bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of C/EBPδ‐dependent transactivation by histone deacetylases in intestinal epithelial cells
Authors: Turgeon Naomie , Valiquette Caroline , Blais Mylène , Routhier Sophie , Seidman Ernest G. , Asselin Claude 
Published: October 2007

AbstractThe C/EBPδ transcription factor is involved in the positive regulation of the intestinal epithelial cell acute phase response. C/EBPδ regulation by histone deacetylases (HDACs) during the course of inflammation remains to be determined. Our aim was to examine the effect of HDACs on C/EBPδ‐dependent regulation of haptoglobin, an acute phase protein induced in intestinal epithelial cells in response to pro‐inflammatory cytokines. HDAC1, HDAC3, and HDAC4 were expressed in intestinal epithelial cells, as determined by Western blot. GST pull‐down assays showed specific HDAC1 interactions with the transcriptional activation and the b‐ZIP C/EBPδ domains, while the co‐repressor mSin3A interacts with the C‐terminal domain. Immunoprecipitation assays confirmed the interaction between HDAC1 and the N‐terminal C/EBPδ amino acid 36–164 domain. HDAC1 overexpression decreased C/EBPδ transcriptional activity of the haptoglobin promoter, as assessed by transient transfection and luciferase assays. Chromatin immunoprecipitation analysis showed a displacement of HDAC1 from the haptoglobin promoter in response to inflammatory stimuli and an increased acetylation of histone H3 and H4. HDAC1 silencing by shRNA expression increased both basal and IL‐1β‐induced haptoglobin mRNA levels in epithelial intestinal cells. Our results suggest that interactions between C/EBPs and HDAC1 negatively regulate C/EBPδ‐dependent haptoglobin expression in intestinal epithelial cells. J. Cell. Biochem. 103: 1573–1583, 2008. © 2007 Wiley‐Liss, Inc.
Immunosuppressive drug‐free operational immune tolerance in human kidney transplant recipients: Part I. blood gene expression statistical analysis
Authors: Braud Christophe , Baeten Dominique , Giral Magali , Pallier Annaïck , Ashton‐Chess Joanna , Braudeau Cecile , Chevalier Catherine , Lebars Alice , Léger Jean , Moreau Anne , Pechkova Eugenia , Nicolini Claudio , Soulillou Jean‐Paul , Brouard Sophie 
Published: October 2007

AbstractSurvival of solid organ grafts depends on life‐long immunosuppression, which results in increased rates of infection and malignancy. Induction of tolerance to allografts would represent the optimal solution for controlling both chronic rejection (CR) and side effects of immunosuppression. Although spontaneous “operational tolerance” can occur in human kidney transplantation, the lack of noninvasive peripheral blood biological markers of this rare phenomenon precludes the identification of potentially tolerant patients in whom immunosuppression could be tapered as well as the development of new tolerance inducing strategies. Here, the potential of high throughput microarray technology to decipher complex pathologies allowed us to study the peripheral blood specific gene expression profile and corresponding EASE molecular pathways associated to operational tolerance in a cohort of human kidney graft recipients. In comparison with patients with CR, tolerant patients displayed a set of 343 differentially expressed genes, mainly immune and defense genes, in their peripheral blood mononuclear cells (PBMC), of which 223 were also different from healthy volunteers. Using the expression pattern of these 343 genes, we were able to classify correctly >80% of the patients in a cross‐validation experiment and classified correctly all of the samples over time. Collectively, this study identifies a unique PBMC gene signature associated with human operational tolerance in kidney transplantation by a classical statistical microarray analysis and, in the second part, by a nonstatistical analysis. J. Cell. Biochem. 103: 1681–1692, 2008. © 2007 Wiley‐Liss, Inc.
Structure and dynamics of phospholipid bilayers using recently developed general all‐atom force fields
Authors: Rosso Lula , Gould Ian R. 
Published: October 2007

AbstractTwo fully hydrated pure‐species phospholipids bilayers, 1,2‐dimyristoyl‐sn‐glycero‐3‐phosphocholine (DMPC) and 1,2‐dioleoyl‐sn‐glycero‐3‐phosphorylcholine (DOPC), in the fluid phase and explicit solvent have been studied using molecular dynamics simulation. Atom interactions were modeled using recently developed force fields based on AMBER with full atomistic details. Several representative liquid phase properties for the structure and dynamics of lipids with different length of hydrocarbon chains and different level of saturation have been reproduced without artificially biasing the system in order to match experimental data. In particular, as the new GAFF (General Amber Force Field) has not been explicitly developed to reproduce lipid characteristics and is naturally compatible with standard AMBER nucleic acids and proteins parameters, it is here proven a promising tool to study mixed lipid–protein processes as protein activity dependence on membrane composition, permeation of solute across membranes, and other cellular processes. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Applications of deuterium isotope effects for probing aspects of reactions involving oxidative addition and reductive elimination of H–H and C–H bonds
Authors: Parkin Gerard 
Published: October 2007

AbstractThe various types of deuterium isotope effects that are observed for reactions involving oxidative addition and reductive elimination reactions of H–H and C–H bonds with a transition metal center are reviewed. Copyright © 2007 John Wiley & Sons, Ltd.
Ligand–receptor interactions and membrane structure investigated by AFM and time‐resolved fluorescence microscopy
Authors: Thormann Esben , Simonsen Adam C. , Nielsen Lars K. , Mouritsen Ole G. 
Published: October 2007

AbstractThe atomic force microscope (AFM) and the associated dynamic force spectroscopy technique have been exploited to quantitatively assess the interaction between proteins and their binding to specific ligands and membrane surfaces. In particular, we have studied the specific interaction between lung surfactant protein D and various carbohydrates. In addition, we have used scanning AFM and time‐resolved fluorescence microscopy to image the lateral structure of different lipid bilayers and their morphological changes as a function of time. The various systems studied illustrate the potential of modern AFM techniques for application to biomedical research, specifically within immunology and liposome‐based drug delivery. Copyright © 2007 John Wiley & Sons, Ltd.
Effects of supercritical carbon dioxide on volatile formation from Maillard reaction between ribose and cysteine
Authors: Xu Honggao , Gao Yanxiang , Liu Xuan , Zhao Jian 
Published: October 2007

AbstractBACKGROUND: Supercritical carbon dioxide (SC‐CO2) technology is being used in an increasing number of food‐manufacturing applications; however, its effect on the Maillard reaction is not well studied. The objective of this study was to investigate the effect of SC‐CO2 treatment (140 °C, 40 MPa) on the Maillard reaction of an aqueous ribose–cysteine model system under varying pH conditions (5.6, 7.0 and 8.0), with emphasis on the formation of volatile compounds.RESULTS: SC‐CO2 had a suppressing effect on the browning stages of the reaction under acidic and neutral pH conditions, while it appeared to have an accelerating effect at pH 8.0. Over 70 volatile compounds were positively identified from the headspace of the model system by gas chromatography–mass spectrometry. The volatiles were dominated by sulfur‐containing compounds including thiophenes and fused bicyclic sulfur‐containing compounds under all experimental conditions. Several compounds, including 2‐methyl‐3‐furanthiol, 2‐furanmethanethiol, 3‐thiophenethiol, and 2‐methyl‐3‐thiophenethiol, and one of the intermediates, furfural, were generated in much higher amounts in the SC‐CO2‐treated samples, especially at alkaline and neutral pH values.CONCLUSION: SC‐CO2 treatment was inhibitory to the formation of most volatiles in the Maillard reaction, but enhanced the formation of some intermediates and well‐known meaty flavoured compounds. Copyright © 2007 Society of Chemical Industry
Fast nosological imaging using canonical correlation analysis of brain data obtained by two‐dimensional turbo spectroscopic imaging
Authors: Laudadio Teresa , Martínez‐Bisbal M. Carmen , Celda Bernardo , Van Huffel Sabine 
Published: October 2007

AbstractA new fast and accurate tissue typing technique has recently been successfully applied to prostate MR spectroscopic imaging (MRSI) data. This technique is based on canonical correlation analysis (CCA), a statistical method able to simultaneously exploit the spectral and spatial information characterizing the MRSI data. Here, the performance of CCA is further investigated by using brain data obtained by two‐dimensional turbo spectroscopic imaging (2DTSI) from patients affected by glioblastoma. The purpose of this study is to investigate the applicability of CCA when typing tissues of heterogeneous tumors. The performance of CCA is also compared with that of ordinary correlation analysis on simulated as well as in vivo data. The results show that CCA outperforms ordinary correlation analysis in terms of robustness and accuracy. Copyright © 2007 John Wiley & Sons, Ltd.
Quantitative ATP synthesis in human liver measured by localized 31P spectroscopy using the magnetization transfer experiment
Authors: Schmid A. I. , Chmelík M. , Szendroedi J. , Krššák M. , Brehm A. , Moser E. , Roden M. 
Published: October 2007

AbstractThe liver plays a central role in intermediate metabolism. Accumulation of liver fat (steatosis) predisposes to various liver diseases. Steatosis and abnormal muscle energy metabolism are found in insulin‐resistant and type‐2 diabetic states. To examine hepatic energy metabolism, we measured hepatocellular lipid content, using proton MRS, and rates of hepatic ATP synthesis in vivo, using the 31P magnetization transfer experiment. A suitable localization scheme was developed and applied to the measurements of longitudinal relaxation times (T1) in six healthy volunteers and the ATP‐synthesis experiment in nine healthy volunteers. Liver 31P spectra were modelled and quantified successfully using a time domain fit and the AMARES (advanced method for accurate, robust and efficient spectral fitting of MRS data with use of prior knowledge) algorithm describing the essential components of the dataset. The measured T1 relaxation times are comparable to values reported previously at lower field strengths. All nine subjects in whom saturation transfer was measured had low hepatocellular lipid content (1.5 ± 0.2% MR signal; mean ± SEM). The exchange rate constant (k) obtained was 0.30 ± 0.02 s−1, and the rate of ATP synthesis was 29.5 ± 1.8 mM/min. The measured rate of ATP synthesis is about three times higher than in human skeletal muscle and human visual cortex, but only about half of that measured in perfused rat liver. In conclusion, 31P MRS at 3 T provides sufficient sensitivity to detect magnetization transfer effects and can therefore be used to assess ATP synthesis in human liver. Copyright © 2007 John Wiley & Sons, Ltd.
Optimal state filtering and parameter identification for linear systems
Authors: Basin Michael , Perez Joel , Skliar Mikhail 
Published: October 2007

AbstractThis paper presents the optimal filtering and parameter identification problem for linear stochastic systems with unknown multiplicative and additive parameters over linear observations, where unknown parameters are considered Wiener processes. The original problem is reduced to the filtering problem for an extended state vector that incorporates parameters as additional states. The obtained optimal filter for the extended state vector also serves as the optimal identifier for the unknown parameters. Performance of the designed optimal state filter and parameter identifier is verified for both stable and unstable linear uncertain systems. Copyright © 2007 John Wiley & Sons, Ltd.
Comparison of individual factors in school psychology graduate students: Why do students pursue a degree in school psychology?
Authors: JR. Scott L. Graves , Wright Lynda Brown 
Published: October 2007

AbstractThe purpose of this study was to investigate what factors influenced students to enter the field of school psychology. Although numerous studies have documented the thoughts and perspectives of practitioners regarding why they have chosen to become school psychologists, attempts to recruit and retain an adequate number of school psychology practitioners and researchers have shown limited success. A national sample of 307 school psychology graduate students responded to a survey designed to measure issues related to the current state of professional practice, the influence of parental education, and professional organization recruitment. Results indicated that working with children and personal experiences within the school system were highly related to participant's decisions to become school psychologists. In addition, doctoral level and nondoctoral level students present similar reasons for entering the field. This research is discussed in terms of its implications for future research and the current shortage of school psychology practitioners and faculty. © 2007 Wiley Periodicals, Inc. Psychol Schs 44: 865–872, 2007.
An organelle proteomic method to study neurotransmission‐related proteins, applied to a neurodevelopmental model of schizophrenia
Authors: Vercauteren Freya G. G. , Flores Gonzalo , Ma Weiya , Chabot Jean‐Guy , Geenen Lieve , Clerens Stefan , Fazel Ali , Bergeron John J. M. , Srivastava Lalit K. , Arckens Lutgarde , Quirion Rémi 
Published: October 2007

AbstractLimited information is currently available on molecular events that underlie schizophrenia‐like behaviors in animal models. Accordingly, we developed an organelle proteomic approach enabling the study of neurotransmission‐related proteins in the prefrontal cortex (PFC) of postpubertal (postnatal day 60 (PD60)) neonatally ventral hippocampal (nVH) lesioned rats, an extensively used neurodevelopmental model of schizophrenia‐like behaviors. The PFC was chosen because of its purported role in the etiology of the disease. Statistical analysis of 392 reproducible spots on 2‐D organelle proteomic patterns revealed significant changes in intensity of 18 proteinous spots in plasma membrane‐enriched fractions obtained from postpubertal nVH lesioned rats compared to controls. Mass spectrometric analysis and database searching allowed the identification of a single protein in each of the nine differential spots, including proteins of low abundance, such as neurocalcin δ. Most of the identified dysregulated proteins, including clathrin light chain B, syntaxin binding protein 1b and visinin‐like protein 1 are known to be linked to various neurotransmitter systems and to play key roles in plasma membrane receptor expression and recycling as well as synaptic vesicle exocytosis/recycling. Organelle proteomic approaches have hence proved to be most useful to identify key proteins linked to a given behavior in animal models of brain diseases.
Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO‐Proteomics Standards Initiative April 23–25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France
Authors: Orchard Sandra , Montechi‐Palazzi Luisa , Deutsch Eric W. , Binz Pierre‐Alain , Jones Andrew R. , Paton Norman , Pizarro Angel , Creasy David M. , Wojcik Jérôme , Hermjakob Henning 
Published: October 2007

AbstractOver the last five years, the Human Proteome Organisation Proteomics Standards Initiative (HUPO PSI) has produced and released community‐accepted XML interchange formats in the fields of mass spectrometry, molecular interactions and gel electrophoresis, have led the field in the discussion of the minimum information with which such data should be annotated and are now in the process of publishing much of this information. At this 4th Spring workshop, the emphasis was on consolidating this effort, refining and improving the existing models and in pushing these forward to align with more broadly encompassing efforts such as FuGE (Jones, A.R., Pizarro, A., Spellman, P., Miller, M., FuGE Working Group FuGE: Functional Genomics Experiment Object Model. OMICS 2006, 10, 179‐184) and the Ontology for Biomedical Investigation (OBI). The effort to merge the existing mass spectrometry XML interchange formats, mzData and mzXML, into one single standard mzML yielded significant progress. Also the preliminary design of AnalysisXML was extended to include several new use cases and better support for quantification information. Finally the Molecular Interaction group discussed the development of a molecular interaction scoring system with accompanying gold standard data test sets.
Ab initiostudy onN,N′,N″‐triaminoguanidine
Authors: Iqbal Pansy , Patel Dhilon S. , Bharatam Prasad V. 
Published: October 2007

AbstractElectronic structure calculations and second‐order delocalizations inN,N′,N′′‐triaminoguanidine (TAG) have been studied by employingab initioMO and density functional methods. There are total 10 rotational isomers on the potential energy (PE) surface ofTAG. The effect of three amino groups substitution on guanidine (Gu) has been studied in terms of the primary and the secondary electron delocalizations inTAGby employing Natural Population Analysis (NPA). An increased electron delocalization is observed in protonated triaminoguanidine (TAGP) due to the three strong intramolecular hydrogen bonds and hence accounts for its extra stability. The increase in the electron delocalization upon protonation inTAGcan be compared to that in guanidine. The absolute proton affinity (APA) ofTAGis less than that ofGu. HOMA and NICS studies have been carried out to understand electron delocalization inTAGP. Copyright © 2007 John Wiley & Sons, Ltd.
Synthesis and self‐assembly behavior study of α,ω‐dicarboxyl‐poly(ethylene glycol)–permethyl‐6‐amino‐6‐deoxy‐β‐cyclodextrin‐monoamide: A new β‐cyclodextrin conjugate
Authors: Nagy Miklós , Szőllősi László , Kéki Sándor , Herczegh Pál , Batta Gyula , Jicsinszky László , Zsuga Miklós 
Published: October 2007

AbstractA new type of amphiphilic macromolecule was synthesized through the attachment of a poly(ethylene glycol) chain to a permethyl‐amino‐β‐cyclodextrin ring. The structure of the product was studied with 1D and 2D NMR experiments and with MALDI‐TOF MS. The resulting comet‐shaped molecule showed self‐assembly behavior in polar solvents. The presence of supramolecular structures in aqueous media was detected with dynamic light scattering and proven also by 2D NOESY and DOSY experiments. The supramolecular structures that formed could serve as starting materials for new types of drug delivery bioconjugates containing two independent dopable sites, that is, the cyclodextrin ring and the core of the supramolecular structure. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 5149–5155, 2007
Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms2io6A37 in tRNA
Authors: Kaminska Katarzyna H. , Baraniak Urszula , Boniecki Michal , Nowaczyk Katarzyna , Czerwoniec Anna , Bujnicki Janusz M. 
Published: October 2007

AbstracttRNAs from all organisms contain posttranscriptionally modified nucleosides, which are derived from the four canonical nucleosides. In most tRNAs that read codons beginning with U, adenosine in the position 37 adjacent to the 3′ position of the anticodon is modified to N6‐(Δ2‐isopentenyl) adenosine (i6A). In many bacteria, such as Escherichia coli, this residue is typically hypermodified to N6‐isopentenyl‐2‐thiomethyladenosine (ms2i6A). In a few bacteria, such as Salmonella typhimurium, ms2i6A can be further hydroxylated to N6‐(cis‐4‐hydroxyisopentenyl)‐2‐thiomethyladenosine (ms2io6A). Although the enzymes that introduce the respective modifications (prenyltransferase MiaA, methylthiotransferase MiaB, and hydroxylase MiaE) have been identified, their structures remain unknown and sequence‐function relationships remain obscure. We carried out sequence analysis and structure prediction of MiaA, MiaB, and MiaE, using the protein fold‐recognition approach. Three‐dimensional models of all three proteins were then built using a new modeling protocol designed to overcome uncertainties in the alignments and divergence between the templates. For MiaA and MiaB, the catalytic core was built based on the templates from the P‐loop NTPase and Radical‐SAM superfamilies, respectively. For MiaB, we have also modeled the C‐terminal TRAM domain and the newly predicted N‐terminal flavodoxin‐fold domain. For MiaE, we confidently predict that it shares the three‐dimensional fold with the ferritin‐like four‐helix bundle proteins and that it has a similar active site and mechanism of action to diiron carboxylate enzymes, in particular, methane monooxygenase (E.C.1.14.13.25) that catalyses the biological hydroxylation of alkanes. Our models provide the first structural platform for enzymes involved in the biosynthesis of i6A, ms2i6A, and ms2io6A, explain the data available from the literature and will help to design further experiments and interpret their results. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Biophysical characterization of Vpu from HIV‐1 suggests a channel‐pore dualism
Authors: Mehnert T. , Routh A. , Judge P. J. , Lam Y. H. , Fischer D. , Watts A. , Fischer W. B. 
Published: October 2007

AbstractVpu from HIV‐1 is an 81 amino acid type I integral membrane protein which consists of a cytoplasmic and a transmembrane (TM) domain. The TM domain is known to alter membrane permeability for ions and substrates when inserted into artificial membranes. Peptides corresponding to the TM domain of Vpu (Vpu1‐32) and mutant peptides (Vpu1‐32‐W23L, Vpu1‐32‐R31V, Vpu1‐32‐S24L) have been synthesized and reconstituted into artificial lipid bilayers. All peptides show channel activity with a main conductance level of around 20 pS. Vpu1‐32‐W23L has a considerable flickering pattern in the recordings and longer open times than Vpu1‐32. Whilst recordings for Vpu1‐32‐R31V are almost indistinguishable from those of the WT peptide, recordings for Vpu1‐32‐S24L do not exhibit any noticeable channel activity. Recordings of WT peptide and Vpu1‐32‐W23L indicate Michaelis–Menten behavior when the salt concentration is increased. Both peptide channels follow the Eisenman series I, indicative for a weak ion channel with almost pore like characteristics. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Evaluating conformational changes in protein structures binding RNA
Authors: Ellis Jonathan J. , Jones Susan 
Published: October 2007

AbstractMany protein–RNA recognition events are known to exhibit conformational changes from qualitative observations of individual complexes. However, a quantitative estimation of conformational changes is required if protein–RNA docking and template‐based methods for RNA binding site prediction are to be developed. This study presents the first quantitive evaluation of conformational changes that occur when proteins bind RNA. The analysis of twelve RNA‐binding proteins in the bound and unbound states using error‐scaled difference distance matrices is presented. The binding site residues are mapped to each structure, and the conformational changes that affect these residues are evaluated. Of the twelve proteins four exhibit greater movements in nonbinding site residues, and a further four show the greatest movements in binding site residues. The remaining four proteins display no significant conformational change. When interface residues are found to be in conformationally variable regions of the protein they are typically seen to move less than 2 Å between the bound and unbound conformations. The current data indicate that conformational changes in the binding site residues of RNA binding proteins may not be as significant as previously suggested, but a larger data set is required before wider conclusions may be drawn. The implications of the observed conformational changes for protein function prediction are discussed. Proteins 2008. © 2007 Wiley‐Liss, Inc.