bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncoupled investigation of scaffold modulus and mesh size on smooth muscle cell behavior
Authors: Munoz‐Pinto Dany J. , Bulick Allen S. , Hahn Mariah S. 
Published: April 2009

AbstractAlthough scaffold material properties are known to critically impact cell behavior, it has proven difficult to correlate specific cell responses to isolated scaffold parameters, inhibiting rational design of scaffold material properties. The aim of this study was to validate a systematic approach for evaluating the influence of initial scaffold modulus and mesh size on cell extracellular matrix (ECM) deposition and phenotype. Poly(ethylene glycol) diacrylate (PEGDA) hydrogels were selected for this study because of their tunable material properties. Following screening of six distinct PEGDA hydrogels, three formulations were identified which permitted uncoupled investigation of scaffold mesh size and modulus within the target incremental modulus range of ∼100–300 kPa. Smooth muscle cells (SMCs) were encapsulated within these three formulations, and cell ECM deposition and phenotype were evaluated following 21 days of culture. Although elastin content appeared to be correlated with scaffold mesh size and modulus to a similar degree, levels of collagen and serum response factor (SRF), a key regulator of SMC phenotype, were more strongly correlated with mesh size. To gain insight into the cell signaling underlying these observed correlations, variations in cell metabolic state and in RhoA signaling were semi‐quantitatively evaluated. Both RhoA activity, which is largely modulated by scaffold mechanics in 2D, and cell metabolic activity were highly correlated with hydrogel mesh size. These results indicate that the effects of scaffold mechanics on RhoA activity in 3D may be distinct from those in 2D and underscore the need for uncoupled investigation of scaffold parameters on cell behavior. Furthermore, the present data suggest that RhoA signaling and cell metabolic regulation may be closely linked. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res, 2009
Calcium phosphate/DNA co‐precipitates encapsulated fast‐degrading polymer films for substrate‐mediated gene delivery
Authors: Zhang Qiao , Zhao Dong , Zhang Xian‐Zheng , Cheng Si‐Xue , Zhuo Ren‐Xi 
Published: April 2009

AbstractCalcium‐phosphate/deoxyribose nucleic acid (Ca‐P/DNA) co‐precipitates were deposited on or encapsulated in fast‐degrading polymer films with surface erosion degradation mechanism to mediate cell transfection. The polymer, cholic acid functionalized star poly(DL‐lactide), was synthesized through the ring‐opening polymerization of DL‐lactide initiated by cholic acid. The releases of DNA from the Ca‐P/DNA co‐precipitates deposited film and the Ca‐P/DNA co‐precipitates encapsulated film were determined and compared. The in vitro gene transfections of HEK293 cells, Hela cells, and NIH 3T3 cells showed that the expression of pGL3‐Luc plasmid could be effectively mediated by the Ca‐P/DNA co‐precipitates deposited and encapsulated polymer films. In addition, the films did not exhibit any additional cytotoxicity to the cells during the transfections, indicating that the fast‐degrading polymer films have great potential in localized gene delivery. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2009
Trypsin‐ligand binding free energies from explicit and implicit solvent simulations with polarizable potential
Authors: Jiao Dian , Zhang Jiajing , Duke Robert E. , Li Guohui , Schnieders Michael J. , Ren Pengyu 
Published: April 2009

AbstractWe have calculated the binding free energies of a series of benzamidine‐like inhibitors to trypsin with a polarizable force field using both explicit and implicit solvent approaches. Free energy perturbation has been performed for the ligands in bulk water and in protein complex with molecular dynamics simulations. The binding free energies calculated from explicit solvent simulations are well within the accuracy of experimental measurement and the direction of change is predicted correctly in all cases. We analyzed the molecular dipole moments of the ligands in gas, water and protein environments. Neither binding affinity nor ligand solvation free energy in bulk water shows much dependence on the molecular dipole moments of the ligands. Substitution of the aromatic or the charged group in the ligand results in considerable change in the solvation energy in bulk water and protein whereas the binding affinity varies insignificantly due to cancellation. The effect of chemical modification on ligand charge distribution is mostly local. Replacing benzene with diazine has minimal impact on the atomic multipoles at the amidinium group. We have also utilized an implicit solvent based end‐state approach to evaluate the binding free energies of these inhibitors. In this approach, the polarizable multipole model combined with Poisson‐Boltzmann/surface area (PMPB/SA) provides the electrostatic interaction energy and the polar solvation free energy. Overall the relative binding free energies obtained from the MM‐PMPB/SA model are in good agreement with the experimental data. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009
Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity
Authors: Das Payel , Li Jingyuan , Royyuru Ajay K. , Zhou Ruhong 
Published: April 2009

AbstractHistorically, influenza pandemics have been triggered when an avian influenza virus or a human/avian reassorted virus acquires the ability to replicate efficiently and become transmissible in the human population. Most critically, the major surface glycoprotein hemagglutinin (HA) must adapt to the usage of human‐like (α‐2,6‐linked) sialylated glycan receptors. Therefore, identification of mutations that can switch the currently circulating H5N1 HA receptor binding specificity from avian to human might provide leads to the emergence of pandemic H5N1 viruses. To define such mutations in the H5 subtype, here we provide a computational framework that combines molecular modeling with extensive free energy simulations. Our results show that the simulated binding affinities are in good agreement with currently available experimental data. Moreover, we predict that one double mutation (V135S and A138S) in HA significantly enhances α‐2,6‐linked receptor recognition by the H5 subtype. Our simulations indicate that this double mutation in H5N1 HA increases the binding affinity to α‐2,6‐linked sialic acid receptors by 2.6 ± 0.7 kcal/mol per HA monomer that primarily arises from the electrostatic interactions. Further analyses reveal that introduction of this double mutation results in a conformational change in the receptor binding pocket of H5N1 HA. As a result, a major rearrangement occurs in the hydrogen‐bonding network of HA with the human receptor, making the human receptor binding pattern of double mutant H5N1 HA surprisingly similar to that observed in human H1N1 HA. These large scale molecular simulations on single and double mutants thus provide new insights into our understanding toward human adaptation of the avian H5N1 virus. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009
Time‐dependent density functional theory study on the electronic excited‐state geometric structure, infrared spectra, and hydrogen bonding of a doubly hydrogen‐bonded complex
Authors: Liu Yufang , Ding Junxia , Liu Ruiqiong , Shi Deheng , Sun Jinfeng 
Published: April 2009

AbstractThe geometric structures and infrared (IR) spectra in the electronically excited state of a novel doubly hydrogen‐bonded complex formed by fluorenone and alcohols, which has been observed by IR spectra in experimental study, are investigated by the time‐dependent density functional theory (TDDFT) method. The geometric structures and IR spectra in both ground state and the S1 state of this doubly hydrogen‐bonded FN‐2MeOH complex are calculated using the DFT and TDDFT methods, respectively. Two intermolecular hydrogen bonds are formed between FN and methanol molecules in the doubly hydrogen‐bonded FN‐2MeOH complex. Moreover, the formation of the second intermolecular hydrogen bond can make the first intermolecular hydrogen bond become slightly weak. Furthermore, it is confirmed that the spectral shoulder at around 1700 cm−1 observed in the IR spectra should be assigned as the doubly hydrogen‐bonded FN‐2MeOH complex from our calculated results. The electronic excited‐state hydrogen bonding dynamics is also studied by monitoring some vibraitonal modes related to the formation of hydrogen bonds in different electronic states. As a result, both the two intermolecular hydrogen bonds are significantly strengthened in the S1 state of the doubly hydrogen‐bonded FN‐2MeOH complex. The hydrogen bond strengthening in the electronically excited state is similar to the previous study on the singly hydrogen‐bonded FN‐MeOH complex and play important role on the photophysics of fluorenone in solutions. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009
Evaluation of the searching abilities of HBOP and HBSITE for binding pocket detection
Authors: Oda Akifumi , Yamaotsu Noriyuki , Hirono Shuichi 
Published: April 2009

AbstractWe evaluated the pocket‐searching abilities of the computer programs HBOP and HBSITE, in which hydrophobic potentials calculated on grid points generated around a protein function as an indicator of the pocket‐like property‐using a test set of 458 experimentally observed structures of protein–ligand complexes. The results were compared with those obtained using the alternative algorithms PASS and SiteID, which only consider geometric properties, and Q‐SiteFinder, which considers not only geometry but also physicochemical properties. The comparison revealed that HBOP and HBSITE could detect experimentally observed ligand‐binding pockets for more test complexes than PASS and SiteID. In addition, the success rate of HBOP for detecting binding pockets was higher than that of Q‐SiteFinder, and that of HBSITE was comparable with that of Q‐SiteFinder. Results of tests for ligand‐unbound state proteins indicated that HBSITE was more appropriate than Q‐SiteFinder for pocket searches of ligand‐unbound proteins, and HBSITE was more robust than Q‐SiteFinder against structural differences between ligand‐bound and ‐unbound state proteins. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009
The subnuclear organization of histone gene regulatory proteins and 3′ end processing factors of normal somatic and embryonic stem cells is compromised in selected human cancer cell types
Authors: Ghule Prachi N. , Dominski Zbigniew , Lian Jane B. , Stein Janet L. , van Wijnen Andre J. , Stein Gary S. 
Published: April 2009

AbstractHuman histone gene expression is controlled at the level of transcription initiation and subsequent 3′end processing to generate non‐polyadenylated stem‐loop containing histone mRNAs. Transcription is controlled at the G1/S phase transition by the Cyclin E/CDK2 mediated induction of p220NPAT/HiNF‐P complexes at subnuclear domains designated Histone Locus Bodies (HLBs) that associate with histone gene clusters. Histone mRNA maturation is mediated by Lsm10 containing U7snRNP complexes. In normal human somatic and embryonic stem cells, the 6p histone locus, the transcription marker p220NPAT and the 3′end processing marker Lsm10 (but not the Cajal Body marker coilin) co‐localize, reflecting the assembly of an integrated factory for histone gene expression. Using in situ immuno‐fluorescence microscopy and fluorescence in situ hybridization (FISH), we show that this subnuclear organization is compromised in some cancer cell lines. In aneuploid cells, the presence of HLBs correlates with the number of histone gene loci. More importantly, the in situ co‐localization of p220NPAT and Lsm10 is disrupted in HeLa S3 cervical carcinoma cells and MCF7 breast adenocarcinoma cells, with most Lsm10 residing in Cajal Bodies. The finding that the subnuclear integration of transcriptional initiation and 3′end processing of histone gene transcripts is deregulated may be causally linked to tumor‐related modifications in molecular pathways controlling histone gene expression during the cell cycle. J. Cell. Physiol. 220: 129–135, 2009. © 2009 Wiley‐Liss, Inc.
Adsorption and desorption behaviour of Pb(II) on a natural kaolin: equilibrium, kinetic and thermodynamic studies
Authors: Tang Qiang , Tang Xiaowu , Li Zhenze , Chen Yunmin , Kou Naiyu , Sun Zufeng 
Published: April 2009

AbstractBACKGROUND: Pb(II) is common in both waste‐waters and gas emissions. In developing countries, public health problems have been reported concerning Pb(II) pollution, so that stringent measures are required to deal with it.MAJOR RESULTS: The adsorption and desorption behaviour of Pb(II) has been investigated on a natural Chinese kaolin. Several factors, including initial concentration, pH, equilibration time, dosage and temperature correlated positively with Pb(II) adsorption. The Pb(II) adsorption capacity of natural kaolin was 165.117 mg g−1. A kinetic study shows that Pb(II) adsorption on purified kaolin equilibrates within 35 min. The enthalpy changes of Pb(II) adsorption on purified kaolin were 63.683, 20.488 and 21.371 kJ mol−1 with entropy changes 262.250, 112.210 and 105.120 J mol−1 K−1 for solutions containing 50, 100 and 200 mg L−1 Pb(II) respectively, indicating an endothermic and spontaneous adsorption process. The desorption of Pb(II) from kaolin was difficult with more than 85% Pb(II) removal. Based on X‐ray diffraction (XRD) analysis, the Pb(II) adsorption on natural and purified kaolin was attributed mainly to the magnesite component and complexation with the mineral surface.CONCLUSIONS: Natural kaolin exhibits a satisfactory performance for adsorption of Pb(II) from aqueous solution. The optimum conditions for adsorption were: ionic strength = 0.01 mol L−1; pH ≥ 7.2; dosage = 10 g L−1; temperature = 25 °C; duration ≥ 16 h (Ci = 80 mg L−1); and the optimum conditions for desorption were ionic strength = 0.1 mol L−1 and pH ≤ 5.0. Copyright © 2009 Society of Chemical Industry
Adsorption of fluoride from aqueous solution by magnesia‐amended silicon dioxide granules
Authors: Zhu Peiyi , Wang Haizeng , Sun Baowei , Deng Peichang , Hou Shaoqin , Yu Yanwei 
Published: April 2009

AbstractBACKGROUND: A new kind of adsorbent, magnesia‐amended silicon dioxide granules (MAS), has been prepared by wet impregnation of silicon dioxide with magnesium chloride solution. The physicochemical properties were characterized using X‐ray diffraction (XRD), Fourier transform infrared (FT‐IR) and Brunauer, Emmett, Teller (BET) studies. The porous structure and high surface area of these granules make them suitable for sorption. The aim of this study was to show the possibility of defluoridation of water using MAS and to demonstrate the advantage of its use compared with silicon dioxide.RESULTS: XRD and FT‐IR analysis showed that amorphous magnesia was loaded on silicon dioxide after treating with magnesium chloride solution and calcining at 500 °C. Batch sorption experiments indicated that MAS is more effective than silicon dioxide for fluoride adsorption. The sorption capacities of MAS decreased as the solution pH rose. At pH 3, the maximum defluoridation capacity of MAS was 12.6 mg g−1. The adsorption process fitted the Dubinin–Radushkevich isotherm and kinetic studies revealed that the adsorption followed second‐order rate kinetics.CONCLUSION: The results indicate that it is feasible to modify both the physical and chemical properties of silicon dioxide with magnesia so that it can be used as a potential adsorbent to adsorb fluoride from aqueous solution. Copyright © 2009 Society of Chemical Industry
Thiotaurine and hypotaurine contents in hydrothermal‐vent polychaetes without thiotrophic endosymbionts: correlation With sulfide exposure
Authors: Yancey Paul H. , Ishikawa Joanne , Meyer Brigitte , Girguis Peter R. , Lee Raymond W. 
Published: April 2009

AbstractInvertebrates at hydrothermal vents and cold seeps must cope with toxic H2S. One proposed protection mechanism involves taurine derivatives: At vents and seeps, many animals have high levels of hypotaurine and thiotaurine (a product of hypotaurine and HS), originally found in animals with thiotrophic endosymbionts. To further test the role of these compounds, we analyzed them in vent polychaetes without endosymbionts: Paralvinella sulfincola, P. palmiformis and P. pandorae (paralvinellids) and Nicomache venticola (maldanid). P. sulfincola were collected from a high temperature (42–68°C) and a warm site (21–35°C). P. palmiformis and pandorae were from cool sites (12–18°C) and N. venticola were from a cold site (4°C). H2S concentrations in vent effluent largely correlate with temperature. Some specimens were frozen; other ones were kept alive in laboratory chambers, with and without sulfide. Tissues were analyzed for taurine derivatives and other solutes that serve as organic osmolytes. The major osmolyte of all species was glycine. Thiotaurine contents were significantly different among all species, in the order P. sulfincola hot>P. sulfincola warm>P. pandorae>P. palmiformis>N. venticola. P. sulfincola also had high levels of sarcosine; others species had none. Sarcosine and hypotaurine contents of P. sulfincola's branchiae were higher, while glycine contents were lower, than in main body. In P. palmiformis kept in pressure chambers with sulfide, thiotaurine contents were higher and hypotaurine lower than in those kept without sulfide. These results support the hypothesis that conversion of hypotaurine to thiotaurine detoxifies sulfide in vent animals without endosymbionts. J. Exp. Zool. 311A:439–447, 2009. © 2009 Wiley‐Liss, Inc.
Osteoinduction by microbubble‐enhanced transcutaneous sonoporation of human bone morphogenetic protein‐2
Authors: Osawa Kenji , Okubo Yasunori , Nakao Kazumasa , Koyama Noriaki , Bessho Kazuhisa 
Published: April 2009

AbstractBackgroundBone morphogenetic protein‐2 (BMP‐2) is believed to participate in bone healing and regeneration. Previous studies using BMP‐2 in clinical applications have encountered difficulties that include the lack of an efficient, safe and simple delivery system, and expensive proteins and matrices. The gene transfer approach is a promising option for utilizing BMP‐2. Viral vector‐mediated gene transfer is efficient, but safety concerns prevent its clinical application for common diseases. Sonoporation is a simple and inexpensive method that only requires a plasmid and a sonoporation device.MethodsWe used a plasmid‐based human BMP‐2 construct (pCAGGS‐BMP‐2) and examined the induction of bone in the skeletal muscle of mice after plasmid transfer by transcutaneous sonoporation. First, an in vitro study was performed to confirm the expression of BMP‐2 after gene transfer by sonoporation using pCAGGS‐BMP‐2. Next, the BMP‐2 gene was transferred into the skeletal muscle of mice by transcutaneous sonoporation using pCAGGS‐BMP‐2. BMP‐2 production was assessed via immunohistochemistry, and osteoinduction was verified by radiography, histology and biochemical assays.ResultsThe presence of human BMP‐2, alkaline phosphatase and osteocalcin mRNA and the production of the alkaline phosphatase were observed in vitro. Moreover, mature bone was observed in mice sonoporated with pCAGGS‐BMP‐2, confirming that transcutaneous sonoporation with pCAGGS‐BMP‐2 caused osteoinduction in the skeletal muscle of mice.ConclusionsThese results suggest the possibility of the effective clinical use of human BMP‐2 gene therapy using transcutaneous sonoporation, and should facilitate clinical applications of BMP‐2 gene therapy. Copyright © 2009 John Wiley & Sons, Ltd.
Facile synthesis of 4‐alkoxycarbonylisoquinoline‐1,3‐diones and 5‐alkoxycarbonyl‐2‐benzazepine‐1,3‐diones via a mild alkaline cyclization
Authors: Billamboz Muriel , Bailly Fabrice , Cotelle Philippe 
Published: April 2009

Abstract
magnified imageA series of 4‐methoxycarbonylisoquinoline‐1,3‐diones was obtained from homophthalic acid in four steps. The key step was the quantitative and rapid alkaline cyclization of 2‐methoxycarbonyl‐2‐(2‐methoxycarbonylphenyl) acetamides. Homologation easily afforded in the same conditions 5‐carboxy‐2‐benzazepine‐1,3‐dione. J. Heterocyclic Chem., 46, 392 (2009).
N‐methyl‐D‐aspartate‐stimulated ERK1/2 signaling and the transcriptional up‐regulation of plasticity‐related genes are developmentally regulated following in vitro neuronal maturation
Authors: Zhou Xianju , Moon Changjong , Zheng Fei , Luo Yongneng , Soellner Deborah , Nuñez Joseph L. , Wang Hongbing 
Published: April 2009

AbstractThe general features of neuroplasticity are developmentally regulated. Although it has been hypothesized that the loss of plasticity in mature neurons may be due to synaptic saturation and functional reduction of N‐methyl‐D‐aspartate receptors (NMDAR), the molecular mechanisms remain largely unknown. We examined the effects of NMDAR activation and KCl‐mediated membrane depolarization on ERK1/2 signaling following in vitro maturation of cultured cortical neurons. Although NMDA stimulated a robust increase in intracellular calcium at both DIV (day in vitro) 3 and 14, the activation of ERK1/2 and cAMP responsive element‐binding protein (CREB) was impaired at DIV 14. Specifically, the phosphorylation of ERK1/2 was stimulated by both NMDA and KCl at DIV 3. However, at DIV 14, NMDA‐ but not KCl‐stimulated ERK1/2 and CREB phosphorylation was significantly diminished. Consistently, the NMDA‐induced transcription of ERK/CREB‐regulated genes Bdnf exon 4, Arc, and zif268 was significantly attenuated at DIV 14. Moreover, in comparison with 3 DIV neurons, the phosphorylated‐ERK1/2 in 14 DIV neurons displayed a tremendous increase following maturation and was more susceptible to dephosphorylation. Blocking calcium channels by nifedipine or NMDAR by APV caused a more dramatic ERK dephosphorylation in 14 DIV neurons. We further demonstrate that the loss of plasticity‐related signaling is unrelated to NMDA‐induced cell death of the 14 DIV neurons. Taken together, these results suggest that the attenuation of certain aspects of neuroplasticity following maturation may be due to the reduction of NMDAR‐mediated gene transcription and a saturation of ERK1/2 activity. © 2009 Wiley‐Liss, Inc.