bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of microRNA‐regulated protein‐protein interaction network
Authors: Hsu Chun‐Wei , Juan Hsueh‐Fen , Huang Hsuan‐Cheng 
Published: May 2008

AbstractWe have performed topological analysis to elucidate the global correlation between microRNA (miRNA) regulation and protein‐protein interaction network in human. The analysis showed that target genes of individual miRNA tend to be hubs and bottlenecks in the network. While proteins directly regulated by miRNA might not form a network module themselves, the miRNA‐target genes and their interacting neighbors jointly showed significantly higher modularity. Our findings shed light on how miRNA may regulate the protein interaction network.
Identification of differentially expressed proteins in Ficedula flycatchers
Authors: Buggiotti Laura , Primmer Craig R. , Kouvonen Petri , Bureš Stanislav , Corthals Garry L. , Leder Erica H. 
Published: May 2008

AbstractThis is the first report on the large‐scale identification and comparison of proteins in non‐model organisms, Ficedula flycatchers. It highlights the potential of proteomics approaches in both non‐sequenced and non‐model organisms for identification of differentially expressed proteins. Not surprisingly, more than 55% of the proteins failed to be identified even though the MS spectra were of high quality. Nevertheless, the protein information obtained in this study will serve as a valuable resource for continued research.
Quantitative analysis of Streptococcus pneumoniae TIGR4 response to in vitro iron restriction by 2‐D LC ESI MS/MS
Authors: Nanduri Bindu , Shah Pratik , Ramkumar Mahalingam , Allen Edward B. , Swiatlo Edwin , Burgess Shane C. , Lawrence Mark L. 
Published: May 2008

AbstractUnderstanding the growth of bacterial pathogens in a micronutrient restricted host environment can identify potential virulence proteins that help overcome this nutritional barrier to productive infection. In this study, we investigated the pneumococcal protein expression response to iron limitation using an in vitro model. We identified S. pneumoniae TIGR4 proteins by 2‐D LC ESI MS/MS and determined significant changes in protein expression in response to iron restriction using computer‐intensive random resampling methods. Differential protein expression was studied in the context of a S. pneumoniae TIGR4 protein interaction network using Pathway Studio. Our analysis showed that pneumococcal iron restriction response was marked by increased expression of known virulence factors like PsaA. It involved changes in the expression of stress response, and phase variation and biofilm formation proteins. The net effect of changes in all these biological processes could increase the virulence of S. pneumoniae TIGR4 during in vivo infection.
Identification of novel substrates for Cdk5 and new targets for Cdk5 inhibitors using high‐density protein microarrays
Authors: Schnack Cathrin , Hengerer Bastian , Gillardon Frank 
Published: May 2008

AbstractCyclin‐dependent kinase (Cdk) 5 is a serine/threonine kinase that plays an important role during CNS development and its dysregulation is causally involved in the process of neuronal degeneration. To date more than 20 Cdk5 substrates have been identified and the number of Cdk5 substrates is still increasing. The different cellular functions of Cdk5 and its substrates are not completely known at present. High‐throughput protein microarray technology is a powerful tool to identify a large number of potential kinase substrates in parallel under the same experimental conditions. Using Protoarray protein microarrays we identified protein phosphatase 1, regulatory subunit 14A (PPP1R14A) as a novel substrate of Cdk5/p25. Phosphorylation was confirmed in two secondary assays. Our findings may contribute to the elucidation of the physiological function of Cdk5 in synaptic signalling. Functional Kinome Arrays were validated in a second set of experiments to characterize the selectivity of the Cdk5 inhibitor indolinone A. This lead to the identification of two additional kinases that are targeted by this compound and may provide a deeper understanding of its neuroprotective mode of action. However, several false negative results possibly due to a denatured or inactive conformation of the arrayed proteins, sound a note of caution when using protein array techniques.
Monitoring of changes in the membrane proteome during stationary phase adaptation of Bacillus subtilis using in vivo labeling techniques
Authors: Dreisbach Annette , Otto Andreas , Becher Dörte , Hammer Elke , Teumer Alexander , Gouw Joost W. , Hecker Michael , Völker Uwe 
Published: May 2008

AbstractBacillus subtilis has been developed as a model system for physiological proteomics. However, thus far these studies have mainly been limited to cytoplasmic, extracellular, and cell‐wall attached proteins. Although being certainly important for cell physiology, the membrane protein fraction has not been studied in comparable depth due to inaccessibility by traditional 2‐DE‐based workflows and limitations in reliable quantification. In this study, we now compare the potential of stable isotope labeling with amino acids (SILAC) and 14N/15N‐labeling for the analysis of bacterial membrane fractions in physiology‐driven proteomic studies. Using adaptation of B. subtilis to amino acid (lysine) and glucose starvation as proof of principle scenarios, we show that both approaches provide similarly valuable data for the quantification of bacterial membrane proteins. Even if labeling with stable amino acids allows a more straightforward analysis of data, the 14N/15N‐labeling has some advantages in general such as labeling of all amino acids and thereby increasing the number of peptides for quantification. Both, SILAC as well as 14N/15N‐labeling are compatible with 2‐DE, 2‐D LC‐MS/MS, and GeLC‐MS/MS and thus will allow comprehensive simultaneous interrogation of cytoplasmic and enriched membrane proteomes.
How broad band (from radio frequency to microwaves) dielectric parameters describe synthetic chemical reactions
Authors: Meyer Olivier , Delmotte Michel , Lacroix Jean‐Christophe , Weil Raphaël , Loupy André , Maurel François , Fourrier‐Lamer Arlette 
Published: May 2008

AbstractLarge differences in the dielectric responses of isolated molecules and associated reactive mixtures are observed over a wide frequency spectrum ranging from low to microwave frequencies. We present the results obtained for the curing (cross‐linking) of a resin mixed with a hardener. Electrical dipoles contribute to orientation polarization whose responses lie in the 1 kHz to over 1 GHz frequency range, which is predominantly higher than the 0.1 Hz–10 kHz range in which ionic conductivity is observed. It is the relaxation frequency of the reactive mixture that will be considered as the reaction marker. We also describe the results obtained with the saponification of an ester in the presence of a catalyst, with the reactive mixture containing – as in the previous case – electric dipoles and ions, but with responses superimposed in the 1 MHz–10 GHz frequency band. In this case, and for simplification reasons, the low frequency band ionic conductivity is the reaction marker. The aim of this paper is to translate synthetic chemical reactions into electronic terms, in order to allow electronics engineers to understand the interaction between electromagnetic waves and materials. Copyright © 2008 John Wiley & Sons, Ltd.
Waste‐free synthesis and production all across chemistry with the benefit of self‐assembled crystal packings
Authors: Kaupp Gerd 
Published: May 2008

AbstractA systematic mechanistic discussion of solid‐state reactions (intracrystalline, intercrystalline, gas–solid thermal, or photochemical) at local molecular resolution is the basis for industrial sustainable production with waste‐free solid–gas and stoichiometric solid–solid reactions at low energy requirement. These profit from the bargain of the self‐assembled crystal packing. They rapidly complete to give 100% yield and require no solvent for workup. The basic requirements are thermodynamic feasibility and anisotropic molecular migrations at local pressure or suction in opposition to claims of ‘minimal atomic and molecular movements’ that do not know gas–solid and solid–solid reactions. Topochemical failures are settled on that experimental basis by atomic force microscopy (AFM), correlation with the crystal packing, scanning near field optical microscopy (SNOM), and nanoscratching. A general three‐step phase rebuilding mechanism is derived that provides directions for all experimental situations including stereoregular polymerizations. Heat control in gas–solid equipment and solid–solid small‐scale vibration or large‐scale rotation ball‐mills is essential. If AFM identifies (nano)liquids cooling is required. Also rare cases of surface passivation are detected by AFM. Molecular solid‐state chemistry and mechanochemistry are differentiated. Solid‐state techniques easily exclude moisture and are able to synthesize hitherto inaccessible compounds. Some of the latter are selected for discussion out of more than 1000 waste‐free solid‐state reactions in addition to already executed kg‐scale productions using reasonably inexpensive starting materials with promise for industrial applications and extensions. They cover salt formations, complexations, additions, eliminations, substitutions, esterifications, carboxylations, rearrangements, linear dimerizations, cycloreversions, cyclizations, ring openings, cascade reactions, and CC‐couplings (Knoevenagel, Michael, aminomethylation). Copyright © 2008 John Wiley & Sons, Ltd.
Excess polarizabilities upon the first dipole‐allowed excitation of some conjugated oligomers
Authors: Ye J. F. , Chen H. , Note R. , Mizuseki H. , Kawazoe Y. 
Published: May 2008

AbstractThis paper presents theoretical predictions for the excess polarizabilities upon excitation from the ground state to the first dipole‐allowed excited state (11Bu) of some conjugated oligomers. The excess polarizability was obtained by simulating the Stark shift, which was predicted by the time‐dependent density functional theory (TDDFT) with the hybrid Becke‐3 Lee–Yang–Parr (B3LYP) potential. The Stark shift in solution was simulated by employing the non‐equilibrium integral equation formalism polarizable continuum model (IEFPCM). All the model molecules considered in this study were fully optimized by the Hartree–Fock (HF) method and the density functional theory (DFT) with the B3LYP potential, respectively. For diphenylpolyenes, the excess polarizabilities displayed by the DFT/B3LYP‐optimized geometries are more reasonable than those displayed by the HF‐optimized geometries when compared with the experimental results. However, this feature is not clearly demonstrated by our results in the cases of oligo(phenylenevinylene)s (OPVs). Copyright © 2008 John Wiley & Sons, Ltd.
Preparation and characterization of polypyrrole/magnetite nanocomposites synthesized by in situ chemical oxidative polymerization
Authors: Yen Shiang‐Jie , Chen Erh‐Chiang , Chiang Ray‐Kuang , Wu Tzong‐Ming 
Published: May 2008

AbstractThis work describes the preparation and characterization of polypyrrole (PPy)/iron oxide nanocomposites fabricated from monodispersed iron oxide nanoparticles in the crystalline form of magnetite (Fe3O4) and PPy by in situ chemical oxidative polymerization. Two spherical nanoparticles of magnetite, such as 4 and 8 nm, served as cores were first dispersed in an aqueous solution with anionic surfactant sodium bis(2‐ethylhexyl) sulfosuccinate to form micelle/magnetite spherical templates that avoid the aggregation of magnetite nanoparticles during the further preparation of nanocomposites. The PPy/magnetite nanocomposites were then synthesized on the surface of the spherical templates. Structural and morphological analysis showed that the fabricated PPy/magnetite nanocomposites are core (magnetite)‐shell (PPy) structures. Morphology of the PPy/magnetite nanocomposites containing monodispersed 4‐nm magnetite nanoparticles shows a remarkable change from spherical to tube‐like structures as the content of nanoparticles increases from 12 to 24 wt %. Conductivities of these PPy/magnetite nanocomposites show significant enhancements when compared with those of PPy without magnetite nanoparticles, in particular the conductivities of 36 wt % PPy/magnetite nanocomposites with 4‐nm magnetite nanoparticles are about six times in magnitude higher than those of PPy without magnetite nanocomposites. These results suggest that the tube‐like structures of 36 wt % PPy/magnetite nanocomposites may be served as conducting network to enhance the conductivity of nanocomposites. The magnetic properties of 24 and 36 wt % PPy/magnetitenanocomposites show ferromagnetic behavior and supermagnetism, respectively. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1291–1300, 2008
Electrical strength in ramp voltage AC tests of LDPE and its nanocomposites with silica and fibrous and laminar silicates
Authors: Hoyos M. , García N. , Navarro R. , Dardano A. , Ratto A. , Guastavino F. , Tiemblo P. 
Published: May 2008

AbstractThe electrical strength of a set of LDPE micro and nanocomposites with silica, laminar silicates and fibrous silicates has been studied. A significant 60% increase of the breakdown electrical field is shown by the microsized microdispersed LDPE/montmorillonite composites while only a 20% increase is obtained with a nanosized laminar silicate. Nanosized nanodispersed composites of the spherical silica and fibrous silicate with LDPE show a lower increase of the breakdown electrical field. The data point scatter in repeated tests is very high in the case of the microcomposites, indicating strong morphological heterogeneity, while it is very low in the nanocomposites. This implies that these nanocomposites are remarkably defect‐free as regards electrically “weak” sites. An analysis of the crystalline structure, semicrystalline morphology and inorganic particle size and distribution evidences the importance of the role played not only by the inorganic particles but also by the semicrystalline morphology in the final dielectric performance of the composite. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1301–1311, 2008
Quantum carpets of a slightly relativistic particle
Authors: Marzoli I. , Kaplan A.E. , Saif F. , Schleich W.P. 
Published: May 2008

AbstractWe analyze the structures emerging in the spacetime representation of the probability density woven by a slightly relativistic particle caught in a one‐dimensional box. In particular, we evaluate the relativistic effects on the revival time and the specific changes produced in the intermode traces, which quantum carpets consist of. Moreover, we present a detailed mathematical analysis of such quantum carpets pursuing the approach of a kernel. Here we represent the probability distribution as a superposition of interfering Airy function‐type structures along straight world lines. We also show that this phenomenon can be enhanced by many orders of magnitude in semiconductors with narrow band‐gap (e.g. as in InSb) and small effective mass of the electron, whereby due to the strong nonparabolicity of the semiconductor conduction band, the electron energy vs momentum dispersion relation behaves in a pseudo‐relativistic way.
Inhibitory effects of nordihydroguaiaretic acid (NDGA) on the IGF‐1 receptor and androgen dependent growth of LAPC‐4 prostate cancer cells
Authors: Ryan Charles J. , Zavodovskaya Marianna , Youngren Jack F. , Campbell Michael , Diamond Marc , Jones Jeremy , Shiry Laura , Allan Geoffrey , Maddux Betty A. , Goldfine Ira D. 
Published: May 2008

AbstractBACKGROUNDNordihydroguaiaretic acid (NDGA) is an inhibitor of the IGF‐1 receptor (IGF‐1R) in breast and other cancers, and concomitantly inhibits tumor growth both in cultured cells and animals. The current study evaluates the effect of NDGA on the androgen‐stimulated growth of human prostate cancer cells.METHODSLAPC‐4 prostate cancer cells in tissue culture were androgen starved for 3 days, 1 nM dihydrotestosterone (DHT) and other androgens were then added for up to 7 days, and cell proliferation measured. IGF‐1R protein expression was measured by Western blot, and IGF‐1R mRNA expression by quantitative PCR. IGF‐1R receptor kinase activation was measured by ELISA.RESULTSAfter 7 days, LAPC‐4 growth was doubled by 1 nM DHT. NDGA had a rapid effect to inhibit IGF‐1R autophosphorylation induced by IGF‐1. DHT increased the expression of IGF‐1R protein and mRNA levels. Maximal IGF‐1R protein levels were observed 3 days after the addition of androgen. In addition, NDGA, at 10 µM or less, inhibited DHT‐induced proliferation in both cells grown in plates and cells grown in soft agar. Androgen receptor (AR) studies by FRET revealed that NDGA had no conformational effects on the AR in response to ligand.CONCLUSIONSNDGA blocks the DHT‐induced growth of LAPC‐4 prostate cancer cells by several mechanisms including rapid inhibition of the IGF‐1R kinase, and a dose‐dependent inhibition of androgen stimulation of IGF‐1R expression. Clinical studies of this agent will determine its efficacy in the setting of androgen‐dependent prostate cancer. Prostate 68: 1232–1240, 2008. © 2008 Wiley‐Liss, Inc.
Cumulative effect of five genetic variants on prostate cancer risk in multiple study populations
Authors: Sun Jielin , Chang Bao‐Li , Isaacs Sarah D. , Wiley Kathleen E. , Wiklund Fredrik , Stattin Pär , Duggan David , Carpten John D. , Trock Bruce J. , Partin Alan W. , Walsh Patrick C. , Grönberg Henrik , Xu Jianfeng , Isaacs William B. , Zheng S. Lilly 
Published: May 2008

AbstractBACKGROUNDA strong cumulative effect of five genetic variants and family history on prostate cancer risk was recently reported in a Swedish population (CAPS). We carried out this study to confirm the finding in two U.S. study populations and perform a combined analysis to obtain a more stable estimate of the odds ratio (OR) for prostate cancer.METHODSWe evaluated three SNPs at 8q24 and one SNP each at 17q12 and 17q24.3 in two study populations in the U.S. The first was a hospital‐based case–control study population at Johns Hopkins Hospital (JHH), including 1,563 prostate cancer patients and 576 control subjects. The second was the National Cancer Institute Cancer Genetic Markers of Susceptibility (CGEMS) Initiative, including 1,172 prostate cancer patients and 1,157 control subjects.RESULTSWe confirmed a cumulative effect of five risk variants on prostate cancer risk. Based on a total of 5,628 cases and 3,514 controls from JHH, CGEMS, and CAPS, men who carry any combination of 1, 2, 3, and 4 or more of these five risk variants have an estimated OR (95% CI) of 1.41 (1.20–1.67), 1.88 (1.59–2.22), 2.36 (1.95–2.85), and 3.80 (2.77–5.22) for prostate cancer, respectively, compared to men who do not have any of these five risk variants. When family history was included, the cumulative effect was stronger.DISCUSSIONThese results provide an important confirmation for the cumulative effect of five genetic risk variants on prostate cancer risk. The more stable OR estimates of the cumulative effect of these six risk factors are a major step toward individual risk characterization for this disease. Prostate 68:1257–1262, 2008. © 2008 Wiley‐Liss, Inc.
A novel method to map and compare protein–protein interactions in spherical viral capsids
Authors: Carrillo‐Tripp Mauricio , Brooks Charles L. , Reddy Vijay S. 
Published: May 2008

AbstractViral capsids are composed of multiple copies of one or a few chemically distinct capsid proteins and are mostly stabilized by inter subunit protein–protein interactions. There have been efforts to identify and analyze these protein–protein interactions, in terms of their extent and similarity, between the subunit interfaces related by quasi‐ and icosahedral symmetry. Here, we describe a new method to map quaternary interactions in spherical virus capsids onto polar angle space with respect to the icosahedral symmetry axes using azimuthal orthographic diagrams. This approach enables one to map the nonredundant interactions in a spherical virus capsid, irrespective of its size or triangulation number (T), onto the reference icosahedral asymmetric unit space. The resultant diagrams represent characteristic fingerprints of quaternary interactions of the respective capsids. Hence, they can be used as road maps of the protein–protein interactions to visualize the distribution and the density of the interactions. In addition, unlike the previous studies, the fingerprints of different capsids, when represented in a matrix form, can be compared with one another to quantitatively evaluate the similarity (S‐score) in the subunit environments and the associated protein–protein interactions. The S‐score selectively distinguishes the similarity, or lack of it, in the locations of the quaternary interactions as opposed to other well‐known structural similarity metrics (e.g., RMSD, TM‐score). Application of this method on a subset of T = 1 and T = 3 capsids suggests that S‐score values range between 1 and 0.6 for capsids that belong to the same virus family/genus; 0.6–0.3 for capsids from different families with the same T‐number and similar subunit fold; and <0.3 for comparisons of the dissimilar capsids that display different quaternary architectures (T‐numbers). Finally, the sequence conserved interface residues within a virus family, whose spatial locations were also conserved have been hypothesized as the essential residues for self‐assembly of the member virus capsids. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Interplay between structural rigidity and electrostatic interactions in the ligand binding domain of GluR2
Authors: Mamonova Tatyana , Speranskiy Kirill , Kurnikova Maria 
Published: May 2008

AbstractUsing molecular dynamics (MD) simulations, computational protein modifications, and a novel theoretical methodology that determines structural rigidity/flexibility (the FIRST algorithm), we investigate how molecular structure and dynamics of the glutamate receptor ligand binding domain (GluR2 S1S2) facilitate its conformational transition. S1S2 is a two‐lobe protein, which undergoes a cleft closure conformational transition upon binding an agonist in the cleft between the two lobes; hence it is expected that the mechanism of this conformational transition can be characterized as a hinge‐type. However, in the rigidity analysis one lobe of the protein is identified as a single rigid cluster while the other one is structurally flexible, inconsistent with a presumed mechanical hinge mechanism. Instead, we characterize the cleft‐closing transition as a load and lock mechanism. We find that when two cross‐cleft hydrogen bonds are disrupted the protein undergoes a rapid cleft opening transition. At the same time, the dynamical behavior of the cleft in the presence of the glutamate ligand is only weakly affected by the S652 peptide bond in its flipped conformation observed in the crystal structure. The residue E705 plays significant role in stabilization of the closed conformation via electrostatic interactions. The presence of the E705‐K730 salt bridge seems to correlate strongly withthe cleft opening transition in the MD simulations. Proteins 2008. © 2008 Wiley‐Liss, Inc.