bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptional profiling defines the effects of nickel in human epidermal keratinocytes
Authors: Gazel Alix , Rosdy Martin , Tornier Carine , De Fraissinette Anne De Brugerolle , Blumenberg Miroslav
Published: July 2008

Nickel is a ubiquitous and virtually unavoidable environmental pollutant and occupational hazard, but its molecular and cellular effects are not well understood. Human epidermal keratinocytes are the sentinel and the primary target for nickel. We treated with nickel salts skin equivalents containing differentiating epidermal keratinocytes grown on air–liquid interface in standard cell culture conditions. We identified the transcriptional profiles affected by nickel in reconstructed human epidermis (RHE) using DNA microarrays. The Ni‐regulated genes were determined at two time points, immediate‐early, 30 min after treatment, and late, at 6 h. Using in silico data analysis, we determined that 134 genes are regulated by nickel; of these, 97 are induced and 37 suppressed. Functional categories of regulated genes suggest that Ni inhibits apoptosis, promotes cell cycle and induces synthesis of extracellular matrix proteins and extracellular proteases. Importantly, Ni also regulates a set of secreted signaling proteins, inducing VEGF, amphiregulin, PGF, GDF15, and BST2, while suppressing IL‐18, galectin‐3, and LITAF. These secreted proteins may be important in Ni‐caused allergic reactions. Ni induced inhibitors of the NFκB signaling pathway, and suppressed its activators. Correspondingly, NFκB binding sites were found to be overrepresented in the Ni‐suppressed genes, whereas cFOS/AP1 binding sites were common in the Ni‐induced genes. Significant parallels were found between the Ni‐regulated genes and the genes regulated by TGFβ, EGF, glucocorticoids, or Oncostatin‐M. The comprehensive identification of Ni‐regulated genes in human epidermal equivalents significantly advances our understanding of the molecular effects of nickel in skin. J. Cell. Physiol. 217: 686–692, 2008. © 2008 Wiley‐Liss, Inc.
Induction of HIF‐1α expression by intermittent hypoxia: Involvement of NADPH oxidase, Ca2+ signaling, prolyl hydroxylases, and mTOR
Authors: Yuan Guoxiang , Nanduri Jayasri , Khan Shakil , Semenza Gregg L. , Prabhakar Nanduri R.
Published: July 2008

Sleep‐disordered breathing with recurrent apnea (periodic cessation of breathing) results in chronic intermittent hypoxia (IH), which leads to cardiovascular and respiratory pathology. Molecular mechanisms underlying IH‐evoked cardio‐respiratory co‐morbidities have not been delineated. Mice with heterozygous deficiency of hypoxia‐inducible factor 1α (HIF‐1α) do not develop cardio‐respiratory responses to chronic IH. HIF‐1α protein expression and HIF‐1 transcriptional activity are induced by IH in PC12 cells. In the present study, we investigated the signaling pathways associated with IH‐evoked HIF‐1α accumulation. PC12 cells were exposed to aerobic conditions (20% O2) or 60 cycles of IH (30 sec at 1.5% O2 followed by 5 min at 20% O2). Our results show that IH‐induced HIF‐1α accumulation is due to increased generation of ROS by NADPH oxidase. We further demonstrate that ROS‐dependent Ca2+ signaling pathways involving phospholipase Cγ (PLCγ) and protein kinase C activation are required for IH‐evoked HIF‐1α accumulation. IH leads to activation of mTOR and S6 kinase (S6K) and rapamycin partially inhibited IH‐induced HIF‐1α accumulation. IH also decreased hydroxylation of HIF‐1α protein and anti‐oxidants as well as inhibitors of Ca+2 signaling prevented this response. Thus, both increased mTOR‐dependent HIF‐1α synthesis and decreased hydroxylase‐dependent HIF‐1α degradation contribute to IH‐evoked HIF‐1α accumulation. Following IH, HIF‐1α, and phosphorylated mTOR levels remained elevated during 90 min of re‐oxygenation despite re‐activation of prolyl hydroxylase. Rapamycin or cycloheximide, blocked increased HIF‐1α levels during re‐oxygenation indicating that mTOR‐dependent protein synthesis is required for the persistent elevation of HIF‐1α levels during re‐oxygenation. J. Cell. Physiol. 217: 674–685, 2008. © 2008 Wiley‐Liss, Inc.
Stimulation of macrophage TNFα production by orthopaedic wear particles requires activation of the ERK1/2/Egr‐1 and NF‐κB pathways but is independent of p38 and JNK
Authors: Beidelschies Michelle A. , Huang Honglian , McMullen Megan R. , Smith Matthew V. , Islam Andrew S. , Goldberg Victor M. , Chen Xin , Nagy Laura E. , Greenfield Edward M.
Published: July 2008

Bone loss that causes aseptic loosening of orthopedic implants is initiated by pro‐inflammatory cytokines produced by macrophages in response to implant‐derived wear particles. MAPK and NF‐κB signaling pathways are activated by the particles; however, it is not clear which of the signaling pathways are important for the initial response to the wear particles and which are only involved at later steps in the process, such as osteoclast differentiation. Here, we show that the ERK1/2, p38, JNK, and NF‐κB pathways are rapidly activated by the wear particles but that only the ERK1/2 and NF‐κB pathways are required for the initial response to the wear particles, which include increases in TNFα promoter activity, TNFα mRNA expression, and secretion of TNFα protein. Moreover, ERK1/2 activation by wear particles is also required for increased expression of the transcription factor Egr‐1 as well as Egr‐1's ability to bind to and activate the TNFα promoter. These results, together with our previous studies of the PI3K/Akt pathway, demonstrate that wear particles coordinately activate multiple signaling pathways and multiple transcription factors to stimulate production of pro‐inflammatory cytokines, such as TNFα. The current study also demonstrates that the signaling pathways are activated to a much greater extent by wear particles with adherent endotoxin than by “endotoxin‐free” wear particles. These results, together with those demonstrating the requirement for ERK1/2/Egr‐1 and NF‐κB, show that activation of these signaling pathways is responsible for the ability of adherent endotoxin to potentiate cytokine production, osteoclast differentiation, and bone loss induced by wear particles. J. Cell. Physiol. 217: 652–666, 2008. © 2008 Wiley‐Liss, Inc.
Synergistic anti‐proliferative and pro‐apoptotic activity of combined therapy with bortezomib, a proteasome inhibitor, with anti‐epidermal growth factor receptor (EGFR) drugs in human cancer cells
Authors: Cascone Tina , Morelli Maria Pia , Morgillo Floriana , Kim Woo‐Young , Rodolico Gabriella , Pepe Stefano , Tortora Giampaolo , Berrino Liberato , Lee Ho‐Young , Heymach John V. , Ciardiello Fortunato
Published: July 2008

The article to which this erratum refers was published in J Cell Physiol (2008) 216: 698–707. © 2008 Wiley‐Liss, Inc. DOI: 10.1002/jcp.21444
Cancer initiating cells or cancer stem cells in the gastrointestinal tract and liver
Authors: Zou Gang‐Ming
Published: July 2008

It has been suggested that cancer stem cells population within the solid tumor with indefinite proliferation potential drives the growth and metastasis of cancer. In literature, these malignant stem cells also named Cancer initiating cells. Cancer stem cells exhibit low rate of division and proliferation in their niche that help them to avoid chemotherapy and radiation. Epithelial cancers are believed to originate from transformation of tissue stem cells. Bone marrow‐derived cells, which are frequently recruited to sites of tissue injury and inflammation, might also represent a potential source of malignancy in the gastrointestinal tract. Pancreatic cancer is one of most common cause of cancer‐related death. Pancreatic cancer stem cells have been characterized recently through serial transplantation of human pancreatic cancer cells. The phenotype of Pancreatic cancer stem cells has been defined as CD24+CD44+CD326 (ESA)+. CD133 antigen has been also suggested as a potential marker for cancer stem cell in gastrointestinal tract but recently there is also debate in this regard. More recently, other cancer stem cells in gastrointestinal tract, such as colon cancer stem cells, liver cancer stem cells, have been also characterized in their phenotype. These advances clearly will bring the new strategy in cancer treatment and control in the gastrointestinal tract. In this review, the author will discuss the current status and progress about cancer stem cell research in gastrointestinal tract and liver. J. Cell. Physiol. 217: 598–604, 2008. © 2008 Wiley‐Liss, Inc.
Signaling pathways in medulloblastoma
Authors: Guessous Fadila , Li Yunqing , Abounader Roger
Published: July 2008

Medulloblastoma is the most common brain tumor of childhood. Multiple signaling pathways have been associated with medulloblastoma formation and growth. These include the developmental pathways Hedgehog, (Hh) Notch, and Wnt as well as the receptor tyrosine kinases (RTK) c‐Met, erbB2, IGF‐R and TrkC, and the oncoprotein Myc. Here we review the involvement of these pathways in medulloblastoma malignancy with a focus on their mode of deregulation, prognostic value, functional effects, cellular and molecular mechanisms of action, and implications for therapy. J. Cell. Physiol. 217: 577–583, 2008. © 2008 Wiley‐Liss, Inc.
The common house spider alters the material and mechanical properties of cobweb silk in response to different prey
Authors: Boutry Cecilia , Blackledge Todd A.
Published: July 2008

Many spiders depend upon webs to capture prey. Web function results from architecture and mechanical performance of the silk. We hypothesized that the common house spider, Achaearanea tepidariorum, would alter the mechanical performance of its cobweb in response to different prey by varying the structural and material properties of its silk. We fed spiders either large, high kinetic energy crickets or small, low kinetic energy pillbugs for 1 week and then examined their freshly spun silk. We separated mechanical performance into structural and material effects. We measured both types of properties for silk threads collected directly from cobwebs to test for “tuning” of silk performance to different aspects of prey capture. We compared silk from two different functional regions of the cobweb—sticky gumfooted threads that adhere directly to prey and supporting threads that maintain web integrity. Supporting threads from cricket‐fed spiders were stiffer and tougher than supporting threads from pillbug‐fed spiders. Both types of silk from cricket‐fed spiders broke at higher loads than silk from pillbug‐fed spiders. We explain this variation using a simple model of forces exerted by prey and spiders on single threads and propose potential mechanisms for this change in material properties. Two alternative, nonexclusive, hypotheses are suggested by our data. Spiders may tune silk to different types of prey by spinning threads that are able to hold prey without deforming permanently. Alternatively, as spider's body mass differed dramatically between the two feeding regimes, spiders may tune silk to their own body mass. J. Exp. Zool. 309A:542–552, 2008. © 2008 Wiley‐Liss, Inc.
Incremental effects of reward on experienced performance pressure: positive outcomes for intrinsic interest and creativity
Authors: Eisenberger Robert , Aselage Justin
Published: July 2008

Two field studies and a laboratory study examined the influence of reward for high performance on experienced performance pressure, intrinsic interest and creativity. Study 1 found that employees' expected reward for high performance was positively related to performance pressure which, in turn, was positively associated with the employees' interest in their jobs. Study 2 replicated this finding and showed that intrinsic interest, produced by performance pressure, was positively related to supervisors' ratings of creative performance. Study 3 found that college students' receipt of reward for high performance increased their experienced performance pressure which, in turn, was positively related to intrinsic interest and creativity. Copyright © 2008 John Wiley & Sons, Ltd.
Boundaryless careers, social capital, and knowledge management: Implications for organizational performance
Authors: Lazarova Mila , Taylor Sully
Published: July 2008

The purpose of this paper is to critically assess the utilization of boundaryless careers in organizations through the lens of how they impact the formation and deployment of organizational social capital. We build a model of the positive and negative effects of boundaryless careers on social capital formation by proposing a more nuanced picture of boundaryless careers. We divide boundaryless careers into four types: internal psychological, internal enacted, external psychological and external enacted. Our model delineates the conditions under which different types of boundaryless careers affect the formation and deployment of organizational structural, relational and cognitive social capital and offer propositions based on our analysis. In addition we examine type of knowledge (exploratory or exploitative) pursued by the firm as a key moderator for the relationships we propose. Copyright © 2008 John Wiley & Sons, Ltd.
Polymeric Microcapsules for Synthetic Applications
Authors: Lensen Dennis , Vriezema Dennis M. , van Hest Jan C. M.
Published: July 2008

For decades scientists have been working on closed systems for transportation, catalysis and protection, which are inspired by natural cells. Only recently polymer based systems have emerged for these systems, since they are more robust, give protection from the environment and give a more stable membrane. Various methods have been developed to prepare polymer based capsules. They can be made by self‐assembly, templating, in situ polymerization or precipitation. Their application has been explored in various areas e.g. drug delivery, diagnostics, sensors and nano reactors. Considering the output in this field has substantially grown, more developments can be expected from this latter application.

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Test results regarding the corrosion protection of the reinforcement at the application of acrylate gels in concrete cracks
Authors: Raupach M. , Harnisch J. , Wolff L.
Published: July 2008

This paper deals with the possible corrosion risk for steel rebars in cracked reinforced concrete structures by using acrylate gels for grouting. In the course of this project, 19 customary acrylate gels were analysed. The results of the conducted test procedures revealed that none of the tested acrylate gels can provide an active corrosion protection for the steel rebars due to their low electrolytic resistivity and low pH values. Just when applied in very thin layers (e.g., fine cracks) it seems to be possible that alkaline components of the surrounding concrete can penetrate through the gel to form a passive layer on the embedded steel rebar.
Multisecular corrosion behaviour of low carbon steel in anoxic soils: Characterisation of corrosion system on archaeological artefacts
Authors: Saheb M. , Neff D. , Dillmann P. , Matthiesen H. , Foy E. , Bellot‐Gurlet L.
Published: July 2008

In the context of the prediction of materials behaviour used in the nuclear waste storage, the understanding of iron corrosion mechanisms in anoxic environment is of great importance. Information can be obtained using complementary analytical tools. Interactions between burial soil and archaeological artefacts are studied by performing on site soil measurements. Moreover, archaeological artefacts are studied on transverse sections using a combination of microbeam techniques. The specific interest of this project lies in the study of ferrous thick corrosion layers formed in anoxic environments.
Characterization of long‐term corrosion of rebars embedded in concretes sampled on French historical buildings aged from 50 to 80 years
Authors: L'Hostis V. , Neff D. , Bellot‐Gurlet L. , Dillmann P.
Published: July 2008

The aim of this paper is to understand what the chemical influence of the concrete on the corrosion form present is, on rebars embedded for tens or hundreds years. Therefore, metal/concrete interface of samples coming from two French Historical Monuments has been characterized: ‘Bourse du Travail’, Bordeaux, 80 years old and ‘Maison du Brésil de la Cité Internationale de Paris’, 50 years old. The collected samples have been observed on transverse section in order to observe the whole corrosion system (metal/corrosion products/concrete). Morphology, elementary composition and structure have been studied with complementary analytical approaches (optical microscope, scanning electron microscope coupled to energy dispersive spectroscopy and Raman microspectroscopy). Thus, a fine description of the corrosion scales formed on the metallic rebars can be schematized. On the basis of these results, mechanisms hypotheses are proposed in the discussion.
Effect of humidity and chloride content on the corrosion of steel embedded in LWA concrete
Authors: Vennesland Ø. , Havdahl J.
Published: July 2008

Measurements have been made with mortar specimens with light aggregates (LWA) and the cements Norcem HS65 and MP30, corresponding to CEM I and CEM II. The w/b ratio was 0.30 and 0.40 and in one mix prewetted LWA was used. The silica fume addition was 8%. The specimens have two sets of electrodes consisting of a 10 mm reinforcing steel and a 10 mm rod of stainless steel.

In the start of the experiment the chloride penetration was accelerated by applying a voltage between a negatively charged steel plate within the salt solution and a positively charged net of stainless steel embedded in the concrete above the reinforcing steels. This caused some problems and the set‐up was changed to using a Plexiglas brim and a solution of calcium hydroxide and sodium chloride was applied. In the solution, a titanium net was placed and a positive voltage of 12 V was applied between the embedded steels and the net with the titanium net as the positive pole.

Measuring galvanic currents, electrochemical potential and polarisation resistances have presented a good picture of the corrosion activity of the embedded steels. There is a distinct effect of the humidity upon the corrosion activity registered by the electrochemical measurements.

There is a good relation between the electrochemical measurements and the observed corrosion attacks at the end of the experiments.

The LWA concrete with water saturated aggregates showed more corrosion than the corresponding LWA concrete with dry aggregates. The rates of corrosion measured both as a galvanic current and as a function of the polarisation resistance showed that the concrete with watered aggregate concrete had a corrosion rate about twice as high as the corresponding LWA concrete with dry aggregates.

There are marked differences in the chloride penetration for the different cements. Effects have been observed on the chloride content of the different concretes. Lower w/b ratio, MP30 cement compared to HS65 and no prewatering of the LWA gave less chloride penetration.
A Strategy for Synthesis of Ion‐Bonded Supramolecular Star Polymers by Reversible Addition‐Fragmentation Chain Transfer (RAFT) Polymerization
Authors: Tao Kang , Lu Dairen , Bai Ruke , Li Hongfei , An Lijia
Published: July 2008

We have developed a novel strategy for the preparation of ion‐bonded supramolecular star polymers by RAFT polymerization. An ion‐bonded star supramolecule with six functional groups was prepared from a triphenylene derivative containing tertiary amino groups and trithiocarbonate carboxylic acid, and used as the RAFT agent in polymerizations of tert‐butyl acrylate (tBA) and styrene (St). Molecular weights and structures of the polymers were characterized by 1H NMR and GPC. The results show that the polymerization possesses the character of living free‐radical polymerization and the ion‐bonded supramolecular star polymers PSt, PtBA, and PSt‐b‐PtBA, with six well‐defined arms, were successfully synthesized.

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Hybrid Process for Fabricating 3D Hierarchical Scaffolds Combining Rapid Prototyping and Electrospinning
Authors: Kim GeunHyung , Son JoonGon , Park SuA , Kim WanDoo
Published: July 2008

An ideal scaffold should have good mechanical properties and provide a biologically functional implant site. A rapid prototyping system has been introduced as a good method of fabricating 3D scaffolds that mimic the structure in the human body. However, the scaffolds have strands that are too smooth and a pore size that is too large relative to the seeded cells and present unfavorable conditions for initial cell attachment. To overcome these problems, we propose a hybrid technology combining a 3D rapid prototyping system and an electrospinning process to produce a hierarchical 3D biomedical scaffold. The resulting structure consists of alternating layers of 3D‐structured/microsized polymer strands and nanofiber webs. The results of cell culturing of chondrocytes indicate that this technique is a feasible new method for fabricating high quality 3D polymeric scaffolds.

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Macromol. Rapid Commun. 15/2008
Authors: Choi Sung‐Ho , Jung Hyun‐Ho , Kim Jae‐Il , Furusho Horotoshi , Geckeler Kurt E
Published: July 2008

Front Cover: The cover picture displays a section of a novel supramolecular, nanoscaled network with a nexus unit in the center that was obtained by self‐assembly via host‐guest inclusion complexation from bifunctional cyclodextrin and trifunctional melamine precursors. This is the first example of a guest‐core supramolecular network. Further details can be found in the article by S.‐H. Choi, H.‐H. Jung, J.‐I. Kim, H. Furusho, and K. E. Geckeler* on page 1279.
Macromol. Rapid Commun. 15/2008
Authors: Tanaka Hiroyuki , Isojima Tatsushi , Hanasaki Minako , Ifuku Yasuo , Takeuchi Hisao , Kawaguchi Haruma , Shiroya Toshifumi
Published: July 2008

Back Cover: A novel method to prepare a three‐dimensional nano‐structured protein hydrogel (3‐D NPH), which is composed of protein‐polymer hybrid nanoparticles has been discovered. The 3‐D NPH can be easily prepared by dispensing a protein and polymer mixture on a substrate (as shown on the cover). Surprisingly, gold particles conjugated with protein A diffuse into the 3‐D NPH which is made of Mouse IgG through the pores. The protein chips made using this 3‐D NPH method show a tremendously improved sensitivity in detecting protein‐protein interactions as compared to that of direct protein immobilization methods. Further details can be found in the article by H. Tanaka, T. Isojima, M. Hanasaki, Y. Ifuku, H. Takeuchi, H. Kawaguchi, and T. Shiroya* on page 1287.
Recent advances in breast MRI and MRS
Authors: Sinha S. , Sinha U.
Published: July 2008

Breast MRI is an area of intense research and is fast becoming an important tool for the diagnosis of breast cancer. This review covers recent advances in breast MRI, MRS, and image post‐processing and analysis. Several studies have explored a multi‐parametric approach to breast imaging that combines analysis of traditional contrast enhancement patterns and lesion architecture with novel methods such as diffusion, perfusion, and spectroscopy to increase the specificity of breast MRI studies. Diffusion‐weighted MRI shows some potential for increasing the specificity of breast lesion diagnosis and is even more promise for monitoring early response to therapy. MRS also has great potential for increasing specificity and for therapeutic monitoring. A limited number of studies have evaluated perfusion imaging based on first‐pass contrast bolus tracking, and these clearly identify that vascular indices have great potential to increase specificity. The review also covers the relatively new acquisition technique of MR elastography for breast lesion characterization. A brief survey of image processing algorithms tailored for breast MR, including registration of serial dynamic images, segmentation and extraction of morphological features of breast lesions, and contrast uptake modeling, is also included. Recent advances in MRI, MRS, and automated image analysis have increased the utility of breast MR in diagnosis, screening, management, and therapy monitoring of breast cancer. Copyright © 2008 John Wiley & Sons, Ltd.
Dynamic contrast‐enhanced MRI in the diagnosis and management of breast cancer
Authors: Turnbull Lindsay W.
Published: July 2008

Dynamic contrast‐enhanced MRI (DCE‐MRI) is an evolving tool for determining breast disease, which benefits from the move to imaging at 3 T. It has major capabilities for the diagnosis, detection and monitoring of malignancy. It benefits from being non‐invasive and three‐dimensional, allowing visualisation of the extent of disease and its angiogenic properties, visualisation of lesion heterogeneity, detection of changes in angiogenic properties before morphological alterations, and the potential to predict the overall response either before the start of therapy or early during treatment. In addition, DCE‐MRI is emerging as a powerful tool for screening high‐risk patients and for detecting high‐grade ductal carcinomain situ. However, there are also a number of limitations, including the overlap in enhancement patterns between malignant and benign disease, the failure to resolve microscopic disease particularly in the neoadjuvant setting, and the inconsistent predictive value of the enhancement pattern for clinical outcome. Careful consideration should be given to the technical requirements of individual examinations and the need for automation of post‐processing techniques to appropriately handle the growing volume of data acquired. Research continues, focusing on the use of higher field strengths with improved spatial and temporal resolution data, improving understanding of the mechanism of contrast enhancement at the cellular level, and developing macromolecular and targeted contrast agents. Copyright © 2008 John Wiley & Sons, Ltd.
Avulsion fractures of the transverse processes of the first thoracic vertebra: an archaeological case study from Raunds
Authors: Upex B. R. , Knüsel C. J.
Published: July 2008

Avulsion fractures of the transverse processes of vertebrae have not been previously identified in the archaeological record. This paper provides a case study of a 21–25 year old male skeleton from the 10th century cemetery at Raunds Furnells (Northamptonshire, UK) with bilateral avulsion fractures of the transverse processes of the first thoracic vertebra. Possible aetiologies of this condition are discussed and conclusions drawn about the impact of this condition upon the individual. Copyright © 2008 John Wiley & Sons, Ltd.
Comparative proteomic and transcriptional profiling of a bread wheat cultivar and its derived transgenic line overexpressing a low molecular weight glutenin subunit gene in the endosperm
Authors: Scossa Federico , Laudencia‐Chingcuanco Debbie , Anderson Olin D. , Vensel William H. , Lafiandra Domenico , D'Ovidio Renato , Masci Stefania
Published: July 2008

We carried out a parallel transcriptional and proteomic comparison of seeds from a transformed bread wheat line that overexpresses a transgenic low molecular weight glutenin subunit gene relative to the corresponding nontransformed genotype. Proteomic analyses showed that, during seed development, several classes of endosperm proteins were differentially accumulated in the transformed endosperm. As a result of the strong increase in the amount of the transgenic protein, the endogenous glutenin subunit, all subclasses of gliadins, and metabolic as well as chloroform/methanol soluble proteins were diminished in the transgenic genotype. The differential accumulation detected by proteomic analyses, both in mature and developing seeds, was paralleled by the corresponding changes in transcript levels detected by microarray experiments. Our results suggest that the most evident effect of the strong overexpression of the transgenic glutenin gene consists in a global compensatory response involving a significant decrease in the amounts of polypeptides belonging to the prolamin superfamily. It is likely that such compensation is a consequence of the diversion of amino acid reserves and translation machinery to the synthesis of the transgenic glutenin subunit.
Facile synthesis of C8‐functionalized magnetic silica microspheres for enrichment of low‐concentration peptides for direct MALDI‐TOF MS analysis
Authors: Chen Hemei , Xu Xiuqing , Yao Ning , Deng Chunhui , Yang Pengyuan , Zhang Xiangmin
Published: July 2008

In this study, novel C8‐functionalized magnetic polymer microspheres were prepared by coating single submicron‐sized magnetite particle with silica and subsequent modification with chloro (dimethyl) octylsilane. The resulting C8‐functionalized magnetic silica (C8‐f‐M‐S) microspheres exhibit well‐defined magnetite‐core‐silica‐shell structure and possess high content of magnetite, which endow them with high dispersibility and strong magnetic response. With their magnetic property, the synthesized C8‐f‐M‐S microspheres provide a convenient and efficient way for enrichment of low‐abundance peptides from tryptic protein digest and human serum. The enriched peptides/proteins were subjected for MALDI‐TOF MS analysis and the enrichment efficiency was documented. In a word, the facile synthesis and efficient enrichment process of the novel C8‐f‐M‐S microspheres make them promising candidates for isolation of peptides even in complex biological samples such as serum, plasma, and urine.
Analysis of immunoglobulin glycosylation by LC‐ESI‐MS of glycopeptides and oligosaccharides
Authors: Stadlmann Johannes , Pabst Martin , Kolarich Daniel , Kunert Renate , Altmann Friedrich
Published: July 2008

Two LC‐ESI‐MS methods for the analysis of antibody glycosylation are presented. In the first approach, tryptic glycopeptides are separated by RP chromatography and analyzed by ESI‐MS. This “glycopeptide strategy” allows a protein‐ and subclass‐specific quantitation of both neutral and sialylated glycan structures. Additional information about under‐ or deglycosylation and the protein backbone, e.g., termini, can be extracted from the same data. In the second LC‐ESI‐MS method, released oligosaccharides are separated on porous graphitic carbon (PGC). A complete structural assignment of neutral and sialylated oligosaccharides occurring on antibodies is thereby achieved in one chromatographic run. The two methods were applied to polyclonal human IgG, to commercial mAb expressed in CHO cells (Rituximab, Xolair, and Herceptin), in SP2/0 (Erbitux and Remicade) or NS0 cells (Zenapax) and the anti‐HIV antibody 4E10 produced either in CHO cells or in a human cell line. Both methods require comparably little sample preparation and can be applied to SDS‐PAGE bands. They both outperform non‐MS methods in terms of reliability of peak assignment and MALDI‐MS of underivatized glycans with regard to the recording of sialylated structures. Regarding fast and yet detailed structural assignment, LC‐MS on graphitic carbon supersedes all other current methods.
O‐acetylation of sialic acids in N‐glycans of Atlantic salmon (Salmo salar) serum is altered by handling stress
Authors: Liu Xin , Afonso Luis , Altman Eleonora , Johnson Stewart , Brown Laura , Li Jianjun
Published: July 2008

O‐acetylation is one of the major modifications of sialic acids that significantly alters biological properties of the parent molecule. These O‐acetylated forms are components of the cellular membrane and can affect physiological and pathological responses. Understanding the role of N‐glycans in physiology is of increasing relevance to cellular biologists in various disciplines who study glycoproteomics yet lack information regarding the function of the attached glycans. It is well known that stress may decrease immune function in fish; however, there are only few suitable biomarkers available to monitor the physiological responses under the stress conditions. This study is the first report on the effect of stress on the profile of O‐acetylation of sialic acids in fish serum. In order to preserve the relevant structural characteristics as much as possible, native N‐glycans were directly analyzed using CE‐MS. We have characterized the N‐glycans in serum of salmon (Salmo salar) exposed to long‐term handling stress (15 s out of the water, daily for 4 wk) and compared with the results obtained from sera of control fish. The results indicated that major N‐glycans in salmon serum contained mono‐acetylated sialic acids (83%), and that the O‐acetylation pattern of sialic acids could be altered by long‐term stress.
Increasing information from shotgun proteomic data by accounting for misassigned precursor ion masses
Authors: Scherl Alexander , Tsai Yihsuan Shannon , Shaffer Scott A. , Goodlett David R.
Published: July 2008

Although mass spectrometers are capable of providing high mass accuracy data, assignment of true monoisotopic precursor ion mass is complicated during data‐dependent ion selection for LC‐MS/MS analysis of complex mixtures. The complication arises when chromatographic peak widths for a given analyte exceed the time required to acquire a precursor ion mass spectrum. The result is that many measured monoisotopic masses are misassigned due to calculation from a single mass spectrum with poor ion statistics based on only a fraction of the total available ions for a given analyte. Such data in turn produces errors in automated database searches, where precursor m/z value is one search parameter. We propose here a postacquisition approach to correct misassigned monoisotopic m/z values that involves peak detection over the entire elution profile and correction of the precursor ion monoisotopic mass. As a result of using this approach to reprocess shotgun proteomic data we increased peptide sequence assignments by 10% while reducing the estimated false positive ratio from 1 to 0.2%. We also show that 4% of the salvaged identifications may be accounted for by correction of mixed tandem mass spectra resulting from fragmentation of multiple peptides simultaneously, a situation which we refer to as accidental CID.
Proteomic analysis of hypoxia‐induced tube breakdown of an in vitro capillary model composed of HUVECs: Potential role of p38‐regulated reduction of HSP27
Authors: Eguchi Ryoji , Naitou Hirotaka , Kunimasa Kazuhiro , Ayuzawa Rie , Fujimori Yoshihiro , Ohashi Norio , Kaji Kazuhiko , Ohta Toshiro
Published: July 2008

We recently reported that hypoxia could induce the breakdown of capillary‐like tubes formed by human umbilical vein endothelial cells (HUVECs) and that this breakdown was regulated by p38 and not by a caspase cascade, although the exact molecular mechanisms remain unknown. The aim of this study was to identify proteins that regulated hypoxia‐induced tube breakdown through p38‐regulated and caspase‐independent mechanisms. The involvement of adhesion proteins, integrins, VE‐cadherin, PECAM‐1, and occludin was first investigated. Although some of these proteins decreased after hypoxia, none of them met the conditions of being quantitatively restored by p38 inhibition but not by caspase inhibition. We then conducted 2‐D DIGE coupled with MALDI‐TOF/TOF‐MS to identify altered protein expression. The differential proteomic analysis of tube‐forming HUVECs treated with normoxia or hypoxia and treated with hypoxia in the presence or absence of SB203580, a specific p38 inhibitor, revealed the involvement of heat shock proteins in this tube breakdown. We also confirmed that the amount of HSP27 and HSP70 changed in a p38‐regulated and caspase‐independent manner during hypoxia. Knocking down HSP27 expression using RNAi further augmented hypoxia‐induced tube breakdown. Taken together, it was shown that p38‐regulated and caspase‐independent reduction of HSP27 plays an important role in hypoxia‐induced tube breakdown.
Inhaled anesthetics elicit region‐specific changes in protein expression in mammalian brain
Authors: Pan Jonathan Z. , Xi Jin , Eckenhoff Maryellen F. , Eckenhoff Roderic G.
Published: July 2008

Inhaled anesthetics bind specifically to many proteins in the mammalian brain. Within the subgroup of proteins whose activity is substantially modulated by anesthetic binding, it is reasonable to expect anesthetic‐induced alterations in host expression level. Thus, in an attempt to define the group of functional targets for these commonly used drugs, we examined changes in protein expression after anesthetic exposure in both intact rodent brains and in neuronal cell culture. Differential in‐gel electrophoresis was used to minimize variance, in order to detect small changes. Quantitative analysis shows that 5 h exposures to 1 minimum alveolar concentration (1 MAC) halothane caused changes in the expression of ∼2% of detectable proteins, but only at 2–24 h after awakening, and only in the cortex. An equipotent concentration of isoflurane altered the expression of only ∼1% of detectable proteins, and only in the hippocampus. Primary cortical neurons were exposed to three‐fold higher concentrations of anesthetics with no evidence of cytotoxicity. Small changes in protein expression were elicited by both drugs. Despite the fact that anesthetics produce profound changes in neurobiology and behavior, we found only minor changes in brain protein expression. A pronounced degree of regional selectivity was noted, indicating an under appreciated degree of specificity for these promiscuous drugs.
Free‐flow electrophoresis for top‐down proteomics by Fourier transform ion cyclotron resonance mass spectrometry
Authors: Ouvry‐Patat Séverine A. , Torres Matthew P. , Quek Hung‐Hiang , Gelfand Craig A. , O'Mullan Patrick , Nissum Mikkel , Schroeder Gottfried K. , Han Jun , Elliott Monica , Dryhurst Deanna , Ausio Juan , Wolfenden Richard , Borchers Christoph H.
Published: July 2008

High‐efficiency prefractionation of complex protein mixtures is critical for top‐down proteomics, i.e., the analysis of intact proteins by MS. Free‐flow electrophoresis (FFE) can be used for IEF to separate proteins within a pH gradient according to their pIs. In an FFE system, this separation is performed entirely in the liquid phase, without the need for particulate chromatographic media, gels, or membranes. Herein, we demonstrated the compatibility of IEF‐FFE with ESI‐Fourier transform ICR MS (ESI‐FTICR‐MS) for top‐down experiments. We demonstrated that IEF‐FFE of intact proteins were highly reproducible between FFE instruments, between laboratories, and between analyses. Applying native (0.2% hydroxypropylmethyl cellulose) IEF‐FFE to an enzyme resulted in no decrease in enzyme activity; applying either native or denaturing (8 M urea) IEF‐FFE to a four‐protein mixture with different pIs resulted in isolation of each protein into separate fractions in a 96‐well plate. After desalting, each protein was sequenced by top‐down MS/MS. As an application of this technique, chicken erythrocyte histone H2A‐IV and its major modified forms were enriched by IEF‐FFE. Top‐down analysis revealed Lys‐5 to be a major acetylation site, in addition to N‐terminal acetylation.
Proteomic identification of a PSF/p54nrb heterodimer as RNF43 oncoprotein‐interacting proteins
Authors: Miyamoto Kentaro , Sakurai Hidetaka , Sugiura Takeyuki
Published: July 2008

RNF43 is an oncogenic RING finger protein overexpressed in colorectal cancer. To dissect its biological functions, we explored RNF43‐interacting proteins by pull‐down assay and MS. We identified a heterodimer, p54nrb and PSF, as RNF43's binding partners and confirmed their physical interaction in vivo by the co‐immunoprecipitation experiment. Immunofluorescence analysis revealed that co‐expression of PSF relocates RNF43 from the nuclear periphery to the nucleoplasm. Thus, proteomic identification of RNF43‐associated proteins sheds light on its dynamic interaction network in nuclear events.
A whole‐genome bioinformatics approach to selection of antigens for systematic antibody generation
Authors: Berglund Lisa , Björling Erik , Jonasson Kalle , Rockberg Johan , Fagerberg Linn , Al‐Khalili Szigyarto Cristina , Sivertsson Åsa , Uhlén Mathias
Published: July 2008

Here, we present an antigen selection strategy based on a whole‐genome bioinformatics approach, which is facilitated by an interactive visualization tool displaying protein features from both public resources and in‐house generated data. The web‐based bioinformatics platform has been designed for selection of multiple, non‐overlapping recombinant protein epitope signature tags by display of predicted information relevant for antigens, including domain‐ and epitope sized sequence similarities to other proteins, transmembrane regions and signal peptides. The visualization tool also displays shared and exclusive protein regions for genes with multiple splice variants. A genome‐wide analysis demonstrates that antigens for approximately 80% of the human protein‐coding genes can be selected with this strategy.
Surface segregation of highly branched polymer additives in linear hosts
Authors: Qian Zhenyu , Minnikanti Venkatachala S. , Archer Lynden A.
Published: July 2008

Entropy‐driven segregation of various branched and hyperbranched polymeric additives in chemically similar linear polymer hosts is studied using self‐consistent (SCF) mean‐field lattice simulations. The simulations account for the effect of molecular architecture on local configurational entropy in the blends, but ignores the effect of architecture on local density and blend compressibility. Star, dendrimer, and comb‐like additives are all found to be enriched at the surface of chemically identical linear host polymers. The magnitude of their surface excess increases with increased number of chain ends and decreases with increased segmental crowding near the branch point. Provided the number of arms and molecular weight of the branched additives are maintained constant, we find that the simplest branched architecture, the symmetric star, exhibits the strongest preference for the surface of binary polymer blends. We show that a single variable, here termed the “entropic driving force density,” controls the relative surface affinities of branched additives possessing a wide range of architectures. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1788–1801, 2008
An acrylic acid modified polypropylene as a compatibilizing agent for the intercalation/exfoliation of an organically modified montmorillonite in polypropylene
Authors: Chinellato A. C. , Vidotti S. E. , Hu G.‐H. , Pessan L. A.
Published: July 2008

This work dealt with the effect of using an acrylic acid modified polypropylene (PP‐g‐AA) as a compatibilizing agent for the intercalation/exfoliation of an organically modified montmorillonite (o‐MMT) in a polypropylene matrix (PP). Two PP‐g‐AA containing the same AA content (6 wt %) and having different molar masses were used. The o‐MMT content was 0, 1, or 5 wt % of total mass and the PP‐g‐AA/o‐MMT mass ratio was 0/1, 1/1, 2/1, or 5/1. Results of wide angle X‐ray scattering (WAXS) and transmission electronic microscopy (TEM) showed that without the PP‐g‐AA, the o‐MMT was dispersed in the PP/o‐MMT in a micrometer scale, similar to a conventional microcomposite. With the PP‐g‐AA, the o‐MMT was much better dispersed and its interlayers were intercalated and partly exfoliated by the polymer chains. Compared with the neat PP, some PP/PP‐g‐AA/o‐MMT systems exhibited higher G′ values and a yield stress at low frequencies, indicating that the PP‐g‐AA promoted the intercalation/exfoliation of the o‐MMT. The compatibilizing efficiency of those two PP‐g‐AA was very similar. Generally speaking, the higher the PP‐g‐AA/o‐MMT mass ratio, the better the state of dispersion and the degree of intercalation/exfoliation. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1811–1819, 2008
Delayed Effects of Cold Atmospheric Plasma on Vascular Cells
Authors: Stoffels Eva , Roks Anton J. M. , Deelman Leo E.
Published: July 2008

We investigated the long‐term behaviour of vascular cells (endothelial and smooth muscle) after exposure to a cold atmospheric plasma source. The cells were treated through a gas‐permeable membrane, in order to simulate intravenous treatment with a gas plasma‐filled catheter. Such indirect treatment resulted in (dose‐dependent) apoptosis and necrosis in smooth muscle cells; these effects were visible 6–10 h after exposure. We ascribed cell damage to poisoning by active nitrogen species. A not yet resolved phenomenon of total (irreversible) cell inactivation without necrosis was observed in endothelial cells. Conditions for non‐inflammatory plasma treatment (no cell necrosis) can be realized. Furthermore, the current experiments have brought new insights in the mechanism of cell detachment, which was observed in many previous studies.

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Finite temperature behaviour of O'KKLT model
Authors: Anguelova L. , Calo V.
Published: July 2008

We summarize our work on the O'Raifeartaigh uplifted KKLT model at finite temperature. We study the system for parameter values for which the zero temperature potential for the volume modulus has a dS minimum. The temperature‐dependent part of the effective potential has a runaway behaviour for one exponent in the superpotential, whereas it can have local minima at finite field vevs for two exponents in the superpotential. However, it turns out that, despite the presence of those minima, the zero temperature dS vacuum is not destabilized by thermal corrections within the whole range of validity of our approximations.
Backreacting flavors in the Klebanov‐Witten model via D7‐branes
Authors: Benini F.
Published: July 2008

We discuss the addition of backreacting D7‐branes to (fractional) D3‐brane solutions in IIB supergravity which is dual to the addition of a large number of fields in the fundamental representation to known field theories in the Veneziano limit. We specialize to D7/D3‐branes on the conifold (flavored Klebanov‐Witten theory); we then generalize to massive flavors and to the case of fractional D3‐branes and D7‐branes with gauge flux (flavored Klebanov‐Tseytlin theory). This talk is mainly based on [16, 18].
(D)‐instanton effects in magnetized brane worlds
Authors: Billó M.
Published: July 2008

We consider systems of magnetized D9 branes on orbifolds supporting 𝒩 = 1 gauge theories. In such realizations, the matter multiplets arise from “twisted” strings connecting different stacks of branes. The introduction of Euclidean 5‐branes wrapped on the six‐dimensional compact space leads to instanton effects. We examine the interplay between the annuli diagrams with an E5 boundary and the holomorphicity properties of the effective low‐energy supergravity action which describes the system, including its instanton corrections. This talk is mostly based on [1].
E7(7) invariant measures of entanglement
Authors: Borsten L.
Published: July 2008

A study, centred on the Freudenthal triple system, of the E7(7) invariant tripartite entanglement of seven qubits and its relationship to black hole entropy in N = 8 supergravity. Based on work done in collaboration with D. Dahanayake, M. J. Duff and H. Ebrahim.
String dual of 𝒩 = 1 super Yang‐Mills on the cylinder
Authors: Canoura F.
Published: July 2008

We study the stringy description of 𝒩 = 1 supersymmetric SU(N) gauge theory on ℝ1,2 × S1. Our description is based on the known Maldacena‐Núñez solution, properly modified to account for the compact dimension. The most interesting of its properties is that extra BPS M‐branes are present, which generate a non‐perturbative superpotential that we explicitly compute.
Instantons and Donaldson–Thomas invariants
Authors: Cirafici M. , Sinkovics A. , Szabo R.J.
Published: July 2008

We review some recent progress in understanding the relation between a six dimensional topological Yang–Mills theory and the enumerative geometry of Calabi–Yau threefolds. The gauge theory localizes on generalized instanton solutions and is conjecturally equivalent to Donaldson–Thomas theory. We evaluate the partition function of the U(N) theory in its Coulomb branch on flat space by employing equivariant localization techniques on its noncommutative deformation. Geometrically this corresponds to a higher dimensional generalization of the ADHM formalism. This formalism can be extended to a generic toric Calabi–Yau.