bluuebunny/crossref_metadata_2025 huggingface dataset:
Microbial induction of inflammatory bowel disease associated gene TL1A (TNFSF15) in antigen presenting cells
Authors: Shih David Q. , Kwan Lola Y. , Chavez Valerie , Cohavy Offer , Gonsky Rivkah , Chang Elmer Y. , Chang Christopher , Elson Charles O. , Targan Stephan R.
Published: October 2009

TL1A is a member of the TNF superfamily and its expression is increased in the mucosa of inflammatory bowel disease patients. Neutralizing anti‐mouse TL1A Ab attenuates chronic colitis in two T‐cell driven murine models, suggesting that TL1A is a central modulator of gut mucosal inflammation in inflammatory bowel disease. We showed previously that TL1A is induced by immune complexesviathe FcγR signaling pathway. In this study, we report that multiple bacteria, including gram negative organisms (E. coli,E. coliNissle 1917,Salmonella typhimurium), gram positive organisms (Listeria monocytogenes,Staphylococcus epidermidis), partial anaerobes (Campylobacter jejuni), and obligate anaerobes (Bacteroides thetaiotaomicron,Bifidobacterium breve,Clostridium A4) activate TL1A expression in human APC, including monocytes and monocyte‐derived DC. Bacterially induced TL1A mRNA expression correlates with the detection of TL1A protein levels. TL1A induced by bacteria is mediated in part by the TLR signaling pathway and inhibited by downstream blockade of p38 MAPK and NF‐κB activation. Microbial induction of TL1A production by human APC potentiated CD4+T‐cell effector function by augmenting IFN‐γ production. Our findings suggest a role for TL1A in pro‐inflammatory APC–T cell interactions and implicate TL1A in host responses to enteric microorganisms.
Depletion of tumor‐induced Treg prior to reconstitution rescues enhanced priming of tumor‐specific, therapeutic effector T cells in lymphopenic hosts
Authors: Poehlein Christian H. , Haley Daniel P. , Walker Edwin B. , Fox Bernard A.
Published: October 2009

We reported previously that vaccination of reconstituted, lymphopenic mice resulted in a higher frequency of tumor‐specific effector T cells with therapeutic activity than vaccination of normal mice. Here, we show that lymphopenic mice reconstituted with spleen cells from tumor‐bearing mice (TBM), a situation that resembles the clinical condition, failed to generate tumor‐specific T cells with therapeutic efficacy. However, depletion of CD25+ Treg from the spleen cells of TBM restored tumor‐specific priming and therapeutic efficacy. Adding back TBM CD25+ Treg to CD25− naïve and TBM donor T cells prior to reconstitution confirmed their suppressive role. CD25+ Treg from TBM prevented priming of tumor‐specific T cells since subsequent depletion of CD4+ T cells did not restore therapeutic efficacy. This effect may not be antigen‐specific as three histologically distinct tumors generated CD25+ Treg that could suppress the T‐cell immune response to a melanoma vaccine. Importantly, since ex vivo depletion of CD25+ Treg from TBM spleen cells prior to reconstitution and vaccination fully restored the generation of therapeutic effector T cells, even in animals with established tumor burden, we have initiated a translational clinical trial of this strategy in patients with metastatic melanoma.
2′‐O‐Alkyl Derivatives and 5′‐Analogues of 5‐Aminoimidazole‐4‐carboxamide‐1‐β‐D‐ribofuranoside (AICAR) as Potential Hsp90 Inhibitors
Authors: Bracci Antonio , Colombo Giorgio , Ronchetti Fiamma , Compostella Federica
Published: October 2009

Some selective preparations of AICAR‐related compounds modified at the 2′‐ or 5′‐position of the ribose moiety are reported herein. In particular, 5′‐azido, 5′‐amino, 5′‐O‐benzyl and a series of 2′‐O‐alkylated AICAR derivatives have been synthesized. These compounds were derived from appropriately functionalized inosines by opening the pyrimidine ring at the hypoxanthine residue. The target derivatives were designed with the purpose of studying the effect of AICAR structural modifications on its ability to inhibit Hsp90, one of the biological targets for the development of anticancer agents. Nevertheless, the development of AICAR‐like compounds is an appealing objective also because of their potential therapeutic application in the field of metabolic studies.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
Breath gas aldehydes as biomarkers of lung cancer
Authors: Fuchs Patricia , Loeseken Christian , Schubert Jochen K. , Miekisch Wolfram
Published: October 2009

There is experimental evidence that volatile substances in human breath can reflect presence of neoplasma. Volatile aldehydes were determined in exhaled breath of 12 lung cancer patients, 12 smokers and 12 healthy volunteers. Alveolar breath samples were collected under control of expired CO2. Reactive aldehydes were transformed into stable oximes by means of on‐fiber‐derivatization (SPME‐OFD). Aldehyde concentrations in the ppt and ppb level were determined by means of gas chromatography‐mass spectrometry (GC‐MS). Exhaled concentrations were corrected for inspired values. Exhaled C1–C10 aldehydes could be detected in all healthy volunteers, smokers and lung cancer patients. Concentrations ranged from 7 pmol/l (161 pptV) for butanal to 71 nmol/l (1,582 ppbV) for formaldehyde. Highest inspired concentrations were found for formaldehyde and acetaldehyde (0–55 nmol/l and 0–13 nmol/l, respectively). Acetaldehyde, propanal, butanal, heptanal and decanal concentrations showed no significant differences for cancer patients, smokers and healthy volunteers. Exhaled pentanal, hexanal, octanal and nonanal concentrations were significantly higher in lung cancer patients than in smokers and healthy controls (ppentanal = 0.001; phexanal = 0.006; poctanal = 0.014; pnonanal = 0.025). Sensitivity and specificity of this method were comparable to the diagnostic certitude of conventional serum markers and CT imaging. Lung cancer patients could be identified by means of exhaled pentanal, hexanal, octanal and nonanal concentrations. Exhaled aldehydes reflect aspects of oxidative stress and tumor‐specific tissue composition and metabolism. Noninvasive recognition of lung malignancies may be realized if analytical skills, biochemical knowledge and medical expertise are combined into a joint effort.
Amplicons on chromosome 12q13‐21 in glioblastoma recurrences
Authors: Fischer Ulrike , Leidinger Petra , Keller Andreas , Folarin Amos , Ketter Ralf , Graf Norbert , Lenhof Hans‐Peter , Meese Eckart
Published: October 2009

There is limited knowledge on the in vivo behavior of amplified regions in human tumors. First evidence indicates that amplicon structures are largely maintained in recurrent tumors. Here, we investigated the fate of amplified regions in several independent cases of recurrent glioblastoma and the possible association of 12q13–21 amplifications and survival. We analyzed 12q13–21 amplicon numbers and sizes in glioblastoma and their recurrences by array‐CGH. The majority of the 12q13–21 amplicons found in the original tumor are lost in the subsequent recurrence. Likewise, the majority of the amplicons found in the first recurrence are lost in the second recurrence. The remaining amplicons of recurrences often expanded or were maintained in size. Because of re‐emergences and de novo appearances of amplicons, however, the overall number of amplicons did not decrease in the recurrences. Understanding genetic changes including gene amplifications in the development of tumor recurrences will contribute to rational therapeutic strategies for an improved patient survival. We recognized a significant longer survival time in glioblastoma patients that lack amplifications of either CDK4, CYP27B1, XRCC6BP1 (KUB3), or MDM2.
Tonsillitis, tonsillectomy and Hodgkin's lymphoma
Authors: Vestergaard Hanne , Westergaard Tine , Wohlfahrt Jan , Hjalgrim Henrik , Melbye Mads
Published: October 2009

It has been debated whether the reported increased risk of Hodgkin's lymphoma (HL) after tonsillectomy could be due to some underlying factor rather than the surgery itself. We studied whether not only tonsillectomy but also tonsillitis was associated with HL. This nationwide cohort study included all Danish residents during 1977–2001. Information on a diagnosis of tonsillitis, tonsillectomy, or HL was obtained from national registries. During 124 million person‐years we observed 2,988 HL patients of whom 58 were tonsillectomized (most with preceding tonsillitis) and 14 were diagnosed with only tonsillitis at more than 1 year before HL diagnosis. Tonsillectomy was associated with a significantly increased HL risk in persons under 15 years of age as follows: 1–4 years after tonsillectomy, relative risk (RR) = 3.9 [95% CI: 1.4–11; n = 4]; >5 years after tonsillectomy, RR = 3.5 [1.4–8.5; n = 5]. No young cases of HL occurred among persons diagnosed with only tonsillitis. In contrast, 1–4 years after a hospital diagnosis of tonsillitis without subsequent tonsillectomy we found an increased HL risk in persons aged 15 years or above as follows: 15–34 years of age at HL diagnosis, RR = 3.5 [1.6–7.7; n = 6]; 35+ years, RR = 5.9 [2.2–16; n = 4]. Age at tonsillitis or tonsillectomy did not modify HL risk within the 3 age strata. An increased HL risk was found both after tonsillectomy and after an isolated diagnosis of tonsillitis. These results suggest that tonsillitis is a risk factor for HL and not that, as previously reported, only the surgical removal of tonsils is a risk factor.
Age‐related differences in susceptibility to cisplatin‐induced renal toxicity
Authors: Espandiari P. , Rosenzweig B. , Zhang J. , Zhou Y. , Schnackenberg L. , Vaidya V. S. , Goering P. L. , Brown R. P. , Bonventre J. V. , Mahjoob K. , Holland R. D. , Beger R. D. , Thompson K. , Hanig J. , Sadrieh N.
Published: October 2009

Limited experimental models exist to assess drug toxicity in pediatric populations. We recently reported how a multi‐age rat model could be used for pre‐clinical studies of comparative drug toxicity in pediatric populations. The objective of this study was to expand the utility of this animal model, which previously demonstrated an age‐dependent sensitivity to the classic nephrotoxic compound, gentamicin, to another nephrotoxicant, namely cisplatin (Cis). Sprague–Dawley rats (10, 25, 40 and 80 days old) were injected with a single dose of Cis (0, 1, 3 or 6 mg kg−1 i.p.). Urine samples were collected prior and up to 72 h after treatment in animals that were ≥ 25 days old. Several serum, urinary and ‘omic’ injury biomarkers as well as renal histopathology lesions were evaluated. Statistically significant changes were noted with different injury biomarkers in different age groups. The order of age‐related Cis‐induced nephrotoxicity was different than our previous study with gentamicin: 80 > 40 > 10 > 25 day‐old vs 10 ≥ 80 > 40 > 25‐day‐old rats, respectively. The increased levels of kidney injury molecule‐1 (Kim‐1: urinary protein/tissue mRNA) provided evidence of early Cis‐induced nephrotoxicity in the most sensitive age group (80 days old). Levels of Kim‐1 tissue mRNA and urinary protein were significantly correlated to each other and to the severity of renal histopathology lesions. These data indicate that the multi‐age rat model can be used to demonstrate different age‐related sensitivities to renal injury using mechanistically distinct nephrotoxicants, which is reflected in measurements of a variety of metabolite, gene transcript and protein biomarkers. Published in 2009 by John Wiley & Sons, Ltd.
Climatological significance of stable isotopes in precipitation over south‐west China
Authors: Zhang Xin‐Ping , Liu Jing‐Miao , Wang Xiao‐Yun , Nakawo Masayoshi , Xie Zi‐Chu , Zhang Jian‐Ming , Zhang Xin‐Zhu
Published: October 2009

The variations of stable isotopes including deuterium excess d over south‐west China are displayed, and the relationships of the stable isotopes in precipitation with temperature and humidity at different altitudes are also researched. Under the prevailing monsoon system, distinct seasonality for δ18O and d in precipitation are shown and the reverse correlations with vapour pressure and atmospheric precipitable water (PW) are marked clearly for the sampling at the Mengzi, Tengchong and Simao stations. Analyses indicate that the relationship between δ18O and d in precipitation with temperature and humidity in the middle and low troposphere is consistent. Taking into account the relationships of δ18O and d in precipitation with atmospheric humidity comprehensively, it is deduced that the main causation affecting stable isotopic variations in precipitation over south‐west China is mainly related to the property of air mass for rainfall, whereas the evaporation‐enrichment action in a falling raindrop works in a relatively weaker manner. During the rainy season, vapour generating precipitation with high humidity and low stable isotopic ratios owing to the rainout of vapour on the transport routine, and also the small d in precipitation, comes primarily from low‐latitude oceans. In contrast, vapour generating precipitation with low humidity and great stable isotopic ratios and high d in precipitation in dry seasons is assumed to be primarily from the westerlies' transportation and results, with high probability, from the replenishment of re‐evaporated vapour inland. On an annual timescale, the precipitation amount weighted mean δ18O values suggest negative correlations not only with annual precipitation but also with annual mean temperature at 500 hPa. Copyright © 2010 Royal Meteorological Society
Utilization of dual retention mechanism on columns with bonded PEG and diol stationary phases for adjusting the separation selectivity of phenolic and flavone natural antioxidants
Authors: Jandera Pavel , Hájek Tomáš
Published: October 2009

The retention of phenolic acid and flavone antioxidants was investigated on three columns with bonded PEG, hydroxy (DIOL) and mixed oxyethylene‐hydroxy (Luna HILIC) stationary phases in buffered aqueous ACN mobile phases. All columns show mixed retention mechanism: reversed phases in highly aqueous mobile phases and normal phases (HILIC, hydrophilic interaction LC) in mobile phases with high concentration of ACN, showing characteristic U‐shape retention versus mobile phase composition plots. Equations enabling description and prediction of retention of sample compounds over the full mobile phase composition range were compared. Dual retention mechanism offers possibilities for using differences in selectivity between the two separation modes on a single column to improve the separation of natural antioxidants. The Luna HILIC column shows larger HILIC retention range, enhanced retention, improved selectivity and better peak symmetry in comparison to the PEG and DIOL columns.
EIS study on pitting corrosion of 7150 aluminum alloy in sodium chloride and hydrochloric acid solution
Authors: Peng G. S , Chen K. H. , Fang H. C. , Chao H. , Chen S. Y.
Published: October 2009

The pitting corrosion behavior of 7150 aluminum alloy was studied by electrochemical impedance spectroscopy (EIS) in the sodium chloride and hydrochloric acid solution. Based on EIS features and corrosion morphologies as well as corrosion potential, the process of pitting corrosion could be clearly divided into four stages: at the first stage, the Nyquist diagram was composed of two overlapping capacitive loops at the high‐medial frequency and one inductive loop at the low frequency. At the second stage (metastable pits developing stage), there existed one small capacitive loop at the high frequency and one big capacitive loop at the medial frequency. At the third stage (stable pits developing stage), two time constants were more clearly distinguished, corresponding to two obvious capacitive loops. At the fourth stage, there appeared one capacitive loop, attributing to uniform corrosion. An equivalent circuit was designed to fit EIS, and the experimental results and the fitted results had good correspondence.
Influential ownership and capital structure
Authors: Pöyry Salla , Maury Benjamin
Published: October 2009

This paper explores the relation between ownership structures and capital structures in Russia—an economy with a state‐run banking sector, weak corporate governance, and highly concentrated ownership. We find that firms with the state as controlling shareholder have significantly higher leverage than firms controlled by domestic private controlling shareholders other than oligarchs. Both firms controlled by the state or oligarchs finance their growth with more debt than other firms. Profitability is negatively related to leverage across all types of controlling owners, indicating a preference for internal funding over debt. The results indicate that firms with owners that have political influence or ties to large financial groups enjoy better access to debt. Copyright © 2009 John Wiley & Sons, Ltd.
A study of Y chromosome gene mRNA in human ejaculated spermatozoa
Authors: Yao Chenjiang , Wang Zhaoxia , Zhou Ying , Xu Wangjie , Li Qiaoli , Ma Duan , Wang Lianyun , Qiao Zhongdong
Published: October 2009

We asked if messenger ribonucleic acid (mRNA) of Y chromosome genes was selectively retained in human ejaculated spermatozoa. A panel of genes on the nonrecombining region of Y chromosome (NRY) and their X homologues were selected and screened in human testis and ejaculated spermatozoa by reverse transcription‐polymerase chain reaction (RT‐PCR). Then, the cellular localization of DBY, RPS4Y and SMCY mRNA in testis and matured spermatozoa were investigated by in situ hybridization. The expression pattern of these three genes in human ejaculated spermatozoa was also tested by Western blot and Immunofluorescence. All 11 Y chromosome gene mRNAs were found in the testis, but the transcripts of only three genes DBY, SRY, and RPS4Y were detected in ejaculated sperm by RT‐PCR. Further investigation showed that DBY and RPS4Y mRNA were present in both human testis and the post‐acrosome region comprising nearly 50% of spermatozoa, while the encoded proteins were not detected in spermatozoa. In contrast, although SMCY mRNA was not detected in mature spermatozoa, the H‐Y antigen encoded by SMCY was expressed on the surface of spermatozoa. We therefore conclude that the spermatozoa mRNA could be selectively reserved in mature ejaculated spermatozoa. They might be useful in early zygotic and embryonic development. Mol. Reprod. Dev. 77: 158–166, 2010. © 2009 Wiley‐Liss, Inc.
Correlation of DTI metrics in the wall and cavity of brain abscess with histology and immunohistochemistry
Authors: Gupta Rakesh K. , Srivastava Savita , Saksena Sona , Rathore Ram K. S. , Awasthi Rishi , Prasad Kashi N. , Husain Mazhar , Pandey Chandra M. , Husain Nuzhat
Published: October 2009

Diffusion tensor imaging (DTI) was performed in eight patients with brain abscess (BA). The aim of this study was to see the difference in the relationship between intercellular cell adhesion molecule‐1 (ICAM‐1) and lymphocyte function‐associated antigen‐1 (LFA‐1) expression and DTI metrics measured in vivo in the wall and cavity of BA and its possible explanation vis‐à‐vis histology and immunohistochemistry. Neuroinflammatory molecules (NMs) were quantified from BA cavity aspirate of the patients and quantitative immunohistochemical analysis was performed for ICAM‐1 and LFA‐1 in the BA wall, showing maximal positive staining and correlated with DTI metrics. The fractional anisotropy (FA) significantly increased while mean diffusivity and spherical anisotropy significantly decreased in the BA wall compared to the BA cavity. In the BA wall, FA and linear anisotropy (CL) showed a significant positive correlation with ICAM‐1 and LFA‐1 expression whereas FA and planar anisotropy positively correlated with NMs quantified from aspirated pus respectively. Higher FA values in the BA wall compared to BA cavity, even when ICAM‐1 and LFA‐1 were expressed only in the macrophages and not in the collagen fibers, suggests that a combination of both concentric layers of collagen fibers as well as neutrophils and macrophages provide structural orientation and are responsible for increased FA. In the BA wall, increased CL was found compared to the cavity, indicating the presence of concentrically laid collagen fibers responsible for the diffusion of water molecules in the direction parallel to the collagen fibers. We conclude that in the BA, different mechanisms are operative for the changes in the DTI metrics in the wall and cavity; these conclusions are validated by histology and immunohistochemistry. Copyright © 2009 John Wiley & Sons, Ltd.
Shape optimization of a body in the Oseen flow
Authors: Wang Axia , Ma Yichen , Gao Zhiming
Published: October 2009

This article is concerned with a numerical simulation of shape optimization of the Oseen flow around a solid body. The shape gradient for shape optimization problem in a viscous incompressible flow is computed by the velocity method. The flow is governed by the Oseen equations with mixed boundary conditions containing the pressure. The structure of continuous shape gradient of the cost functional is derived by using the differentiability of a minimax formulation involving a Lagrange functional with a function space parametrization technique. A gradient type algorithm is applied to the shape optimization problem. Numerical examples show that our theory is useful for practical purpose and the proposed algorithm is feasible. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2010
Fast iterative solver for convection‐diffusion systems with spectral elements
Authors: Lott P. Aaron , Elman Howard
Published: October 2009

We introduce a solver and preconditioning technique based on Domain Decomposition and the Fast Diagonalization Method that can be applied to tensor product based discretizations of the steady convection–diffusion equation. The method is based on a Robin–Robin interface preconditioner coupled to a fast diagonalization solver which is used to efficiently eliminate the interior degrees of freedom and perform subsidiary subdomain solves. Using a spectral element discretization, we first apply our technique to constant wind problems, and then propose a means for applying the technique as a preconditioner for variable wind problems. We demonstrate that iteration counts are mildly dependent on changes in mesh size and convection strength. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2011
An optimization‐based domain decomposition method for numerical simulation of the incompressible Navier‐Stokes flows
Authors: Kong Fande , Ma Yichen , Lu Junxiang
Published: October 2009

This article is concerned about an optimization‐based domain decomposition method for numerical simulation of the incompressible Navier‐Stokes flows. Using the method, an classical domain decomposition problem is transformed into a constrained minimization problem for which the objective functional is chosen to measure the jump in the dependent variables across the common interfaces between subdomains. The Lagrange multiplier rule is used to transform the constrained optimization problem into an unconstrained one and that rule is applied to derive an optimality system from which optimal solutions may be obtained. The optimality system is also derived using “sensitivity” derivatives instead of the Lagrange multiplier rule. We consider a gradient‐type approach to the solution of domain decomposition problem. The results of some numerical experiments are presented to demonstrate the feasibility and applicability of the algorithm developed in this article. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2011
Residual‐based a posteriori error estimator for the mixed finite element approximation of the biharmonic equation
Authors: Gudi Thirupathi
Published: October 2009

A reliable and efficient residual‐based a posteriori error estimator is derived for the Ciarlet‐Raviart mixed finite element method for the biharmonic equation on polygonal domains. The performance of the estimator is illustrated by numerical experiments. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2011
Nano‐emulsion use for the synthesis of polyaniline nano‐grains or nano‐fibers
Authors: Rahy Abdelaziz , Bae Joseph , Wu Aimei , Manohar Sanjeev K. , Yang Duck J.
Published: October 2009

We report that nano‐emulsions can be creatively used as a morphology selective synthesis method to prepare not only nano‐grains but also nano‐fibers with high selectivity. Synthesis of the two different morphological materials was demonstrated using polyaniline synthesis as a model case. Polyaniline nano‐grains were synthesized from aniline molecules in nano‐size aqueous droplets as polymerization sites whose droplets were generated by inverse water‐in‐oil nano‐emulsion use, and polyaniline nano‐fibers were synthesized from aniline in aqueous nano‐dimensional channels as polymerization sites whose channels were generated by direct oil‐in‐water nano‐emulsion use containing high population of oil droplets. Using the approaches, we successfully synthesized nano‐fibers of 60 nm diameter with 0.5 µm length and also nano‐grains having diameter of 60–80 nm. The two different polymerization sites of nano‐scale dimension were made by changing the ratio among surfactant, aqueous aniline/HCl solution, and oil, i.e. organic solvent. We found the nano‐fibers synthesized from the channels formed by the direct oil‐in‐water nano‐emulsion have higher bulk electrical conductivity than the nano‐grains which were synthesized from the droplets formed by the inverse water‐in‐oil emulsion. We also found that the emulsion use allows us to use a room temperature synthesis unlike conventional synthesis methods which require to use ice bath temperature. Physical properties of both nano‐fibers and nano‐grains synthesized were characterized by Fourier transform infrared (FTIR), UV–Vis spectra, scanning electron microscopy (SEM), and four probes conductivity measurement. Copyright © 2009 John Wiley & Sons, Ltd.
Comparative proteomic analysis provides new insights into mulberry dwarf responses in mulberry (Morus alba L.)
Authors: Ji Xianling , Gai Yingping , Zheng Chengchao , Mu Zhimei
Published: October 2009

Mulberry dwarf (MD) is a serious infectious disease of mulberry caused by phytoplasma. Infection with MD phytoplasma results in stress phenotypes of yellowing, phyllody, stunting, proliferation, and witches' broom. Physiological and biochemical analysis has shown that infection with MD phytoplasma causes an increase in soluble carbohydrate and starch content, and a decrease in the net photosynthesis rate, carboxylation efficiency, and pigment content of leaves. Furthermore, damage to the chloroplast ultrastructure was detected in infected leaves. To better understand the pathogen‐stress response of mulberry (Morus alba L.) to MD phytoplasma, we conducted a comparative proteomic analysis using 2‐DE of infected and healthy leaves. Among 500 protein spots that were reproducibly detected, 20 were down‐regulated and 17 were up‐regulated. MS identified 16 differentially expressed proteins. The photosynthetic proteins rubisco large subunit, rubisco activase, and sedoheptulose‐1,7‐bisphosphatase showed enhanced degradation in infected leaves. Based these results, a model for the occurrence mechanism of MD is proposed. In conclusion, this study provides new insights into the mulberry response to MD phytoplasma infection.
Comparative proteomics of a lycopene‐accumulating mutant reveals the important role of oxidative stress on carotenogenesis in sweet orange (Citrus sinensis [L.] osbeck)
Authors: Pan Zhiyong , Liu Qing , Yun Ze , Guan Rui , Zeng Wenfang , Xu Qiang , Deng Xiuxin
Published: October 2009

A spontaneous sweet orange (Citrus sinenesis [L.] Osbeck) mutant ‘Hong Anliu’ is of high value due to lycopene accumulation in the pulp. In this study, we analyzed the proteomic alterations in the pulp of ‘Hong Anliu’ versus its wild type (WT) at four maturing stages by using 2‐DE combined with MALDI‐TOF‐TOF MS. Among the 74 differentially expressed proteins identified, the majority are predicted to be involved in stress response, carbohydrate/energy metabolism and regulation, or protein fate, modification and degradation. Particularly, expression levels of six anti‐oxidative enzymes were altered by the mutation; and assays of their respective enzymatic activities indicated an enhanced level of oxidative stress in ‘Hong Anliu’, implying a regulatory role of oxidative stress on carotenogenesis. This conclusion was further confirmed by our observation that treatment of fruit pulps with tert‐butylhydroperoxide (a ROS progenitor) induced lycopene accumulation in ‘Hong Anliu’ only. Gene expression showed that genes predicted to function upstream of lycopene biosynthesis were generally upregulated in juice sacs, but downregulated in segment membranes in both ‘Hong Anliu’ and its WT. The result suggests an important role of post‐transcriptional regulation on carotenogenesis since lycopene was induced in ‘Hong Anliu’ but not WT. The result also implies that carotenogenesis in juice sacs and segment membranes of citrus fruits may be regulated by different mechanisms.
The PSI semantic validator: A framework to check MIAPE compliance of proteomics data
Authors: Montecchi‐Palazzi Luisa , Kerrien Samuel , Reisinger Florian , Aranda Bruno , Jones Andrew R. , Martens Lennart , Hermjakob Henning
Published: October 2009

The Human Proteome Organization's Proteomics Standards Initiative (PSI) promotes the development of exchange standards to improve data integration and interoperability. PSI specifies the suitable level of detail required when reporting a proteomics experiment (via the Minimum Information About a Proteomics Experiment), and provides extensible markup language (XML) exchange formats and dedicated controlled vocabularies (CVs) that must be combined to generate a standard compliant document. The framework presented here tackles the issue of checking that experimental data reported using a specific format, CVs and public bio‐ontologies (e.g. Gene Ontology, NCBI taxonomy) are compliant with the Minimum Information About a Proteomics Experiment recommendations. The semantic validator not only checks the XML syntax but it also enforces rules regarding the use of an ontology class or CV terms by checking that the terms exist in the resource and that they are used in the correct location of a document. Moreover, this framework is extremely fast, even on sizable data files, and flexible, as it can be adapted to any standard by customizing the parameters it requires: an XML Schema Definition, one or more CVs or ontologies, and a mapping file describing in a formal way how the semantic resources and the format are interrelated. As such, the validator provides a general solution to the common problem in data exchange: how to validate the correct usage of a data standard beyond simple XML Schema Definition validation. The framework source code and its various applications can be found at http://psidev.info/validator.
Relation between pH, structure, and absorption spectrum of Cerulean: A study by molecular dynamics and TD DFT calculations
Authors: Vallverdu Germain , Demachy Isabelle , Mérola Fabienne , Pasquier Hélène , Ridard Jacqueline , Lévy Bernard
Published: October 2009

Molecular dynamics (MD) and quantum mechanical calculations of the Cerulean green fluorescent protein (a variant of enhanced cyan fluorescent protein ECFP) at pH 5.0 and 8.0 are presented, addressing two questions arising from experimental results (Malo et al., Biochemistry 2007;46:9865–9873): the origin of the blue shift of absorption spectrum when the pH is decreased from 8.0 to 5.0, and the lateral chain orientation of the key residue Asp148. We demonstrate that the blue shift is reproduced assuming that a rotation around the single bond of the exocyclic ring of the chromophore takes place when the pH changes from 5.0 to 8.0. We find that Asp148 is protonated and inside the barrel at pH 5.0 in agreement with crystallographic data. However, the hydrogen bond pattern of Asp148 is different in simulations of the solvated protein and in the crystal structure. This difference is explained by a partial closing of the cleft between strands 6 and 7 in MD simulations. This study provides also a structure at pH 8.0: the Asp148 carboxylate group is exposed to the solvent and the chromophore is stabilized in the trans conformation by a tighter hydrogen bond network. This work gives some insight into the relationship between the pH and the chromophore conformation and suggests an interpretation of the very similar fluorescent properties of ECFP and ECFP/H148D. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Computational design of second‐site suppressor mutations at protein–protein interfaces
Authors: Sammond Deanne W. , Eletr Ziad M. , Purbeck Carrie , Kuhlman Brian
Published: October 2009

The importance of a protein–protein interaction to a signaling pathway can be established by showing that amino acid mutations that weaken the interaction disrupt signaling, and that additional mutations that rescue the interaction recover signaling. Identifying rescue mutations, often referred to as second‐site suppressor mutations, controls against scenarios in which the initial deleterious mutation inactivates the protein or disrupts alternative protein–protein interactions. Here, we test a structure‐based protocol for identifying second‐site suppressor mutations that is based on a strategy previously described by Kortemme and Baker. The molecular modeling software Rosetta is used to scan an interface for point mutations that are predicted to weaken binding but can be rescued by mutations on the partner protein. The protocol typically identifies three types of specificity switches: knob‐in‐to‐hole redesigns, switching hydrophobic interactions to hydrogen bond interactions, and replacing polar interactions with nonpolar interactions. Computational predictions were tested with two separate protein complexes; the G‐protein Gαi1 bound to the RGS14 GoLoco motif, and UbcH7 bound to the ubiquitin ligase E6AP. Eight designs were experimentally tested. Swapping a buried hydrophobic residue with a polar residue dramatically weakened binding affinities. In none of these cases were we able to identify compensating mutations that returned binding to wild‐type affinity, highlighting the challenges inherent in designing buried hydrogen bond networks. The strongest specificity switches were a knob‐in‐to‐hole design (20‐fold) and the replacement of a charge–charge interaction with nonpolar interactions (55‐fold). In two cases, specificity was further tuned by including mutations distant from the initial design. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Cooperative nature of gating transitions in K+ channels as seen from dynamic importance sampling calculations
Authors: Denning Elizabeth J. , Woolf Thomas B.
Published: October 2009

The growing dataset of K+ channel x‐ray structures provides an excellent opportunity to begin a detailed molecular understanding of voltage‐dependent gating. These structures, while differing in sequence, represent either a stable open or closed state. However, an understanding of the molecular details of gating will require models for the transitions and experimentally testable predictions for the gating transition. To explore these ideas, we apply dynamic importance sampling to a set of homology models for the molecular conformations of K+ channels for four different sets of sequences and eight different states. In our results, we highlight the importance of particular residues upstream from the Pro‐Val‐Pro (PVP) region to the gating transition. This supports growing evidence that the PVP region is important for influencing the flexibility of the S6 helix and thus the opening of the gating domain. The results further suggest how gating on the molecular level depends on intra‐subunit motions to influence the cooperative behavior of all four subunits of the K+ channel. We hypothesize that the gating process occurs in steps: first sidechain movement, then inter‐S5‐S6 subunit motions, and lastly the large‐scale domain rearrangements. Proteins 2010. © 2009 Wiley‐Liss, Inc.
MUFOLD: A new solution for protein 3D structure prediction
Authors: Zhang Jingfen , Wang Qingguo , Barz Bogdan , He Zhiquan , Kosztin Ioan , Shang Yi , Xu Dong
Published: October 2009

There have been steady improvements in protein structure prediction during the past 2 decades. However, current methods are still far from consistently predicting structural models accurately with computing power accessible to common users. Toward achieving more accurate and efficient structure prediction, we developed a number of novel methods and integrated them into a software package, MUFOLD. First, a systematic protocol was developed to identify useful templates and fragments from Protein Data Bank for a given target protein. Then, an efficient process was applied for iterative coarse‐grain model generation and evaluation at the Cα or backbone level. In this process, we construct models using interresidue spatial restraints derived from alignments by multidimensional scaling, evaluate and select models through clustering and static scoring functions, and iteratively improve the selected models by integrating spatial restraints and previous models. Finally, the full‐atom models were evaluated using molecular dynamics simulations based on structural changes under simulated heating. We have continuously improved the performance of MUFOLD by using a benchmark of 200 proteins from the Astral database, where no template with >25% sequence identity to any target protein is included. The average root‐mean‐square deviation of the best models from the native structures is 4.28 Å, which shows significant and systematic improvement over our previous methods. The computing time of MUFOLD is much shorter than many other tools, such as Rosetta. MUFOLD demonstrated some success in the 2008 community‐wide experiment for protein structure prediction CASP8. Proteins 2010. © 2009 Wiley‐Liss, Inc.
The effect of calcium on the conformation of cobalamin transporter BtuB
Authors: Luan Binquan , Carr Rogan , Caffrey Martin , Aksimentiev Aleksei
Published: October 2009

BtuB is a β‐barrel membrane protein that facilitates transport of cobalamin (vitamin B12) from the extracellular medium across the outer membrane of Escherichia coli. It is thought that binding of B12 to BtuB alters the conformation of its periplasm‐exposed N‐terminal residues (the TonB box), which enables subsequent binding of a TonB protein and leads to eventual uptake of B12 into the cytoplasm. Structural studies determined the location of the B12 binding site at the top of the BtuB's β‐barrel, surrounded by extracellular loops. However, the structure of the loops was found to depend on the method used to obtain the protein crystals, which—among other factors—differed in calcium concentration. Experimentally, calcium concentration was found to modulate the binding of the B12 substrate to BtuB. In this study, we investigate the effect of calcium ions on the conformation of the extracellular loops of BtuB and their possible role in B12 binding. Using all‐atom molecular dynamics, we simulate conformational fluctuations of several X‐ray structures of BtuB in the presence and absence of calcium ions. These simulations demonstrate that calcium ions can stabilize the conformation of loops 3–4, 5–6, and 15–16, and thereby prevent occlusion of the binding site. Furthermore, binding of calcium ions to extracellular loops of BtuB was found to enhance correlated motions in the BtuB structure, which is expected to promote signal transduction. Finally, we characterize conformation dynamics of the TonB box in different X‐ray structures and find an interesting correlation between the stability of the TonB box structure and calcium binding. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Multiscale simulations of protein landscapes: Using coarse‐grained models as reference potentials to full explicit models
Authors: Messer Benjamin M. , Roca Maite , Chu Zhen T. , Vicatos Spyridon , Kilshtain Alexandra Vardi , Warshel Arieh
Published: October 2009

Evaluating the free‐energy landscape of proteins and the corresponding functional aspects presents a major challenge for computer simulation approaches. This challenge is due to the complexity of the landscape and the enormous computer time needed for converging simulations. The use of simplified coarse‐grained (CG) folding models offers an effective way of sampling the landscape but such a treatment, however, may not give the correct description of the effect of the actual protein residues. A general way around this problem that has been put forward in our early work (Fan et al., Theor Chem Acc 1999;103:77–80) uses the CG model as a reference potential for free‐energy calculations of different properties of the explicit model. This method is refined and extended here, focusing on improving the electrostatic treatment and on demonstrating key applications. These applications include: evaluation of changes of folding energy upon mutations, calculations of transition‐states binding free energies (which are crucial for rational enzyme design), evaluations of catalytic landscape, and evaluations of the time‐dependent responses to pH changes. Furthermore, the general potential of our approach in overcoming major challenges in studies of structure function correlation in proteins is discussed. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Study on secondary phase precipitate behavior in Zircaloy‐2 by positron annihilation spectroscopy
Authors: Mulki S. , Pujari P. K. , Srivastava D. , Samajdar I. , Dey G. K. , Sharma S.
Published: October 2009

It is well established that in Zr alloys, secondary phase precipitates (SPP) have a major influence on the corrosion and mechanical properties. Thus it is important to understand the kinetics and growth of precipitates under thermal treatments. In this study, secondary phase precipitates were generated by suitable heat treatment at 800 °C and 840 °C for different duration (1‐1440 minutes). Positron lifetime spectroscopy and Doppler broadening measurements were carried out to examine the nucleation and growth aspects of the precipitates. The variation in lifetime and S‐parameter were seen to be consistent. From the S‐W curve it is seen that the defects associated with precipitation at 800 °C and 840 °C are different. Possible mechanism for precipitation of SPP's has been proposed based on the positron annihilation data. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The responses to stress questionnaire: construct validity and prediction of depressive and social anxiety symptoms in a sample of Chinese adolescents
Authors: Xiao Jing , Yao Shuqiao , Zhu Xiongzhao , Zhang Chenchen , Auerbach Randy P. , McWhinnie Chad M. , Abela John R. Z.
Published: October 2009

The objective of the current study was to develop a Chinese version of the Responses to Stress Questionnaire (RSQ‐C) and to evaluate its reliability and validity. The original version of the RSQ was back‐translated into Chinese and administered to a sample of students recruited from two middle schools in Hunan, China. The final sample consisted of 1068 adolescents (49.9% males and 50.1% females). Participants' ages ranged from 14 to 20 (M = 16.47 years, standard deviation = 1.02). The RSQ‐C exhibited moderate internal consistency (Cronbach's alpha was 0.87), and test–retest reliability (intraclass correlation coefficients was 0.82 over a 1‐month interval). Results of confirmatory factor analyses indicated that the fit of a three‐factor model of voluntary coping and a separate two‐factor model of involuntary coping. With regard to predictive validity, the results of multiple regression analyses suggest that the high levels of Disengagement Coping and low levels of Primary Control Engagement Coping were significant predictors of depressive symptomology. Additionally, high levels of Involuntary Engagement and low levels of Primary Control Engagement Coping predicted higher levels of social anxiety symptoms. Copyright ? 2009 John Wiley & Sons, Ltd.
Surgical Outcomes Auditing Systems in Humanitarian Organizations
Authors: Bermudez Luis , Carter Victoria , Magee William , Sherman Randy , Ayala Ruben
Published: October 2009

Background

Operation Smile is a humanitarian volunteer‐based organization that provides cleft care around the world. Successful primary surgery is the key to improving the quality of life of patients with oral clefts. A cleft surgery outcomes database and evaluation system has been developed and implemented.

Methods

During Operation Smile’s “World Journey of Smiles” in November 2007, a total of 4100 patients were operated on during a 10‐day period at 40 simultaneous missions in 25 countries. Photographs taken before surgery, right after surgery, and at the follow‐up consultations were entered in a database and used as media to evaluate surgical outcomes objectively by independent unbiased evaluators. Data about complications collected during the postoperative consultations were also entered.

Results

A postoperative consultation, 6 months to 1 year after surgery was conducted at 24 sites, 19 of which sent back postoperative images; and most returned postoperative examination forms. At those 19 sites, 703 of 1917 patients returned for a 6‐ to 9‐month postoperative visit, for a 36.67% return rate. After matching before and after pictures, 562 patients were able to be entered into the database, allowing 580 procedures to be evaluated. Feedback reports have been sent to 134 volunteer surgeons around the world. Results were compared among sites and locations; and the places where future actions were needed to improve the quality of surgery were identified.

Conclusions

The current outcomes evaluation system has proven beneficial in tracking patient outcomes, auditing surgical performance, and providing feedback to surgeons and other team members. Challenges are discussed.
Reexcision of Soft Tissue Sarcoma: Sufficient Local Control but Increased Rate of Metastasis
Authors: Rehders A. , Stoecklein N. H. , Poremba C. , Alexander A. , Knoefel W. T. , Peiper M.
Published: October 2009

Background

Assuming a benign tumor, soft tissue sarcomas are often treated by inadequate resection. The concept of reexcision in these patients is still under debate. Therefore, it was our goal to evaluate the results of this treatment with particular respect to residual tumor.

Methods

During a 14‐year period, a total of 143 patients were referred to our institution after unplanned excision. Reexcision was performed in 139 patients. The assessed endpoints were local recurrence‐free survival, distant metastasis‐free survival, and tumor‐related mortality. Univariate and multivariate analyses were performed using a log‐rank test and Cox’s proportional‐hazard models.

Results

Over a median observation period of 109 months, local recurrence appeared in 18 patients (12%) and distant metastasis in 46 patients (33%). Residual tumor was detected in 43 patients (31%) and was significantly associated with reduced relapse‐free and overall survival. Local recurrence, however, was not affected.

Conclusions

Despite an incomplete initial resection, reexcision enables local control similar to that in patients without residual tumor. Still, these patients have a worse prognosis owing to an increased rate of distant metastasis; therefore, patients with soft tissue masses of unknown identity should be transferred to centers that specialize in treating sarcomas for adequate initial resection.