol to give characteristic secondary ellagitannins. The major part of the cinnamon procyanidins is polymerized by copolymerization with cinnamaldehyde. In addition, anthocyanidin structural units are generated in the polymer molecules by oxidation which accounts for the reddish coloration of the cinnamon extract. This reaction is related to the insolubilization of proanthocyanidins in persimmon fruits by condensation with acetaldehyde. In addition to oxidation, the reaction of polyphenols with aldehydes may be important in food processing. http://www.mdpi.com/1422-0067/11/1/14/ Mon, 28 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-28 11 1 Review 14 40 1422-0067 Chemistry of Secondary Polyphenols Produced during Processing of Tea and Selected Foods 2009-12-28 doi: 10.3390/ijms11010014 Takashi Tanaka Yosuke Matsuo Isao Kouno http://www.mdpi.com/1422-0067/11/1/1/ Chalcones exhibit chemopreventive and antitumor effects. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a naturally occurring anticancer agent that induces apoptosis in cancer cells and is not toxic to normal cells. We examined the cytotoxic and apoptotic effect of five chalcones in combination with TRAIL on prostate cancer cells. The cytotoxicity was evaluated by the MTT and LDH assays. The apoptosis was determined using flow cytometry with annexin V-FITC. Our study showed that all five tested chalcones: chalcone, licochalcone-A, isobavachalcone, xanthohumol, butein markedly augmented TRAIL-mediated apoptosis and cytotoxicity in prostate cancer cells and confirmed the significant role of chalcones in chemoprevention of prostate cancer. http://www.mdpi.com/1422-0067/11/1/1/ Thu, 24 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-24 11 1 Article 1 13 1422-0067 Chalcones Enhance TRAIL-Induced Apoptosis in Prostate Cancer Cells 2009-12-24 doi: 10.3390/ijms11010001 Ewelina Szliszka Zenon P. Czuba Bogdan Mazur Lukasz Sedek Andrzej Paradysz Wojciech Krol http://www.mdpi.com/1422-0067/10/12/5513/ Phenolic compounds were extracted from red lentil seeds using 80% (v/v) aqueous acetone. The crude extract was applied to a Sephadex LH-20 column. Fraction 1, consisting of sugars and low-molecular-weight phenolics, was eluted from the column by ethanol. Fraction 2, consisting of tannins, was obtained using acetone-water (1:1; v/v) as the mobile phase. Phenolic compounds present in the crude extract and its fractions demonstrated antioxidant and antiradical activities as revealed from studies using a β-carotene-linoleate model system, the total antioxidant activity (TAA) method, the DPPH radical-scavenging activity assay, and a reducing power evaluation. Results of these assays showed the highest values when tannins (fraction 2) were tested. For instance, the TAA of the tannin fraction was 5.85 μmol Trolox® eq./mg, whereas the crude extract and fraction 1 showed 0.68 and 0.33 μmol Trolox® eq./mg, respectively. The content of total phenolics in fraction 2 was the highest (290 mg/g); the tannin content, determined using the vanillin method and expressed as absorbance units at 500 nm per 1 g, was 129. There were 24 compounds identified in the crude extract using an HPLC-ESI-MS method: quercetin diglycoside, catechin, digallate procyanidin, and p-hydroxybenzoic were the dominant phenolics in the extract. http://www.mdpi.com/1422-0067/10/12/5513/ Wed, 23 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-23 10 12 Article 5513 5527 1422-0067 Antioxidant Activity of a Red Lentil Extract and Its Fractions 2009-12-23 doi: 10.3390/ijms10125513 Ryszard Amarowicz Isabell Estrella Teresa Hernández Montserrat Dueñas Agnieszka Troszyńska Agnieszka Kosińska Ronald B. Pegg http://www.mdpi.com/1422-0067/10/12/5498/ Hyperthermophilic superoxide dismutases (SODs) are of particular interest due to their potential industrial importance and scientific merit in studying the molecular mechanisms of protein folding and stability. Compared to the mesophilic SODs, the hyperthermostable Fe-SODs (TcSOD and ApSOD) have an extended C-terminal helix, which forms an additional ion-pairing network. In this research, the role of the extended C-terminus in the structural stability of TcSOD was studied by investigating the properties of two deletion mutants. The results indicated that the ion-pairing network at the C-terminus had limited contributions to the stability of TcSOD against heat- and GdnHClinduced inactivation. The intactness of the C-terminal helix had dissimilar impact on the two stages of TcSOD unfolding induced by guanidinium chloride. The mutations slightly decreased the Gibbs free energy of the dissociation of the tetrameric enzymes, while greatly affected the stability of the molten globule-like intermediate. These results suggested that the additional ion-pairing network mainly enhanced the structural stability of TcSOD by stabilizing the monomers. http://www.mdpi.com/1422-0067/10/12/5498/ Wed, 23 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-23 10 12 Article 5498 5512 1422-0067 Contributions of the C-Terminal Helix to the Structural Stability of a Hyperthermophilic Fe-Superoxide Dismutase (TcSOD) 2009-12-23 doi: 10.3390/ijms10125498 Sha Wang Yong-Bin Yan Zhi-Yang Dong http://www.mdpi.com/1422-0067/10/12/5485/ The tannin fractions isolated from hazelnuts, walnuts and almonds were characterised by colorimetric assays and by an SE-HPLC technique. The complexation of Cu(II) and Zn(II) was determined by the reaction with tetramethylmurexide, whereas for Fe(II), ferrozine was employed. The walnut tannins exhibited a significantly weaker reaction with the vanillin/HCl reagent than hazelnut and almond tannins, but the protein precipitation capacity of the walnut fraction was high. The SE-HPLC chromatogram of the tannin fraction from hazelnuts revealed the presence of oligomers with higher molecular weights compared to that of almonds. Copper ions were most effectively chelated by the constituents of the tannin fractions of hazelnuts, walnuts and almonds. At a 0.2 mg/assay addition level, the walnut tannins complexed almost 100% Cu(II). The Fe(II) complexation capacities of the tannin fractions of walnuts and hazelnuts were weaker in comparison to that of the almond tannin fraction, which at a 2.5 mg/assay addition level, bound Fe(II) by ~90%. The capacity to chelate Zn(II) was quite varied for the different nut tannin fractions: almond tannins bound as much as 84% Zn(II), whereas the value for walnut tannins was only 8.7%; and for hazelnut tannins, no Zn(II) chelation took place at the levels tested. http://www.mdpi.com/1422-0067/10/12/5485/ Tue, 22 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-22 10 12 Article 5485 5497 1422-0067 Chelation of Cu(II), Zn(II), and Fe(II) by Tannin Constituents of Selected Edible Nuts 2009-12-22 doi: 10.3390/ijms10125485 Magdalena Karamać http://www.mdpi.com/1422-0067/10/12/5471/ Macrocyclic trichothecenes, mycotoxins produced by Stachybotrys chartarum, have been implicated in adverse reactions in individuals exposed to mold-contaminated environments. Cellular and humoral immune responses and the presence of trichothecenes were evaluated in patients with mold-related health complaints. Patients underwent history, physical examination, skin prick/puncture tests with mold extracts, immunological evaluations and their sera were analyzed for trichothecenes. T-cell proliferation, macrocyclic trichothecenes, and mold specific IgG and IgA levels were not significantly different than controls; however 70% of the patients had positive skin tests to molds. Thus, IgE mediated or other non-immune mechanisms could be the cause of their symptoms. http://www.mdpi.com/1422-0067/10/12/5471/ Mon, 21 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-21 10 12 Article 5471 5484 1422-0067 Immune Response among Patients Exposed to Molds 2009-12-21 doi: 10.3390/ijms10125471 David A. Edmondson Christy S. Barrios Trevor L. Brasel David C. Straus Viswanath P. Kurup Jordan N. Fink http://www.mdpi.com/1422-0067/10/12/5455/ Genealogical concordance is a critical overlay of all phylogenetic analyses, irrespective of taxonomic level. To assess such patterns of congruence we have compiled and derived sequence data for two mitochondrial (16S rRNA, COI) and two nuclear (ITS1, p26) markers in 14 American populations of the hypersaline branchiopod Artemia franciscana. Cladistic analysis revealed three reciprocally monophyletic mitochondrial clades. For nuclear DNA, incomplete lineage sorting was evident presumably as a result of slower coalescence or male-mediated dispersal. Our findings capture the genealogical interval between gene splitting and population divergence. In this sense, strong indications are provided in favour of a superspecies status and ongoing speciation in A. franciscana. http://www.mdpi.com/1422-0067/10/12/5455/ Fri, 18 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-18 10 12 Article 5455 5470 1422-0067 Sharp Phylogeographic Breaks and Patterns of Genealogical Concordance in the Brine Shrimp Artemia franciscana 2009-12-18 doi: 10.3390/ijms10125455 Stefania Maniatsi Ilias Kappas Athanasios D. Baxevanis Theodora Farmaki Theodore J. Abatzopoulos http://www.mdpi.com/1422-0067/10/12/5442/ Objective: To demonstrate the inhibitory function of the prodomain of tumor necrosis factor-α (TNF-α) converting enzyme (TACE) on TACE activity and to develop an approach to interfere with inflammation processes. Methods: The cDNA encoding the fulllength ectodomain (T1300) and prodomain (T591) of TACE were amplified by RT-PCR. The expression plasmids (pET-28a (+)-T1300 and pET-28a (+)-T591) were constructed and transformed into E. coli BL21. After Ni2+-NTA resin affinity chromatography, the recombinant T591 protein was obtained and assayed. In order to detect its inhibiton of TACE activity, the mice in the LPS-induced endotoxemia model group were treated with the recombinant TACE prodomain protein prior to the injection of LPS. Murine peritoneal macrophages were isolated from mice abdominal cavity for FCM and the liver, kidney and lung were removed for traditionally histopathology sectioning. Results: The FCM results showed that the recombinant prodomain protein decreased the release of the sTNF-α, which mediated the accumulation of TNF-α on the surface of macrophage cells. HE staining proved that the recombinant protein can decrease the inflammatory response in internal organs of endotoxaemia mice. Conclusions: The recombinant prodomain of TACE has the ability to inhibit sTNF-α release, which indicates that prodomain is an effective antagonist of TACE and might be useful in the molecular design of anti-inflammatory drugs. http://www.mdpi.com/1422-0067/10/12/5442/ Fri, 18 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-18 10 12 Article 5442 5454 1422-0067 The Study of the Inhibition of the Recombinant TACE Prodomain to Endotoxemia in Mice 2009-12-18 doi: 10.3390/ijms10125442 Xiaoou Li Yuan Yan Wei Huang Yuzhen Yang http://www.mdpi.com/1422-0067/10/12/5411/ Microfabricated systems provide an excellent platform for the culture of cells, and are an extremely useful tool for the investigation of cellular responses to various stimuli. Advantages offered over traditional methods include cost-effectiveness, controllability, low volume, high resolution, and sensitivity. Both biocompatible and bioincompatible materials have been developed for use in these applications. Biocompatible materials such as PMMA or PLGA can be used directly for cell culture. However, for bioincompatible materials such as silicon or PDMS, additional steps need to be taken to render these materials more suitable for cell adhesion and maintenance. This review describes multiple surface modification strategies to improve the biocompatibility of MEMS materials. Basic concepts of cell-biomaterial interactions, such as protein adsorption and cell adhesion are covered. Finally, the applications of these MEMS materials in Tissue Engineering are presented. http://www.mdpi.com/1422-0067/10/12/5411/ Fri, 18 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-18 10 12 Review 5411 5441 1422-0067 Cell Culture on MEMS Platforms: A Review 2009-12-18 doi: 10.3390/ijms10125411 Ming Ni Wen Hao Tong Deepak Choudhury Nur Aida Abdul Rahim Ciprian Iliescu Hanry Yu http://www.mdpi.com/1422-0067/10/12/5398/ Dihydrofolate reductase (DHFR) is the subject of intensive investigation since it appears to be the primary target enzyme for antifolate drugs. Fluorescence quenching experiments show that the ester bond-containing tea polyphenols (-)-epigallocatechin gallate (EGCG) and (-)-epicatechin gallate (ECG) are potent inhibitors of DHFR with dissociation constants (KD) of 0.9 and 1.8 μM, respectively, while polyphenols lacking the ester bound gallate moiety [e.g., (-)-epigallocatechin (EGC) and (-)-epicatechin (EC)] did not bind to this enzyme. To avoid stability and bioavailability problems associated with tea catechins we synthesized a methylated derivative of ECG (3-O-(3,4,5-trimethoxybenzoyl)-(-)-epicatechin; TMECG), which effectively binds to DHFR (KD = 2.1 μM). In alkaline solution, TMECG generates a stable quinone methide product that strongly binds to the enzyme with a KD of 8.2 nM. Quercetin glucuronides also bind to DHFR but its effective binding was highly dependent of the sugar residue, with quercetin-3-xyloside being the stronger inhibitor of the enzyme with a KD of 0.6 μM. The finding that natural polyphenols are good inhibitors of human DHFR could explain the epidemiological data on their prophylactic effects for certain forms of cancer and open a possibility for the use of natural and synthetic polyphenols in cancer chemotherapy. http://www.mdpi.com/1422-0067/10/12/5398/ Fri, 18 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-18 10 12 Article 5398 5410 1422-0067 Binding of Natural and Synthetic Polyphenols to Human Dihydrofolate Reductase 2009-12-18 doi: 10.3390/ijms10125398 Luís Sánchez-del-Campo Magalí Sáez-Ayala Soledad Chazarra Juan Cabezas-Herrera José Neptuno Rodríguez-López http://www.mdpi.com/1422-0067/10/12/5381/ The crystallization and melting behaviors of linear polylactic acid (PLA) treated by compressed CO2 was investigated. The isothermal crystallization test indicated that while PLA exhibited very low crystallization kinetics under atmospheric pressure, CO2 exposure significantly increased PLA’s crystallization rate; a high crystallinity of 16.5% was achieved after CO2 treatment for only 1 min at 100 °C and 6.89 MPa. One melting peak could be found in the DSC curve, and this exhibited a slight dependency on treatment times, temperatures, and pressures. PLA samples tended to foam during the gas release process, and a foaming window as a function of time and temperature was established. Based on the foaming window, crystallinity, and cell morphology, it was found that foaming clearly reduced the needed time for PLA’s crystallization equilibrium. http://www.mdpi.com/1422-0067/10/12/5381/ Wed, 16 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-16 10 12 Article 5381 5397 1422-0067 A Study of the Crystallization, Melting, and Foaming Behaviors of Polylactic Acid in Compressed CO2 2009-12-16 doi: 10.3390/ijms10125381 Wentao Zhai Yoorim Ko Wenli Zhu Anson Wong Chul B. Park http://www.mdpi.com/1422-0067/10/12/5370/ The effects of genetic, pre-harvest (season of harvest, spear diameter, spear portion and spear tip color) and post-harvest factors (storage and domestic preparation practices, e.g., peeling and cooking) on total phenolic, flavonoid and ascorbic acid content of white asparagus spears and their correlation with antioxidant capacity (DPPH and FRAP) were studied. Results showed that genetic material was important for the total phenolic content but not season of harvest, spear diameter or storage. Violet spear tips and apical spear portions showed the largest amount of total phenolics. Peeling did not affect total phenolics in fresh asparagus, whereas it reduced their content in stored asparagus, while cooking resulted in an increase in both fresh and stored asparagus. However, the soluble extract of total phenolics and flavonoids were minor and the missing significance of phenolics and flavonoids in antioxidant capacity of white asparagus spears depends on these small amounts. http://www.mdpi.com/1422-0067/10/12/5370/ Wed, 16 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-16 10 12 Article 5370 5380 1422-0067 Effects of Genetic, Pre- and Post-Harvest Factors on Phenolic Content and Antioxidant Capacity of White Asparagus Spears 2009-12-16 doi: 10.3390/ijms10125370 Eleftherios Papoulias Anastasios S. Siomos Athanasios Koukounaras Dimitrios Gerasopoulos Evangelos Kazakis http://www.mdpi.com/1422-0067/10/12/5350/ Genetically-modified, colour-altered varieties of the important cut-flower crop carnation have now been commercially available for nearly ten years. In this review we describe the manipulation of the anthocyanin biosynthesis pathway that has lead to the development of these varieties and how similar manipulations have been successfully applied to both pot plants and another cut-flower species, the rose. From this experience it is clear that down- and up-regulation of the flavonoid and anthocyanin pathway is both possible and predictable. The major commercial benefit of the application of this technology has so far been the development of novel flower colours through the development of transgenic varieties that produce, uniquely for the target species, anthocyanins derived from delphinidin. These anthocyanins are ubiquitous in nature, and occur in both ornamental plants and common food plants. Through the extensive regulatory approval processes that must occur for the commercialization of genetically modified organisms, we have accumulated considerable experimental and trial data to show the accumulation of delphinidin based anthocyanins in the transgenic plants poses no environmental or health risk. http://www.mdpi.com/1422-0067/10/12/5350/ Tue, 15 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-15 10 12 Review 5350 5369 1422-0067 Recent Progress of Flower Colour Modification by Biotechnology 2009-12-15 doi: 10.3390/ijms10125350 Yoshikazu Tanaka Filippa Brugliera Steve Chandler http://www.mdpi.com/1422-0067/10/12/5326/ Skin whitening products are commercially available for cosmetic purposes in order to obtain a lighter skin appearance. They are also utilized for clinical treatment of pigmentary disorders such as melasma or postinflammatory hyperpigmentation. Whitening agents act at various levels of melanin production in the skin. Many of them are known as competitive inhibitors of tyrosinase, the key enzyme in melanogenesis. Others inhibit the maturation of this enzyme or the transport of pigment granules (melanosomes) from melanocytes to surrounding keratinocytes. In this review we present an overview of (natural) whitening products that may decrease skin pigmentation by their interference with the pigmentary processes. http://www.mdpi.com/1422-0067/10/12/5326/ Thu, 10 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-10 10 12 Review 5326 5349 1422-0067 The Hunt for Natural Skin Whitening Agents 2009-12-10 doi: 10.3390/ijms10125326 Nico Smit Jana Vicanova Stan Pavel http://www.mdpi.com/1422-0067/10/12/5296/ We have performed a detailed study of the thermodynamics of the titration Process in an isothermal titration calorimeter with full cells. We show that the relationship between the enthalpy and the heat measured is better described in terms of the equation ΔH = Winj + Q (where Winj is the work necessary to carry out the titration) than in terms of ΔH = Q. Moreover, we show that the heat of interaction between two components is related to the partial enthalpy of interaction at infinite dilution of the titrant component, as well as to its partial volume of interaction at infinite dilution. http://www.mdpi.com/1422-0067/10/12/5296/ Wed, 09 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-09 10 12 Article 5296 5325 1422-0067 On the Physical Meaning of the Isothermal Titration Calorimetry Measurements in Calorimeters with Full Cells 2009-12-09 doi: 10.3390/ijms10125296 Jean-Pierre E. Grolier Jose Manuel del Río http://www.mdpi.com/1422-0067/10/12/5285/ The effects of microwave irradiation (2.45 GHz, 200 W) on glycosylation promoted by a solid super acid in supercritical carbon dioxide was investigated with particular attention paid to the structure of the acceptor substrate. Because of the symmetrical structure and high diffusive property of supercritical carbon dioxide, microwave irradiation did not alter the temperature of the reaction solution, but enhanced reaction yield when aliphatic acceptors are employed. Interestingly, the use of a phenolic acceptor under the same reaction conditions did not show these promoting effects due to microwave irradiation. In the case of aliphatic diol acceptors, the yield seemed to be dependent on the symmetrical properties of the acceptors. The results suggest that microwave irradiation do not affect the reactivity of the donor nor promoter independently. We conclude that the effect of acceptor structure on glycosylation yield is due to electric delocalization of hydroxyl group and dielectrically symmetric structure of whole molecule. http://www.mdpi.com/1422-0067/10/12/5285/ Tue, 08 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-08 10 12 Article 5285 5295 1422-0067 Microwave Effect for Glycosylation Promoted by Solid Super Acid in Supercritical Carbon Dioxide 2009-12-08 doi: 10.3390/ijms10125285 Hiroshi Hinou Naohiro Saito Masato Ogawa Takahiko Maeda Shin-Ichiro Nishimura http://www.mdpi.com/1422-0067/10/12/5257/ This review covers recent advances and work on the microstructure features, mechanical properties and cracking processes of conducting polymer film/coatingsubstrate structures under different testing conditions. An attempt is made to characterize and quantify the relationships between mechanical properties and microstructure features. In addition, the film cracking mechanism on the micro scale and some influencing factors that play a significant role in the service of the film-substrate structure are presented. These investigations cover the conducting polymer film/coating nucleation process, microstructure-fracture characterization, translation of brittle-ductile fractures, and cracking processes near the largest inherent macromolecule defects under thermal-mechanical loadings, and were carried out using in situ scanning electron microscopy (SEM) observations, as a novel method for evaluation of interface strength and critical failure stress. http://www.mdpi.com/1422-0067/10/12/5257/ Tue, 08 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-08 10 12 Review 5257 5284 1422-0067 Investigations on the Mechanical Properties of Conducting Polymer Coating-Substrate Structures and Their Influencing Factors 2009-12-08 doi: 10.3390/ijms10125257 Xi-Shu Wang Hua-Ping Tang Xu-Dong Li Xin Hua http://www.mdpi.com/1422-0067/10/12/5239/ Nanoassemblies are formed via self-assembly of ZnS capped CdSe quantum dots (QD) and perylene bisimide (PBI) dyes. Upon assembly formation the QD photoluminescence is quenched, as can be detected both via single particle detection and ensemble experiments in solution. Quenching has been assigned to FRET and NON-FRET processes. Analysis of FRET allows for a distinction between different geometries of the QD dye assemblies. Time-resolved single molecule spectroscopy reveals intrinsic fluctuations of the PBI fluorescence lifetime and spectrum, caused by rearrangement of the phenoxy side groups. The distribution of such molecular conformations and their changed dynamics upon assembly formation are discussed in the scope of FRET efficiency and surface ligand density. http://www.mdpi.com/1422-0067/10/12/5239/ Tue, 01 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-01 10 12 Article 5239 5256 1422-0067 Identification of Different Donor-Acceptor Structures via Förster Resonance Energy Transfer (FRET) in Quantum-Dot-Perylene Bisimide Assemblies 2009-12-01 doi: 10.3390/ijms10125239 Danny Kowerko Stefan Krause Nicole Amecke Mohamed Abdel-Mottaleb Jörg Schuster Christian von Borczyskowski http://www.mdpi.com/1422-0067/10/12/5224/ Two varieties of foxtail millet protein concentrates (white and yellow) were characterized for in vitro trypsin digestibility, functional and physicochemical properties. Millet protein concentrate was easily digested by trypsin in vitro. Essential amino acids were above the amounts recommended by the Food Agricultural Organization/World Health Organization (FAO/WHO/UNU) for humans. Yellow millet protein concentrate (YMPC) possessed the highest differential scanning calorimetry result (peak temperature of 88.98 °C, delta H = 0.01 J/g), white millet protein concentrate (WMPC) had the lowest (peak temperature 84.06 °C, delta H = 0.10 J/g). The millet protein concentrates had molecular sizes around 14.4 and 97.4 kDa. They have U-shape solubility curves. Waterbinding capacity was in the range of 5.0 and 7.0 g/g, while oil absorption capacity ranged between 4.8 and 5.9 g/g. WMPC had higher bulk density (0.22 g/mL) and emulsifying capacity than YMPC and Soy Protein Concentrate (SPC). Foam capacity and foam stability ranged from 137 to 73 g/mL for WMPC, from 124 to 61 g/mL SPC and from 124 to 46 g/mL for YMPC. Millet protein concentrates are potential functional food ingredients. http://www.mdpi.com/1422-0067/10/12/5224/ Tue, 01 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-01 10 12 Article 5224 5238 1422-0067 Functionality, in Vitro Digestibility and Physicochemical Properties of Two Varieties of Defatted Foxtail Millet Protein Concentrates 2009-12-01 doi: 10.3390/ijms10125224 Tabita Kamara Mohamed Kexue Zhu Amadou Issoufou Tarawalie Fatmata Huiming Zhou http://www.mdpi.com/1422-0067/10/12/5217/ The use of enzymes in supercritical CO2 (SCCO2) has received extensive attention in recent years. Biocatalysts have the advantage of substrate specificity and SCCO2 offers several advantages over liquid solvents. This work deals with the utilization of SCCO2 as a medium for the enzymatic removal of phenol from aqueous solutions using tyrosinase. Since the presence of oxygen is crucial for the enzyme-catalyzed oxidation, the substantial solvating power of SCCO2 makes it a promising medium for such reactions. The conversion of phenol was higher at 10 MPa. Under near critical conditions (7 MPa, 35 ºC), the addition of air at 5 × 105 Pa of pressure improved phenol removal. http://www.mdpi.com/1422-0067/10/12/5217/ Tue, 01 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-01 10 12 Article 5217 5223 1422-0067 Enzymatic Reactions in Near Critical CO2: The Effect of Pressure on Phenol Removal by Tyrosinase 2009-12-01 doi: 10.3390/ijms10125217 Priscilla Amaral Daniela Garcia Miguel Cardoso Marisa Mendes Maria Alice Coelho Fernando Pessoa http://www.mdpi.com/1422-0067/10/12/5135/ This review discusses several computational methods used on different length and time scales for the simulation of material behavior. First, the importance of physical modeling and its relation to computer simulation on multiscales is discussed. Then, computational methods used on different scales are shortly reviewed, before we focus on the molecular dynamics (MD) method. Here we survey in a tutorial-like fashion some key issues including several MD optimization techniques. Thereafter, computational examples for the capabilities of numerical simulations in materials research are discussed. We focus on recent results of shock wave simulations of a solid which are based on two different modeling approaches and we discuss their respective assets and drawbacks with a view to their application on multiscales. Then, the prospects of computer simulations on the molecular length scale using coarse-grained MD methods are covered by means of examples pertaining to complex topological polymer structures including star-polymers, biomacromolecules such as polyelectrolytes and polymers with intrinsic stiffness. This review ends by highlighting new emerging interdisciplinary applications of computational methods in the field of medical engineering where the application of concepts of polymer physics and of shock waves to biological systems holds a lot of promise for improving medical applications such as extracorporeal shock wave lithotripsy or tumor treatment. http://www.mdpi.com/1422-0067/10/12/5135/ Tue, 01 Dec 2009 00:00:00 CET International Journal of Molecular Sciences 2009-12-01 10 12 Review 5135 5216 1422-0067 A Review of Computational Methods in Materials Science: Examples from Shock-Wave and Polymer Physics 2009-12-01 doi: 10.3390/ijms10125135 Martin O. Steinhauser Stefan Hiermaier http://www.mdpi.com/1422-0067/10/12/5115/ This paper deals with the effect of interface structures on the mechanical properties of fiber reinforced composite materials. First, the background of research, development and applications on hybrid composite materials is introduced. Second, metal/polymer composite bonded structures are discussed. Then, the rationale is given for nanostructuring the interface in composite materials and structures by introducing nanoscale features such as nanopores and nanofibers. The effects of modifying matrices and nano-architecturing interfaces on the mechanical properties of nanocomposite materials are examined. A nonlinear damage model for characterizing the deformation behavior of polymeric nanocomposites is presented and the application of this model to carbon nanotube-reinforced and reactive graphite nanotube-reinforced epoxy composite materials is shown. http://www.mdpi.com/1422-0067/10/12/5115/ Wed, 25 Nov 2009 00:00:00 CET International Journal of Molecular Sciences 2009-11-25 10 12 Review 5115 5134 1422-0067 Effect of Interface Structure on Mechanical Properties of Advanced Composite Materials 2009-11-25 doi: 10.3390/ijms10125115 Yong X. Gan http://www.mdpi.com/1422-0067/10/12/5104/ Electronic and structural properties of antiphase boundaries in group III-V semiconductor compounds have been receiving increased attention due to the potential to integration of optically-active III-V heterostructures on silicon or germanium substrates. The formation energies of {110}, {111}, {112}, and {113} antiphase boundaries in GaAs and GaP were studied theoretically using a full-potential linearized augmented plane-wave density-functional approach. Results of the study reveal that the stoichiometric {110} boundaries are the most energetically favorable in both compounds. The specific formation energy γ of the remaining antiphase boundaries increases in the order of γf113g ≈ γf112g < γf111g, which suggests {113} and {112} as possible planes for faceting and annihilation of antiphase boundaries in GaAs and GaP. http://www.mdpi.com/1422-0067/10/12/5104/ Wed, 25 Nov 2009 00:00:00 CET International Journal of Molecular Sciences 2009-11-25 10 12 Article 5104 5114 1422-0067 Formation Energies of Antiphase Boundaries in GaAs and GaP: An ab Initio Study 2009-11-25 doi: 10.3390/ijms10125104 Oleg Rubel Sergei D. Baranovskii http://www.mdpi.com/1422-0067/10/11/5090/ Natural mycoflora and co-occurrence of fumonisins (FB1, FB2) and aflatoxins (AFB1, AFB2, AFG1 and AFG2) in freshly harvested corn grain samples from four regions of Brazil were investigated. Fusarium verticillioides was predominant in all samples. Analysis of fumonisins showed that 98% of the samples were contaminated with FB1 and 74.5% with FB1 + FB2, with toxin levels ranging from 0.015 to 9.67 μg/g for FB1 and from 0.015 to 3.16 μg/g for FB2. Twenty-one (10.5%) samples were contaminated with AFB1, seven (3.5%) with AFB2 and only one (0.5%) with AFG1 and AFG2. Co-contamination with aflatoxins and fumonisins was observed in 7% of the samples. The highest contamination of fumonisins and aflatoxins was observed in Nova Odessa (SP) and Várzea Grande (MT), respectively. The lowest contamination of these mycotoxins was found in Várzea Grande and Nova Odessa, respectively. http://www.mdpi.com/1422-0067/10/11/5090/ Tue, 24 Nov 2009 00:00:00 CET International Journal of Molecular Sciences 2009-11-24 10 11 Article 5090 5103 1422-0067 Mycoflora and Co-Occurrence of Fumonisins and Aflatoxins in Freshly Harvested Corn in Different Regions of Brazil 2009-11-24 doi: 10.3390/ijms10115090 Liliana O. Rocha Viviane K. Nakai Raquel Braghini Tatiana A. Reis Estela Kobashigawa Benedito Corrêa http://www.mdpi.com/1422-0067/10/11/5054/ We review the methodology, algorithmic implementation and performance characteristics of a hierarchical modeling scheme for the generation, equilibration and topological analysis of polymer systems at various levels of molecular description: from atomistic polyethylene samples to random packings of freely-jointed chains of tangent hard spheres of uniform size. Our analysis focuses on hitherto less discussed algorithmic details of the implementation of both, the Monte Carlo (MC) procedure for the system generation and equilibration, and a postprocessing step, where we identify the underlying topological structure of the simulated systems in the form of primitive paths. In order to demonstrate our arguments, we study how molecular length and packing density (volume fraction) affect the performance of the MC scheme built around chain-connectivity altering moves. In parallel, we quantify the effect of finite system size, of polydispersity, and of the definition of the number of entanglements (and related entanglement molecular weight) on the results about the primitive path network. Along these lines we approve main concepts which had been previously proposed in the literature. http://www.mdpi.com/1422-0067/10/11/5054/ Mon, 23 Nov 2009 00:00:00 CET International Journal of Molecular Sciences 2009-11-23 10 11 Review 5054 5089 1422-0067 Combined Molecular Algorithms for the Generation, Equilibration and Topological Analysis of Entangled Polymers: Methodology and Performance 2009-11-23 doi: 10.3390/ijms10115054 Nikos Ch. Karayiannis Martin Kröger http://www.mdpi.com/1422-0067/10/11/5031/ Polyimides having dendritic side chains were investigated. The terphenylene diamine monomer having a first-generation monodendron, 3,4,5-tris(n-dodecyloxy)-benzoate and the monomer having a second-generation monodendron, 3,4,5-tris[-3’,4’,5’-tri(n-dodecyloxy)benzyloxy]benzoate were successfully synthesized and the corresponding soluble dendritic polyimides were obtained by polycondensation with conventional tetracarboxylic dianhydride monomers such as benzophenone tertracarboxylic dianhydride (BTDA). The two-step polymerizations in NMP that is a general method for the synthesis of soluble polyimides is difficult; however, the expected dendritic polyimides can be obtained in aromatic polar solvents such as m-cresol and pyridine. The solubility of these dendoronized polyimides is characteristic; soluble in common organic solvents such as dichloromethane, chloroform, toluene and THF. These dendronized polyimides exhibited high glass transition temperatures and good thermal stability in both air and under nitrogen. Their application as alignment layers for LCDs was investigated, and it was found that these polyimides having dendritic side chains were applicable for the vertically aligned nematic liquid crystal displays (VAN-LCDs). http://www.mdpi.com/1422-0067/10/11/5031/ Thu, 19 Nov 2009 00:00:00 CET International Journal of Molecular Sciences 2009-11-19 10 11 Article 5031 5053 1422-0067 Dendronized Polyimides Bearing Long-Chain Alkyl Groups and Their Application for Vertically Aligned Nematic Liquid Crystal Displays 2009-11-19 doi: 10.3390/ijms10115031 Yusuke Tsuda Jae Min OH Renpei Kuwahara http://www.mdpi.com/1422-0067/10/11/5020/ The efficacyof [bmim][X] ionic liquids (ILs) (X = PF6–, BF4– and NTf2–) as reaction media for methyl oleate metathesis was compared with that of conventional organic solvents (PhCl, PhMe, DCM and DCE) using the well-defined first and second generation Grubbs precatalysts, RuCl2(PCy3)(L)(=CHPh) (L = PCy3 or H2IMes). Best catalytic performance, with excellent selectivity (>98%) at moderate reaction temperatures, was achieved in [bmim][X] ILs compared to conventional solvents. The effects of anion, reaction temperature, solvent polarity, solvent viscosity, and ligand-anion interaction on the reaction are also addressed. http://www.mdpi.com/1422-0067/10/11/5020/ Wed, 18 Nov 2009 00:00:00 CET International Journal of Molecular Sciences 2009-11-18 10 11 Article 5020 5030 1422-0067 C18:1 Methyl Ester Metathesis in [bmim][X] Type Ionic Liquids 2009-11-18 doi: 10.3390/ijms10115020 Priya A. Thomas Bassie B. Marvey http://www.mdpi.com/1422-0067/10/11/5002/ Dietary flavones have promising chemoprotective properties, in particular with regard to cancer, but problems with low oral bioavailability and sometimes unacceptable toxicity have made their use as protective additives to normal diets questionable. However, methylation of free phenolic hydroxyl groups leads to derivatives not susceptible to glucuronic acid or sulfate conjugation, resulting in increased metabolic stability. Methylation also leads to greatly improved transport through biological membranes, such as in intestinal absorption, and much increased oral bioavailability. Recent studies also indicate that methylation results in derivatives with increasing potency to kill cancer cells. They also show high potency towards inhibition of hormone-regulating enzymes, e.g., aromatase, important in the causation of breast cancer. Methylation of the flavones may also result in derivatives with diminished toxic side-effects and improved aqueous solubility. In conclusion, it appears that methylation of dietary flavones as well as of other food products may produce derivatives with much improved health effects. http://www.mdpi.com/1422-0067/10/11/5002/ Wed, 18 Nov 2009 00:00:00 CET International Journal of Molecular Sciences 2009-11-18 10 11 Review 5002 5019 1422-0067 Methylation of Dietary Flavones Increases Their Metabolic Stability and Chemopreventive Effects 2009-11-18 doi: 10.3390/ijms10115002 Thomas Walle http://www.mdpi.com/1422-0067/10/11/4990/ We evaluated the in vitro antioxidant property and phytochemical constituents of the aqueous crude leaf extract of Helichrysum pedunculatum. The scavenging activity on superoxide anions, DPPH, H2O2, NO and ABTS; and the reducing power were determined, as well as the flavonoid, proanthocyanidin and phenolic contents of the extract. The extract exhibited scavenging activity towards all radicals tested due to the presence of relatively high total phenol and flavonoids contents. Our findings suggest that H. pedunculatum is endowed with antioxidant phytochemicals and could serve as a base for future drugs. http://www.mdpi.com/1422-0067/10/11/4990/ Fri, 13 Nov 2009 00:00:00 CET International Journal of Molecular Sciences 2009-11-13 10 11 Article 4990 5001 1422-0067 Phytochemical Screening and Polyphenolic Antioxidant Activity of Aqueous Crude Leaf Extract of Helichrysum pedunculatum 2009-11-13 doi: 10.3390/ijms10114990 Olayinka A. Aiyegoro Anthony I. Okoh http://www.mdpi.com/1422-0067/10/11/4977/ Modification of different zirconium propoxide precursors with H2dea was investigated by characterization of the isolated modified species. Upon modification of zirconium n-propoxide and [Zr(OnPr)(OiPr)3(iPrOH)]2 with ½ a mol equivalent of H2dea the complexes [Zr2(OnPr)6(OCH2CH2)2NH]2 (1) and [Zr2(OnPr)2(OiPr)4(OCH2CH2)2NH]2 (2) were obtained. However, 1H-NMR studies of these tetranuclear compounds showed that these are not time-stable either in solution or solid form. The effect of this time instability on material properties is demonstrated by light scattering and TEM experiments. Modification of zirconium isopropoxide with either ½ or 1 equivalent mol of H2dea results in formation of the trinuclear complex, Zr{η3μ2-NH(C2H4O)2}3[Zr(OiPr)3]2(iPrOH)2 (3) countering a unique nona-coordinated central zirconium atom. This complex 3 is one of the first modified zirconium propoxide precursors shown to be stable in solution for long periods of time. The particle size and morphology of the products of sol-gel synthesis are strongly dependent on the time factor and eventual heat treatment of the precursor solution. Reproducible sol-gel synthesis requires the use of solution stable precursors. http://www.mdpi.com/1422-0067/10/11/4977/ Fri, 13 Nov 2009 00:00:00 CET International Journal of Molecular Sciences 2009-11-13 10 11 Article 4977 4989 1422-0067 Modification of Different Zirconium Propoxide Precursors by Diethanolamine. Is There a Shelf Stability Issue for Sol-Gel Applications? 2009-11-13 doi: 10.3390/ijms10114977 Gerald I. Spijksma Dave H. A. Blank Henny J. M. Bouwmeester Vadim G. Kessler http://www.mdpi.com/1422-0067/10/11/4963/ The aim of this study was to determine the optimal heat treatment conditions for enhancement of pressed silk-mediated 3D-like proliferation of normal human dermal fibroblasts, as well as to determine the responses to heat shock of cells and intracellular signaling pathways. The beginning of 3D-like pattern formation of cells was observed in the second week after the start of the experiment. The mean rates of beginning of 3D-like pattern formation by cells heat-treated at 40 ºC and 43 ºC for 10 min were significantly higher (3.2- and 8.6-fold, respectively) than that of untreated cells. We found that apoptosis had occurred in 7.5% and 50.0% of the cells at one week after heat treatment for 10 min at 43 ºC and 45 ºC, respectively. Western blot analysis demonstrated that phosphorylation of p38 MAPK and that of Hsp27 were markedly increased by heat treatment at 43 ºC for 10 min. The results of an experiment using a p38 MAPK inhibitor and Hsp27 inhibitor suggest that activation of p38 MAPK by heat shock is associated with 3D-like cell proliferation and that Hsp27 contributes to the inhibition of apoptosis. The results of this study should be useful for further studies aimed at elucidation of the physiologic mechanisms underlying thermotherapy. http://www.mdpi.com/1422-0067/10/11/4963/ Thu, 12 Nov 2009 00:00:00 CET International Journal of Molecular Sciences 2009-11-12 10 11 Article 4963 4976 1422-0067 Heat Shock-Induced Three-Dimensional-Like Proliferation of Normal Human Fibroblasts Mediated by Pressed Silk 2009-11-12 doi: 10.3390/ijms10114963 Fukumi Hiragami Hirotoshi Motoda Toshiaki Takezawa Chiyuki Takabayashi Shigeki Inoue Yuji Wakatake Yoshio Kano http://www.mdpi.com/1422-0067/10/11/4954/ Wt% of aragonite, a CaCO3 polymorph, increased with higher hydraulic activity (°C) of limestone in precipitated calcium carbonate (PCC) from the lime-soda process (Ca(OH)2-NaOH-Na2CO3). Only calcite, the most stable polymorph, was crystallized at hydraulic activity under 10 °C, whereas aragonite also started to crystallize over 10 °C. The crystallization of PCC is more dependent on the hydraulic activity of limestone than CaO content, a factor commonly used to classify limestone ores according to quality. The results could be effectively applied to the determination of polymorphs in synthetic PCC for eco-friendly paper manufacture. http://www.mdpi.com/1422-0067/10/11/4954/ Wed, 11 Nov 2009 00:00:00 CET International Journal of Molecular Sciences 2009-11-11 10 11 Article 4954 4962 1422-0067 Effect of Hydraulic Activity on Crystallization of Precipitated Calcium Carbonate (PCC) for Eco-Friendly Paper 2009-11-11 doi: 10.3390/ijms10114954 Jung-Ah Kim Gi-Chun Han Mihee Lim Kwang-Suk You Miyoung Ryu Ji-Whan Ahn Toyohisa Fujita Hwan Kim http://www.mdpi.com/1422-0067/10/11/4953/ Due to personal reasons, I left the research group. In accordance with the regulations of the funding institution, Xiamen Health Administration, China, I hereby declare a withdrawal of my signature, Zhi-Jun Zhang, from this paper. [...] http://www.mdpi.com/1422-0067/10/11/4953/ Wed, 11 Nov 2009 00:00:00 CET International Journal of Molecular Sciences 2009-11-11 10 11 Correction 4953 4953 1422-0067 Correction: Zhou, Z.-B. et al. Receptor-Mediated Vascular Smooth Muscle Migration Induced by LPA Involves p38 Mitogen-Activated Protein Kinase Pathway Activation. Int. J. Mol. Sci. 2009, 10, 3194-3208 2009-11-11 doi: 10.3390/ijms10114953 Zhi-Bin Zhou Jian-Ping Niu Zhi-Jun Zhang http://www.mdpi.com/1422-0067/10/11/4941/ Attempts to establish a relationship between peanut skin color (PSC) and total flavonoid (TF) content have produced inconclusive results. This study investigated the potential of PSC as a biomarker for polyphenol content and antioxidant capacity. Peanut cultivars were objectively evaluated for their skin color, total phenolic (TP), flavonoid (TF), proanthocyanidin (TPC) contents and antioxidant capacities (AC). Their relationship was determined by Pearson’s correlation analyses. TP had stronger correlations with CIE a*, hue angle and AC (r2 = 0.77, 0.82 and 0.80, respectively) compared to TF. Therefore, hue angle of peanut skin may be used as a biomarker for TP content rather than TF. http://www.mdpi.com/1422-0067/10/11/4941/ Wed, 11 Nov 2009 00:00:00 CET International Journal of Molecular Sciences 2009-11-11 10 11 Article 4941 4952 1422-0067 Peanut Skin Color: A Biomarker for Total Polyphenolic Content and Antioxidative Capacities of Peanut Cultivars 2009-11-11 doi: 10.3390/ijms10114941 Yvonne Chukwumah Lloyd T. Walker Martha Verghese