bluuebunny/crossref_metadata_2025_split huggingface dataset:
HTAPP: High‐throughput autonomous proteomic pipeline
Authors: Yu Kebing , Salomon Arthur R. 
Published: March 2010

AbstractRecent advances in the speed and sensitivity of mass spectrometers and in analytical methods, the exponential acceleration of computer processing speeds, and the availability of genomic databases from an array of species and protein information databases have led to a deluge of proteomic data. The development of a lab‐based automated proteomic software platform for the automated collection, processing, storage, and visualization of expansive proteomic data sets is critically important. The high‐throughput autonomous proteomic pipeline described here is designed from the ground up to provide critically important flexibility for diverse proteomic workflows and to streamline the total analysis of a complex proteomic sample. This tool is composed of a software that controls the acquisition of mass spectral data along with automation of post‐acquisition tasks such as peptide quantification, clustered MS/MS spectral database searching, statistical validation, and data exploration within a user‐configurable lab‐based relational database. The software design of high‐throughput autonomous proteomic pipeline focuses on accommodating diverse workflows and providing missing software functionality to a wide range of proteomic researchers to accelerate the extraction of biological meaning from immense proteomic data sets. Although individual software modules in our integrated technology platform may have some similarities to existing tools, the true novelty of the approach described here is in the synergistic and flexible combination of these tools to provide an integrated and efficient analysis of proteomic samples.
Proteomic analysis of Medicago truncatula root plastids
Authors: Daher Zeina , Recorbet Ghislaine , Valot Benoît , Robert Frank , Balliau Thierry , Potin Sophie , Schoefs Benoît , Dumas‐Gaudot Eliane 
Published: March 2010

AbstractDespite the recognized importance of non‐photosynthetic plastids in a wide array of plant processes, the root plastid proteome of soil‐grown plants still remains to be explored. In this study, we used a protocol allowing the isolation of Medicago truncatula root plastids with sufficient protein recovery and purity for their subsequent in‐depth analysis by nanoscale capillary LC‐MS/MS. Besides providing the first picture of a root plastid proteome, the results obtained highlighted the identification of 266 protein candidates whose functional distribution mainly resembled that of wheat endosperm amyloplasts and tobacco proplastids together with displaying major differences to those reported for chloroplasts. Most of the identified proteins have a role in nucleic acid‐related processes (16%), carbohydrate (15%) and nitrogen/sulphur (12%) metabolisms together with stress response mechanisms (10%). It is noteworthy that BLAST searches performed against the proteins reported in different plastidomes allowed detecting 30 putative root plastid proteins for which homologues were previously unsuspected as plastid‐located, most of them displaying a common putative role in participating in the plant cell responses against abiotic and/or biotic stresses. Taken together, the data obtained provide new insights into the functioning of root plastids and reinforce the emerging idea for an important role of these organelles in sustaining plant defence reactions.
Protein expression changes induced in murine peritoneal macrophages by Group B Streptococcus
Authors: Susta Federica , Chiasserini Davide , Fettucciari Katia , Orvietani Pier Luigi , Quotadamo Flavia , Noce Rosina , Bartoli Andrea , Marconi Pierfrancesco , Corazzi Lanfranco , Binaglia Luciano 
Published: March 2010

AbstractProtein expression changes induced in thioglycolate‐elicited peritoneal murine macrophages (MΦ) by infection with type III Group B Streptococcus (GBS) are described. Proteins from control MΦ and MΦ incubated 2 h with live or heat‐inactivated GBS were separated by 2‐DE. Proteins whose expression was significantly different in infected MΦ, as compared with control cells, were identified by MS/MS analysis. Changes in the expression level of proteins involved in both positive and negative modulation of phagocytic functions, stress response and cell death were induced in MΦ by GBS infection. In particular, expression of enzymes playing a key role in production of reactive oxygen species was lowered in GBS‐infected MΦ. Significant alterations in the expression of some metabolic enzymes were also observed, most of the glycolytic and of the pentose‐cycle enzymes being down‐regulated in MΦ infected with live GBS. Finally, evidence was obtained that GBS infection affects the expression of enzymes or enzyme subunits involved in ATP synthesis and in adenine nucleotides interconversion processes.
Identification of ciliary neurotrophic factor receptor α as a mediator of neurotoxicity induced by α‐synuclein
Authors: Liu Jun , Shi Min , Hong Zhen , Zhang JianPeng , Bradner Joshua , Quinn Thomas , Beyer Richard P. , Mcgeer Patrick L. , Chen ShengDi , Zhang Jing 
Published: March 2010

AbstractAccumulating evidence suggests that extracellular α‐synuclein (eSNCA) plays an important role in the pathogenesis of Parkinson's disease or related synucleinopathies by inducing neurotoxicity directly or indirectly via microglial or astroglial activation. However, the mechanisms by which this occurs remain to be characterized. To explore these mechanisms, we combined three biochemical techniques – stable isotope labeling of amino acid in cell cultures (SILAC), biotin labeling of plasma membrane proteins followed by affinity purification, and analysis of unique proteins binding to SNCA peptides on membrane arrays. The SILAC proteomic analysis identified 457 proteins, of which, 245 or 172 proteins belonged to membrane or membrane associated proteins, depending on the various bioinformatics tools used for interpretation. In dopamine neuronal cells treated with eSNCA, the levels of 86 membrane proteins were increased and 35 were decreased compared with untreated cells. In peptide array analysis, 127 proteins were identified as possibly interacting with eSNCA. Of those, seven proteins were overlapped with the membrane proteins that displayed alterations in relative abundance after eSNCA treatment. One was ciliary neurotrophic factor receptor, which appeared to modulate eSNCA‐mediated neurotoxicity via mechanisms related to JAK1/STAT3 signaling but independent of eSNCA endocytosis.
Identification of breast cancer biomarkers in transgenic mouse models: A proteomics approach
Authors: Rodenburg Wendy , Pennings Jeroen L. A. , van Oostrom Conny T. M. , Roodbergen Marianne , Kuiper Raoul V. , Luijten Mirjam , de Vries Annemieke 
Published: March 2010

AbstractPurpose: Transgenic mouse models for cancer circumvent many challenges that hamper human studies aimed at biomarker discovery. Lower biological variances among mice combined with controllable factors such as food uptake and health status may enable the detection of more subtle protein expression differences. This is envisioned to result in the identification of biomarkers better discriminating cancer cases from controls.Experimental design: The current study used two innovative mouse models for breast‐cancer to identify new serum biomarkers. Multi‐analyte profiling technique was used to analyze 70 proteins in individual serum samples of non‐tumor and mammary tumor‐bearing Tg.NK (MMTV/c‐neu) mice.Results: A small set of proteins fully differentiated tumor samples from controls. These comprised osteopontin, interleukin‐18, cystatin C and CD40 antigen. Comparison of protein expression in another breast‐cancer mouse model, the humanized p53.R270H mice, showed common discriminatory expression of osteopontin. However, other biomarkers showed distinct expression in the two different breast‐cancer models, indicating that different mammary tumor sub‐types with respect to molecular and estrogen receptor status reveal divergent serum biomarker sets.Conclusions and clinical relevance: The current study supports the concept that serum proteins can discriminate mammary tumor cases from controls, and yielded interesting biomarkers that need further testing and validation in human studies.
Deep plasma proteomic analysis of patients with left ventricular remodeling after a first myocardial infarction
Authors: Fertin Marie , Beseme Olivia , Duban Sophie , Amouyel Philippe , Bauters Christophe , Pinet Florence 
Published: March 2010

AbstractPurpose: Depletion of major blood proteins is one of the most promising approaches to accessing low abundance biomarkers for proteomics studies. The use of combinatorial peptide ligand library (CPLL) for accessing these low abundance proteins in plasma from patients with a myocardial infarction (MI) was tested to identify candidate protein biomarkers of left ventricular remodeling (LVR).Experimental design: Serial blood samples of MI patients followed for one year (at inclusion, 1 month, 3 months, and 1 year) were treated with CPLL and analyzed by SELDI‐TOF‐MS.Result: The use of CPLL increased resolution, with loss of most abundant plasma proteins, reproducibly and improved the intensity of low‐abundance proteins. Longitudinal information allowed us to reduce by 55% the final number of peaks identified as significantly modulated throughout the 1‐year follow‐up after MI. Interestingly, 19 of the 26 peaks finally selected were detected only in samples treated from CPLL. The 2777 m/z peak, found in less elevated level in high remodeling patients, was identified as being DAHKSEVAHR FKDLGEENFKALVL, the N‐terminal peptide (24–48 aa) generated from albumin by pepsin cleavage.Conclusions and clinical relevance: This finding shows the potential of CPLL in accessing low‐abundance proteins to select and identify candidate biomarkers in patients with LVR.
Identification of diabetic nephropathy‐selective proteins in human plasma by multi‐lectin affinity chromatography and LC‐MS/MS
Authors: Ahn Jung‐Mo , Kim Byung‐Gyu , Yu Myong‐Hee , Lee In‐Kyu , Cho Je‐Yoel 
Published: March 2010

AbstractPurpose: Diabetic nephropathy (DN) is a serious complication of diabetes mellitus. Microalbuminuria has been established as a risk factor for the development of diabetic renal disease. Recently, microalbuminuria has been reported to have limitations in determining disease risk and predicting DN. Therefore, identification of more specific biomarkers for prediction of DN is needed.Experimental design: When kidney damage is initiated, glycoprotein leakage into the blood may occur, thus altering the glycoproteome profile of the blood. Here, we have used a combined approach of glycoprotein enrichment of plasma with a proteomic analysis to discover potential DN biomarkers. We isolated glycoproteins from plasma provided by six type 2 diabetes control (DC) and six type 2 DN patients using multi‐lectin affinity chromatography. Captured glycoproteins were resolved by 1‐D PAGE and tryptic digests of isolated proteins were analyzed by LC‐MS/MS.Results: From the comparative and semi‐quantitative proteome analysis, we identified 13 up‐ and 14 down‐regulated glycoproteins in DN plasma. Among the up‐regulated glycoproteins, the levels of lumican, vasorin and retinol binding protein‐4 were verified by Western blot analysis of individual plasma samples.Conclusion and clinical relevance: Collectively, our findings show that biomarker discovery has considerable potential for predicting diabetic nephropathy in diabetic patients.
Combinatorial vascular targeting in translational medicine
Authors: Staquicini Fernanda I. , Moeller Benjamin J. , Arap Wadih , Pasqualini Renata 
Published: March 2010

AbstractIn the post‐genomic era, the phage display technology surfaces as an alternative approach for large‐scale study of tissue‐specific protein interactions with direct clinical and therapeutic applications. The unbiased identification of molecular complexes expressed on the surface of cells and blood vessels of organs and tissues may eventually lead to a considerably improved understanding of cellular and vascular proteomics. The ultimate value of this technology consists in the conception of a new ligand‐directed pharmacology, with broad implications for both treatment and molecular imaging of cancer patients. In this review, we describe the use and applications of phage display for efficient development of targeted drug discovery and design.
The short‐chain oxidoreductase Q9HYA2 from Pseudomonas aeruginosa PAO1 contains an atypical catalytic center
Authors: Huether Robert , Mao Qilong , Duax William L. , Umland Timothy C. 
Published: March 2010

AbstractThe characteristic oxidation or reduction reaction mechanisms of short‐chain oxidoreductase (SCOR) enzymes involve a highly conserved Asp‐Ser‐Tyr‐Lys catalytic tetrad. The SCOR enzyme Q9HYA2 from the pathogenic bacterium Pseudomonas aeruginosa was recognized to possess an atypical catalytic tetrad composed of Lys118‐Ser146‐Thr159‐Arg163. Orthologs of Q9HYA2 containing the unusual catalytic tetrad along with conserved substrate and cofactor recognition residues were identified in 27 additional species, the majority of which are bacterial pathogens. However, this atypical catalytic tetrad was not represented within the Protein Data Bank. The crystal structures of unligated and NADPH‐complexed Q9HYA2 were determined at 2.3 Å resolution. Structural alignment to a polyketide ketoreductase (KR), a typical SCOR, demonstrated that Q9HYA2's Lys118, Ser146, and Arg163 superimposed upon the KR's catalytic Asp114, Ser144, and Lys161, respectively. However, only the backbone of Q9HYA2's Thr159 overlapped KR's catalytic Tyr157. The Thr159 hydroxyl in apo Q9HYA2 is poorly positioned for participating in catalysis. In the Q9HYA2–NADPH complex, the Thr159 side chain was modeled in two alternate rotamers, one of which is positioned to interact with other members of the tetrad and the bound cofactor. A chloride ion is bound at the position normally occupied by the catalytic tyrosine hydroxyl. The putative active site of Q9HYA2 contains a chemical moiety at each catalytically important position of a typical SCOR enzyme. This is the first observation of a SCOR protein with this alternate catalytic center that includes threonine replacing the catalytic tyrosine and an ion replacing the hydroxyl moiety of the catalytic tyrosine.
Type IIB orientifolds, D‐brane instantons and the LARGE volume scenario
Authors: Plauschinn E. 
Published: March 2010

AbstractThis review article is concerned with three topics important for the construction of four‐dimensional models of particle physics in the context of type II String Theories. Special emphasis is put on a consistent presentation of these topics as well as on highlighting their interconnections. The first of the three topics deals with the tadpole cancellation conditions and the cancellation of chiral anomalies for type IIB orientifolds with orientifold three‐ and seven‐planes. The second topic is related to non‐perturbative effects originating from D‐brane instantons. In particular, in the presence of a realistic particle physics sector, a chiral zero‐mode constraint for contribution of instantons to the superpotential arises. The third topic is about moduli stabilisation in type IIB string compactifications. Two scenarios, the KKLT and Large Volume Scenario, are reviewed and a model for the latter scenario with the chiral zero‐mode constraint taken into account is presented.
High temperature piezoelectric properties of yttrium calcium oxyborate single crystals
Authors: Yu Fapeng , Zhang Shujun , Zhao Xian , Yuan Duorong , Wang Qingming , Shrout Thomas R. 
Published: March 2010

AbstractThe piezoelectric single crystal yttrium calcium oxyborate, YCa4O(BO3)3, was studied as a function of orientation and temperature. The resistivity of Y‐cut samples was found to be 2.7 × 107 Ω cm at 950 °C, three orders of magnitude higher than langatate crystals. The electromechanical coupling k26 and piezoelectric d26 were found to be 22% and 10 pC/N at room temperature for (ZXw)‐30°‐cut samples, respectively, maintaining similar values at elevated temperature of 950 °C, exhibiting temperature independent behavior. Furthermore, the highest temperature frequency coefficient was obtained in (ZXw)‐33°‐cut samples, being –91 ppm/K. The temperature independent piezoelectric properties, together with the high resistivity and mechanical quality factor Q (∼2000 at 950 °C), suggest the YCOB crystal to be a good candidate for high temperature sensing applications. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Extension of potential predictability of Indian summer monsoon dry and wet spells in recent decades
Authors: Neena J. M. , Goswami B. N. 
Published: March 2010

AbstractAn understanding of the limit on potential predictability is crucial for developing appropriate tools for extended‐range prediction of active/break spells of the Indian summer monsoon (ISM). The global low‐frequency changes in climate modulate the annual cycle of the ISM and can influence the intrinsic predictability limit of the ISM intraseasonal oscillations (ISOs). Using 104‐year (1901–2004) long daily rainfall data, the change in potential predictability of active and break spells are estimated by an empirical method. It is found that the potential predictability of both active and break spells have undergone a rapid increase during the recent three decades. The potential predictability of active spells has shown an increase from one week to two weeks while that for break spells increased from two weeks to three weeks. This result is interesting and intriguing in the backdrop of recent finding that the potential predictability of monsoon weather has decreased substantially over the same period compared to earlier decades due to increased potential instability of the atmosphere. The possible role of internal dynamics and external forcing in producing this change has been explored. The changes in energy exchange between the synoptic and ISO scale and the different ISO modes as evidenced by energetics computations in frequency domain also support the increased potential predictability of ISO. Our finding provides optimism for improved and useful extended‐range prediction of monsoon active and break spells. Copyright © 2010 Royal Meteorological Society
Which atomic charges are best adapted to describe polyoxometalates?
Authors: Courcot Blandine , Bridgeman Adam J. 
Published: March 2010

AbstractStudying several polyanions different atomic charges have been considered to determine which scheme can be trusted to describe their chemistry. Focussing on hexa, hepta and octa‐anions, five types of charges evaluated with Density‐functional methods have been compared and discussed: Mulliken, Quantum Theory of Atoms in Molecules (QTAIM), Hirshfeld, Voronoi Deformation Density (VDD), and the net total Voronoi (NTV) charges. It appears that the same two groups of atomic charges predict comparable values. The first group encompasses Mulliken, QTAIM and the NTV charges and the second one Hirshfeld and VDD charges. When the two groups are compared they present two different tendencies regarding the different types of oxygen atoms that can be isolated in the studied polyanions. The absolute value of the first group charges increases with the coordination number of the oxygen atom, whereas Hirshfeld and VDD charges display the opposite variation. These two different tendencies are enhanced by the number of metal atoms in the polyanion. Surprisingly, the NTV charges, which are rarely used in comparison with the VDD, show the same trend as the QTAIM charges which emphasizes the implication of the promolecule's definition in the failure of the Hirshfeld and VDD methods in this study. The Coulomb potential shows that Hirshfeld and VDD atomic charges are not adapted to reproduce the electrostatic properties of the anions which leads to the conclusion that these two partitioning approaches can't describe correctly the chemistry of polyanions and have to be considered with care when dealing with charged species. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Media coverage of sustainable development issues – attention cycles or punctuated equilibrium?
Authors: Holt Diane , Barkemeyer Ralf 
Published: March 2010

AbstractOver the last two decades there has been a marked change in the way that the public perceives environmental issues and the concepts associated with sustainable development. Few would argue that this has moved into the mainstream of public consciousness. Coverage of sustainability related concepts within the media, as illustrated by a sample of 112 worldwide newspapers, shows a clear upward trajectory. Taking the example of climate change and sustainable development, this paper explores this increasing coverage, and arguably awareness, of sustainability concepts, and considers parallels with the concepts of punctuated equilibrium and issue‐attention cycles. Copyright © 2010 John Wiley & Sons, Ltd and ERP Environment.
Florid polypoid endometriosis of the cervix with left ureteric obstruction: a mimic of cervical malignancy
Authors: Kwek J. W. , H'ng M. W. C. , Chew S. H. , Tay E. H. 
Published: March 2010

AbstractPolypoid endometriosis, in contrast to typical (non‐polypoid) endometriosis, presents as masses that project from a serosal or mucosal surface or from the lining of an endometriotic cyst. Generally large, these masses can simulate a malignant tumor on imaging and at surgery. We report a case of florid polypoid endometriosis arising from the cervix with extension into the left parametrium and involving the left ureter, mimicking a locally advanced cervical malignancy on ultrasound and magnetic resonance imaging. Copyright © 2010 ISUOG. Published by John Wiley & Sons, Ltd.
Toward a complete in silico, multi‐layered embryonic stem cell regulatory network
Authors: Xu Huilei , Schaniel Christoph , Lemischka Ihor R. , Ma'ayan Avi 
Published: March 2010

AbstractRecent efforts in systematically profiling embryonic stem (ES) cells have yielded a wealth of high‐throughput data. Complementarily, emerging databases and computational tools facilitate ES cell studies and further pave the way toward the in silico reconstruction of regulatory networks encompassing multiple molecular layers. Here, we briefly survey databases, algorithms, and software tools used to organize and analyze high‐throughput experimental data collected to study mammalian cellular systems with a focus on ES cells. The vision of using heterogeneous data to reconstruct a complete multi‐layered ES cell regulatory network is discussed. This review also provides an accompanying manually extracted dataset of different types of regulatory interactions from low‐throughput experimental ES cell studies available at http://amp.pharm.mssm.edu/iscmid/literature. Copyright © 2010 John Wiley & Sons, Inc.This article is categorized under:

Analytical and Computational Methods > Computational Methods