bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modulation of integrin antagonist signaling by ligand binding of the heparin‐binding domain of vitronectin to the αVβ3 integrin
Authors: Maile Laura A. , Aday Ariel W. , Busby Walker H. , Sanghani Ravi , Veluvolu Umadevi , Clemmons David R. 
Published: July 2008

AbstractThe interaction between the arginine glycine and aspartic acid motif (RGD) of integrin ligands such as vitronectin and the integrin receptor αVβ3 in mediating cell attachment has been well described. Similarly, the ability of disintegrins, small RGD containing peptides, to inhibit cell attachment and other cellular processes has also been studied extensively. Recently, we characterized a second site of interaction between vitronectin and its integrin partner. We determined that amino acids within the heparin‐binding domain of vitronectin bind to a cysteine loop (C‐loop) region of β3 and that this interaction is required for the positive effects of αVβ3 ligand occupancy on IGF‐I signaling in smooth muscle cells. In this study we examine the signaling events activated following ligand binding of disintegrins to the αVβ3 and the ability of these signals to be regulated by binding of the heparin‐binding domain of vitronectin. We demonstrate that disintegrin ligand binding activates a series of events including the sequential activation of the tyrosine kinases c‐Src and Syk. This leads to the activation of calpain and the cleavage of the β3 cytoplasmic tail. Addition of vitronectin or a peptide homologous to the heparin‐binding domain inhibited activation of this pathway. Our results suggest that the signaling events that occur following ligand binding to the αVβ3 integrin reflects a balance between the effects mediated through the RGD binding site interaction and the effects mediated by the heparin binding site interaction and that for intact vitronectin the effect of the heparin‐binding domain predominates. J. Cell. Biochem. 105: 437–446, 2008. © 2008 Wiley‐Liss, Inc.
Valproic acid increases expression of methylenetetrahydrofolate reductase (MTHFR) and induces lower teratogenicity in MTHFR deficiency
Authors: Roy Marc , Leclerc Daniel , Wu Qing , Gupta Sapna , Kruger Warren D. , Rozen Rima 
Published: July 2008

AbstractValproate (VPA) treatment in pregnancy leads to congenital anomalies, possibly by disrupting folate or homocysteine metabolism. Since methylenetetrahydrofolate reductase (MTHFR) is a key enzyme of folate interconversion and homocysteine metabolism, we addressed the possibility that VPA might have different teratogenicity in Mthfr+/+ and Mthfr+/− mice and that VPA might interfere with folate metabolism through MTHFR modulation. Mthfr+/+ and Mthfr+/− pregnant mice were injected with VPA on gestational day 8.5; resorption rates and occurrence of neural tube defects (NTDs) were examined on gestational day 14.5. We also examined the effects of VPA on MTHFR expression in HepG2 cells and on MTHFR activity and homocysteine levels in mice. Mthfr+/+ mice had increased resorption rates (36%) after VPA treatment, compared to saline treatment (10%), whereas resorption rates were similar in Mthfr+/− mice with the two treatments (25–27%). NTDs were only observed in one group (VPA‐treated Mthfr+/+). In HepG2 cells, VPA increased MTHFR promoter activity and MTHFR mRNA and protein (2.5‐ and 3.7‐fold, respectively). Consistent with cellular MTHFR upregulation by VPA, brain MTHFR enzyme activity was increased and plasma homocysteine was decreased in VPA‐treated pregnant mice compared to saline‐treated animals. These results underscore the importance of folate interconversion in VPA‐induced teratogenicity, since VPA increases MTHFR expression and has lower teratogenic potential in MTHFR deficiency. J. Cell. Biochem. 105: 467–476, 2008. © 2008 Wiley‐Liss, Inc.
Single‐molecule analysis of chromatin: Changing the view of genomes one molecule at a time
Authors: Pondugula Santhi , Kladde Michael P. 
Published: July 2008

AbstractWrapping DNA into chromatin provides a wealth of regulatory mechanisms that ensure normal growth and development in eukaryotes. Our understanding of chromatin structure, including nucleosomes and non‐histone protein–DNA interactions, has benefited immensely from nuclease and chemical digestion techniques. DNA‐bound proteins, such as histones or site‐specific factors, protect DNA against nuclease cleavage and generate large nucleosomal or small regulatory factor footprints. Chromatin subject to distinct modes of regulation often coincides with sites of nuclease hypersensitivity or nucleosome positioning. An inherent limitation of cleavage‐based analyses has been the inability to reliably analyze regions of interest when levels of digestion depart from single‐hit kinetics. Moreover, cleavage‐based techniques provide views that are averaged over all the molecules in a sample population. Therefore, in cases of occupancy of multiple regulatory elements by factors, one cannot define whether the factors are bound to the same or different molecules in the population. The recent development of DNA methyltransferase‐based, single‐molecule MAP‐IT technology overcomes limitations of ensemble approaches and has opened numerous new avenues in chromatin research. Here, we review the strengths, limitations, applications and future prospects of MAP‐IT ranging from structural issues to mechanistic questions in eukaryotic chromatin regulation. J. Cell. Biochem. 105: 330–337, 2008. © 2008 Wiley‐Liss, Inc.
Molecular mechanics models for tetracycline analogs
Authors: Aleksandrov Alexey , Simonson Thomas 
Published: July 2008

AbstractTetracyclines (Tcs) are an important family of antibiotics that bind to the ribosome and several proteins. To model Tc interactions with protein and RNA, we have developed a molecular mechanics force field for 12 tetracyclines, consistent with the CHARMM force field. We considered each Tc variant in its zwitterionic tautomer, with and without a bound Mg2+. We used structures from the Cambridge Crystallographic Data Base to identify the conformations likely to be present in solution and in biomolecular complexes. A conformational search by simulated annealing was undertaken, using the MM3 force field, for tetracycline, anhydrotetracycline, doxycycline, and tigecycline. Resulting, low‐energy structures were optimized with an ab initio method. We found that Tc and its analogs all adopt an extended conformation in the zwitterionic tautomer and a twisted one in the neutral tautomer, and the zwitterionic‐extended state is the most stable in solution. Intermolecular force field parameters were derived from a standard supermolecule approach: we considered the ab initio energies and geometries of a water molecule interacting with each Tc analog at several different positions. The final, rms deviation between the ab initio and force field energies, averaged over all forms, was 0.35 kcal/mol. Intramolecular parameters were adopted from either the standard CHARMM force field, the ab initio structure, or the earlier, plain Tc force field. The model reproduces the ab initio geometry and flexibility of each Tc. As tests, we describe MD and free energy simulations of a solvated complex between three Tcs and the Tet repressor protein. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Quantum chemistry in parallel with PQS
Authors: Baker Jon , Wolinski Krzysztof , Malagoli Massimo , Kinghorn Don , Wolinski Pawel , Magyarfalvi Gábor , Saebo Svein , Janowski Tomasz , Pulay Peter 
Published: July 2008

AbstractThis article describes the capabilities and performance of the latest release (version 4.0) of the Parallel Quantum Solutions (PQS) ab initio program package. The program was first released in 1998 and evolved from the TEXAS program package developed by Pulay and coworkers in the late 1970s. PQS was designed from the start to run on Linux‐based clusters (which at the time were just becoming popular) with all major functionality being (a) fully parallel; and (b) capable of carrying out calculations on large—by ab initio standards—molecules, our initial aim being at least 100 atoms and 1000 basis functions with only modest memory requirements. With modern hardware and recent algorithmic developments, full accuracy, high‐level calculations (DFT, MP2, CI, and Coupled‐Cluster) can be performed on systems with up to several thousand basis functions on small (4‐32 node) Linux clusters. We have also developed a graphical user interface with a model builder, job input preparation, parallel job submission, and post‐job visualization and display. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Cognitive–behavioral conjoint therapy for posttraumatic stress disorder: application to operation enduring and Iraqi Freedom veterans
Authors: Monson Candice M. , Fredman Steffany J. , Adair Kathryn C. 
Published: July 2008

AbstractAs the newest generation of veterans returns home from their duties abroad, many face the individual and interpersonal aftereffects of duty‐related traumatic experiences. Despite the established association between posttraumatic stress disorder (PTSD) and relationship problems, there is a lack of evidence‐based conjoint treatments that target both PTSD and relationship distress. Cognitive–behavioral conjoint therapy (CBCT) for PTSD was developed to address this need. The authors summarize knowledge on the association between PTSD and relationship functioning, as well as recent research on veterans and their partners. Following an overview of CBCT for PTSD, the authors present a case study to illustrate the application of CBCT to an Operation Enduring and Iraqi Freedom couple. © 2008 Wiley Periodicals, Inc. J Clin Psychol: In Session 64:1‐14, 2008.
Age‐related differences in insulin‐like growth factor‐1 receptor signaling regulates Akt/FOXO3a and ERK/Fos pathways in vascular smooth muscle cells
Authors: Li Muyao , Chiu Jen‐Fu , Gagne Jessica , Fukagawa Naomi K. 
Published: July 2008

AbstractAdvanced age is a major risk factor for atherosclerosis, but how aging per se influences pathogenesis is not clear. Insulin‐like growth factor‐1 receptor (IGF‐1R) promotes aortic vascular smooth muscle cell (VSMC) growth, migration, and extracellular matrix formation, but how IGF‐1R signaling changes with age in VSMC is not known. We previously found age‐related differences in the activation of Akt/FOXO3a and ERK1/2 pathways in VSMC, but the upstream signaling remains unclear. Using explanted VSMC from Fischer 344/Brown Norway F1 hybrid rats shown to display age‐related vascular pathology similar to humans, we compared IGF‐1R expression in early passages of VSMC and found a constitutive activation of IGF‐1R in VSMC from old compared to young rats, including IGF‐1R expression and its tyrosine kinase activity. The link between IGF‐1R activation and the Akt/FOXO3a and ERK pathways was confirmed through the induction of IGF‐1R with IGF‐1 in young cells and attenuation of IGF‐1R with an inhibitor in old cells. The effects of three kinase inhibitors: AG1024, LY294002, and TCN, were compared in VSMC from old rats to differentiate IGF‐1R from other upstream signaling that could also regulate the Akt/FOXO and ERK pathways. Genes for p27kip‐1, catalase and MnSOD, which play important roles in the control of cell cycle arrest and stress resistance, were found to be FOXO3a‐targets based on FOXO3a‐siRNA treatment. Furthermore, IGF‐1R signaling modulated these genes through activation of the Akt/FOXO3a pathway. Therefore, activation of IGF‐1R signaling influences VSMC function in old rats and may contribute to the increased risk for atherosclerosis. J. Cell. Physiol. 217: 377–387, 2008. © 2008 Wiley‐Liss, Inc.
15‐deoxy‐delta 12,14‐prostaglandin J2 inhibits the synthesis of the acute phase protein SIP24 in cartilage: Involvement of COX‐2 in resolution of inflammation
Authors: Ulivi Valentina , Cancedda Ranieri , Cancedda Fiorella Descalzi 
Published: July 2008

AbstractWe previously demonstrated that, in the MC615 cartilage cell line, the p38/NF‐kB pathway is activated both during differentiation and in response to an inflammatory stimulus. In both cases, the p38/NF‐kB pathway activation leads to the expression of the lipocalin SIP24 and of COX‐2. Given the fact that, in the same cells, the COX‐2 expression is sustained during the inflammation resolution, at the same time that the SIP24 expression is suppressed, in the present study we tested the hypothesis that COX‐2 products play a role in SIP24 repression. Taken together, our results suggest that, during the resolution of inflammation, COX‐2 represses the acute phase protein SIP24 and restores physiological conditions, possibly through a pathway involving PPARγ. Experimental evidences being the following: (1) 15‐deoxy‐delta 12,14‐prostaglandin J2, but not PGE2: (i) inhibits the expression of SIP24 in the inflammatory phase and induces COX‐2 synthesis; (ii) represses NF‐kB activation induced by LPS; (iii) represses the synthesis of microsomal PGE Synthase‐1 induced by LPS. (2) PPARγ and PPARα are present in MC615 cells in both proliferating and hyperconfluent cultures. (3) PPARγ ligand GW7845, but not PPARα ligand GW7647: (i) represses the expression of SIP24 induced by LPS; (ii) induces COX‐2 expression. (4) p38 is involved in the PPARγ mediated induction of COX‐2. In fact 15‐deoxy‐delta 12,14‐prostaglandin J2 activates p38 and the cell pretreatment with the p38 specific inhibitor SB203580 represses the expression of COX‐2 induced by both the 15‐deoxy‐delta12,14‐prostaglandin J2 and the PPARγ ligand GW7845. J. Cell. Physiol. 217: 433–441, 2008. © 2008 Wiley‐Liss, Inc.
The mesenchymal stromal cell contribution to homeostasis
Authors: Valtieri Mauro , Sorrentino Antonio 
Published: July 2008

AbstractAdult mesenchymal stromal cells (MSCs) are undifferentiated multi‐potent cells predominantly residing in the bone marrow (BM), but also present with similar but not identical features in many other tissues such as blood, placenta, dental pulp, and adipose tissue. MSCs have the potential to differentiate into multiple skeletal phenotypes like osteoblasts, chondrocytes, adipocytes, stromal cells, fibroblasts, and possibly tendons. MSCs differentiation potential, ex vivo expansion capacity, nurturing and immunomodulatory proficiencies oriented these versatile cells in several areas of ongoing clinical applications. However, the absence of MSC‐specific markers for isolation and characterization together with the lack of a comprehensive view of the molecular pathways governing their particular biological properties, remains a primary obstacle to their research and application. In this review we discuss some areas of growing interest in MSCs biology: their contribution to the hematopoietic stem cell (HSC) niche, to regenerative medicine, their role in cancer and in therapy as delivery tools and their micro‐RNA (miRNA) signatures. Despite rapid progress in the MSC field, it is generally thought that only a fraction of their full potential has been realized thus far. J. Cell. Physiol. 217: 296–300, 2008. © 2008 Wiley‐Liss, Inc.
Mitotic catastrophe and apoptosis induced by docetaxel in hormone‐refractory prostate cancer cells
Authors: Fabbri Francesco , Amadori Dino , Carloni Silvia , Brigliadori Giovanni , Tesei Anna , Ulivi Paola , Rosetti Marco , Vannini Ivan , Arienti Chiara , Zoli Wainer , Silvestrini Rosella 
Published: July 2008

AbstractStudies performed in different experimental and clinical settings have shown that Docetaxel (Doc) is effective in a wide range of tumors and that it exerts its activity through multiple mechanisms of action. However, the sequence of events induced by Doc which leads to cell death is still not fully understood. Moreover, it is not completely clear how Doc induces mitotic catastrophe and whether this process is an end event or followed by apoptosis or necrosis. We investigated the mechanisms by which Doc triggers cell death in hormone‐refractory prostate cancer cells by analyzing cell cycle perturbations, apoptosis‐related marker expression, and morphologic cell alterations. Doc induced a transient increase in G2/M phase followed by the appearance of G0/1 hypo‐ and hyperdiploid cells and increased p21 expression. Time‐ and concentration‐dependent apoptosis was induced in up to 70% of cells, in concomitance with Bcl‐2 phosphorylation, which was followed by caspase‐2 and ‐3 activation. In conclusion, Doc would seem to trigger apoptosis in hormone‐refractory prostate cancer cells via mitotic catastrophe through two forms of mitotic exit, in concomitance with increased p21 expression and caspase‐2 activation. J. Cell. Physiol. 217: 494–501, 2008. © 2008 Wiley‐Liss, Inc.
Low‐power laser irradiation activates Src tyrosine kinase through reactive oxygen species‐mediated signaling pathway
Authors: Zhang Juntao , Xing Da , Gao Xuejuan 
Published: July 2008

AbstractLow‐power laser therapy in medicine is widespread but the mechanisms are not fully understood. It has been suggested that low‐power laser irradiation (LPLI) could induce photochemical reaction and activate several intracellular signaling pathways. Reactive oxygen species (ROS) are considered to be the key secondary messengers produced by LPLI. Here, we studied the signaling pathway mediated by ROS upon the stimulation of LPLI. Src tyrosine kinases are well‐known targets of ROS and can be activated by oxidative events. Using a Src reporter based on fluorescence resonance energy transfer (FRET) and confocal laser scanning microscope, we visualized the dynamic Src activation in Hela cells immediately after LPLI. Moreover, Src activation by LPLI was in a dose‐dependent manner. The increase of Src phosphorylation at Tyr416 was detected by Western blotting. In the presence of vitamin C, catalase alone, or the combination of catalase and superoxide dismutase (SOD), the activation of Src by LPLI is significantly abolished. In contrast, Gö6983 loading, a PKC inhibitor, did not affect this response. Treatment of Hela cells with exogenous H2O2 also resulted in a concentration‐dependent activation of Src. These results demonstrated that it was ROS that mediated Src activation by LPLI. Cellular viability assay revealed that laser irradiation of low doses (≤25 J/cm2) promoted Hela cells viability while high doses impaired. Therefore, LPLI induces ROS‐mediated Src activation which may play an important role in biostimulatory effect of LPLI. J. Cell. Physiol. 217: 518–528, 2008. © 2008 Wiley‐Liss, Inc.
S10 phosphorylation of p27 mediates atRA induced growth arrest in ovarian carcinoma cell lines
Authors: Radu Maria , Soprano Dianne R. , Soprano Kenneth J. 
Published: July 2008

AbstractAll trans retinoic acid (atRA) has been shown to inhibit the growth of CAOV3 ovarian carcinoma cells and to elevate the level of p27 cyclin‐dependent kinase inhibitor. We report here that phosphorylation at S10 residue is an important event in mediating p27 role in atRA induced growth arrest. atRA treatment of atRA sensitive CAOV3 cells increases the levels of S10 phospho‐p27 in both nuclear and cytoplasmic cell compartments. This increase is accompanied by a decrease in the levels of skp2 protein. This effect was not observed in SKOV3 cells which are resistant to atRA growth inhibitory effect. An A10‐p27 mutant that cannot be phosphorylated at S10 induces a dominant negative effect on the atRA effect on the levels and activity of endogenous p27. Overexpression of A10‐p27 mutant renders CAOV3 cells more resistant to atRA treatment and reverses the effect that atRA has on p27 binding to CDKs, on CDK activity, and on the expression of S phase genes. J. Cell. Physiol. 217: 558–568, 2008. © 2008 Wiley‐Liss, Inc.
Extraction and separation of molybdenum(VI) from acidic media by fatty hydrazides
Authors: Mohamad Sharifah , Wan Yunus Wan Md Zin , Haron Md Jelas , Abdul Rahman Mohd Zaki 
Published: July 2008

AbstractBACKGROUND: The increasing demand for molybdenum has encouraged the development of low‐cost and environmentally friendly extractants to recycle and recover this metal. In the present study, solvent extraction of Mo(VI) from acidic media using a mixture of fatty hydrazides synthesised from palm olein as the extractant was carried out. The effects of various parameters such as acid, diluent, contact time, extractant concentration, metal ion concentration and stripping agent and the separation of Mo(VI) from other metal ions such as Co(II), Ni(II), Al(III) and Mn(II) were investigated.RESULTS: It was found that the extraction of Mo(VI) into the organic phase involved the formation of 1:3 complexes. Mo(VI) was successfully separated from commonly associated metal ions such as Ni(II), Co(II), Al(III) and Mn(II). Mo(VI) stripping from the loaded organic phase was studied using different acidic and alkaline solutions and was found to be optimal with ammonium hydroxide solution.CONCLUSION: These results are useful for the development of a method to recover Mo(VI) from acidic media utilising fatty hydrazides as the extractant. Copyright © 2008 Society of Chemical Industry
Detection of microembolic signals using power M‐mode Doppler sonography in acute stroke patients with intracranial artery stenosis
Authors: Tan Teng‐Yeow , Chen Ting‐Yao 
Published: July 2008

AbstractPurpose.Microembolic signals (MES) can be detected in a variety of clinical situations using conventional transcranial Doppler (TCD) sonography. We studied the prevalence of positive MESs in acute stroke patients with intracranial artery stenosis using power M‐mode Doppler (PMD) sonography and also tested the feasibility of this new technique.Method.Thirty‐three consecutive acute ischemic stroke or transient ischemic attack patients with intracranial large artery occlusive disease were enrolled. PMD/TCD monitoring for 30 minutes was used for MES detection downstream of the stenotic artery within 1 week after stroke onset. Clinical risk factors in emboli‐positive and emboli‐negative patients were assessed.Results.MESs were detected in 21% (7/33) of patients. No significant differences were found in clinical risk factors between emboli‐positive and emboli‐negative patients.Conclusion.PMD sonography to detect MESs in acute stroke patients is feasible and may be used in future clinical trials regarding MES detection. © 2008 Wiley Periodicals, Inc. J Clin Ultrasound, 2008
Retrieval of absorptive potential variation in electron beam sensitive specimens using a single energy‐filtered bright‐field TEM image
Authors: Bhattacharyya Somnath , Jinschek Joerg R. 
Published: July 2008

AbstractA method is presented for retrieving the variation of the absorptive potential in electron beam sensitive soft material. The absorptive potential is directly related to the variations in atomic density and in chemical composition fluctuation. In our approach only a single zero‐loss energy‐filtered bright‐field transmission electron microscopy (TEM) image is sufficient to obtain this information. The accuracy and the effectiveness of this proposed method has been tested using both simulation and experiment. As an experimental example of soft (organic) material, the variation in absorptive potential in an unstained tissue sample of zebrafish gill has been determined. Microsc. Res. Tech., 2008. © 2008 Wiley‐Liss, Inc.
Image signal‐to‐noise ratio estimation using Shape‐Preserving Piecewise Cubic Hermite Autoregressive Moving Average model
Authors: Sim K.S. , Wee M.Y. , Lim W.K. 
Published: July 2008

AbstractWe propose to cascade the Shape‐Preserving Piecewise Cubic Hermite model with the Autoregressive Moving Average (ARMA) interpolator; we call this technique the Shape‐Preserving Piecewise Cubic Hermite Autoregressive Moving Average (SP2CHARMA) model. In a few test cases involving different images, this model is found to deliver an optimum solution for signal to noise ratio (SNR) estimation problems under different noise environments. The performance of the proposed estimator is compared with two existing methods: the autoregressive‐based and autoregressive moving average estimators. Being more robust with noise, the SP2CHARMA estimator has efficiency that is significantly greater than those of the two methods. Microsc. Res. Tech., 2008. © 2008 Wiley‐Liss, Inc.