bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines
Authors: Jones Andrew R. , Siepen Jennifer A. , Hubbard Simon J. , Paton Norman W. 
Published: February 2009

AbstractLC‐MS experiments can generate large quantities of data, for which a variety of database search engines are available to make peptide and protein identifications. Decoy databases are becoming widely used to place statistical confidence in result sets, allowing the false discovery rate (FDR) to be estimated. Different search engines produce different identification sets so employing more than one search engine could result in an increased number of peptides (and proteins) being identified, if an appropriate mechanism for combining data can be defined. We have developed a search engine independent score, based on FDR, which allows peptide identifications from different search engines to be combined, called the FDR Score. The results demonstrate that the observed FDR is significantly different when analysing the set of identifications made by all three search engines, by each pair of search engines or by a single search engine. Our algorithm assigns identifications to groups according to the set of search engines that have made the identification, and re‐assigns the score (combined FDR Score). The combined FDR Score can differentiate between correct and incorrect peptide identifications with high accuracy, allowing on average 35% more peptide identifications to be made at a fixed FDR than using a single search engine.
Glycosylation as means of reducing sample complexity to enable quantitative proteomics
Authors: Domon Bruno 
Published: February 2009

AbstractQuantitative proteomics is a rapidly expanding field, in particular, the application to clinical biomarker studies for diagnosis or prognosis of diseases, and the systematic analysis of protein functions in biological systems. Isolation of a class of peptides or a subproteome enables reduction of sample complexity, which is essential to perform sensitive, quantitative analyses over a wider dynamic range of protein concentrations. Glycosylation is one of the most frequent PTMs, and glycans have unique chemical properties that can be leveraged to selectively enrich for a subset of peptides, and thus facilitate the downstream analysis. The isolation of glycopeptides and its benefits for mass spectrometric measurements is discussed.
Proteomic analysis of human low‐density lipoprotein reveals the presence of prenylcysteine lyase, a hydrogen peroxide‐generating enzyme
Authors: Banfi Cristina , Brioschi Maura , Barcella Simona , Wait Robin , Begum Shajna , Galli Sabrina , Rizzi Andrea , Tremoli Elena 
Published: February 2009

AbstractThe molecular mechanisms underlying the relationship between low‐density lipoprotein (LDL) and the risk of atherosclerosis are not clear. Therefore, detailed information on the protein composition of LDL may help to reveal its role in atherogenesis. Liquid‐phase IEF has been used to resolve LDL proteins into well‐defined fractions on the basis of pI, which improves the subsequent detection and resolution of low abundance proteins. Besides known LDL‐associated proteins, this approach revealed the presence of proteins not previously described to reside in LDL, including prenylcysteine lyase (PCL1), orosomucoid, retinol‐binding protein, and paraoxonase‐1. PCL1, an enzyme crucial for the degradation of prenylated proteins, generates free cysteine, isoprenoid aldehyde and hydrogen peroxide. Addition of the substrate farnesylcysteine to lipoprotein resulted in a time‐dependent generation of H2O2 which was stronger in very low density lipoprotein (VLDL) than in LDL or HDL, reflecting the greater protein content of PCL1 in VLDL. Farnesol, a dead end inhibitor of the PCL1 reaction, reduced H2O2 generation by VLDL. PCL1 is generated along with nascent lipoprotein, as shown by its presence in the lipoprotein secreted by HepG2 cells. The finding that an enzyme associated with atherogenic lipoproteins can itself generate an oxidant suggests that PCL1 may play a significant role in atherogenesis.
Isolation, purification and de novo sequencing of TBD‐1, the first beta‐defensin from leukocytes of reptiles
Authors: Stegemann Christin , Kolobov Alexander , Leonova Yulia F. , Knappe Daniel , Shamova Olga , Ovchinnikova Tatiana V. , Kokryakov Vladimir N. , Hoffmann Ralf 
Published: February 2009

AbstractA novel peptide with antimicrobial activity was isolated from leukocytes of the European pond turtle Emys orbicularis and purified to homogeneity by preparative gel electrophoresis followed by reversed phase chromatography. It was highly active in vitro against Escherichia coli, Listeria monocytogenes, methicillin‐resistant Staphylococcus aureus, and Candida albicans. The isolated peptide was sequenced de novo by tandem mass spectrometry using both collision‐induced and electron‐transfer dissociation in combination with different chemical derivatization techniques. The 40‐residue peptide, called TBD‐1 (turtle β‐defensin 1), represents the first defensin isolated from reptilian leukocytes. It contains three disulfide bonds and shows high structural similarities to β‐defensins isolated from birds and mammals.
Biospecific irreversible fishing coupled with atomic force microscopy for detection of extremely low‐abundant proteins
Authors: Archakov Alexander , Ivanov Yurii , Lisitsa Andrey , Zgoda Victor 
Published: February 2009

AbstractIn the absence of an analog of PCR for proteins, the concentration detection limit (DL) becomes a real challenge. The problem may be solved by means of a combination of biospecific irreversible fishing with atomic force microscopy (AFM). AFM offers the ability to register individual molecules and their complexes, while biospecific fishing takes advantage of an affine interaction between analyte molecules spread over a large volume of biomaterial and ligand molecules immobilized on the chip surface. Fishing may be conducted in Kd‐dependent reversible mode and in Kd‐independent irreversible mode. In this study, the DLs of two previously applied proteomic approaches were determined and compared to the DL of a newly developed analytical method. The first approach, based on MS analysis of biomaterial after 2‐DE or LC separation of proteins, attained a DL at the level of 10−8–10−10 M. The second approach, based on the optical biosensor analysis of molecular interactions in the format of proteomic microarrays, had a DL of 10−9–10−10 M. Our proposed method which combines biospecific fishing with AFM allowed us to attain DL values of 10−11 M under reversible binding conditions and 10−16 M under irreversible binding conditions.
Quantifying proteins by mass spectrometry: The selectivity of SRM is only part of the problem
Authors: Duncan Mark W. , Yergey Alfred L. , Patterson Scott D. 
Published: February 2009

AbstractPrecise and accurate protein quantification is critical to many areas of proteomics. Antibody‐based approaches are costly and time‐consuming to develop, consequently, there is considerable interest in alternative quantitative methods that are versatile and can be implemented without the considerable delays associated with antibody development and characterization. Approaches based on MS have therefore attracted considerable attention and are now frequently touted as the most practical and powerful of all options. Nevertheless, there are serious limitations associated with quantifying a protein based on tandem mass analysis of one or two peptides generated by either chemical or enzymatic cleavage. In an accompanying Viewpoint article, Molloy and coworkers point out that selectivity is not necessarily guaranteed despite the power of SRM. Here we address an additional concern that can also compromise specificity. In complex mammalian systems, multiple proteins can serve as precursors of a single peptide and consequently, depending on the peptide(s) selected, protein levels may be significantly under‐ or overestimated.
Mental health in significant others of patients dying from lung cancer
Authors: Östlund Ulrika , Wennman‐Larsen Agneta , Persson Carina , Gustavsson Petter , Wengström Yvonne 
Published: February 2009

AbstractObjective: Definitions and measures of significant others' mental health vary, but stress processes have been associated with caregiver outcomes of this kind. Thus, various mental health outcomes probably appear, either as specific responses to particular types of caregiver stressors, or as part of a general response resulting from an accumulation of various stressors. The present study explores the occurrence of symptoms of strain with regard to depression, exhaustion, and emotional well‐being in significant others of patients dying from lung cancer, and how these symptoms coexist.Methods: Measures used were the Montgomery Åsberg Depression Rating Scale, the OLdenburg Burnout Inventory, and the Swedish Health‐Related Quality of Life Survey. Data from 84 significant others of patients dying from lung cancer were collected at a time‐point during the last 4 months before the patients died and subsequently analysed. The occurrence of symptoms of strain was established by creating cut‐off scores from the general population. To explore how the different symptoms coexisted, hierarchical agglomerative cluster analyses were conducted using Ward's method.Results: Approximately 40% of the significant others reported symptoms of strain for each of the three outcomes, and a coexistence was found since the significant others clustered as subgroups, ranging from ‘high on all scales’ to ‘low on all scales’.Conclusion: A considerable proportion of the significant others were thus negatively affected in terms of mental health. We conclude that being a significant other of a person dying from lung cancer most likely results in a general response to this major life event. Copyright © 2009 John Wiley & Sons, Ltd.
Protein content in aqueous humor from patients with pseudoexfoliation (PEX) investigated by capillary LC MALDI‐TOF/TOF MS
Authors: Hardenborg Emilia , Botling‐Taube Amelie , Hanrieder Jörg , Andersson Marit , Alm Albert , Bergquist Jonas 
Published: February 2009

AbstractAnalysis of proteins in human body fluids is challenging since the composition of the sample often is rather complex. Here we present a method for analysis of proteins in aqueous humor from two groups of cataract patients, with and without pseudoexfoliation (PEX). Aqueous humor is an extracellular fluid contained in the anterior chamber of the eye between the cornea and iris. The limited volume of sample requires sophisticated analysis techniques. Our method is based on a total tryptic digestion of the sample followed by capillary LC‐MALDI MS and MS/MS analysis of the peptides. The method is rapid, efficient and suitable as a complement or alternative to more commonly used methods based on gel electrophoretic experiments. With this method we found and unambiguously identified 30 nonredundant proteins. Proteins found include general transport proteins such as albumin and apolipoprotein A1 but also specific proteins involved in immune response, such as complement factors. Cystatin C, clusterin, and crystallins were also found. Although the number of proteins was roughly the same in both groups there was a significant difference in their identities. These findings may give some new insights into the pathophysiology of the PEX syndrome.
Spontaneous and induced labour are associated with different myometrial proteomes in the human
Authors: MacIntyre David A. , Smith Roger , Yeo George , Kwek Kenneth , Bisits Andrew M. , Chan Eng‐Cheng 
Published: February 2009

AbstractHuman myometrium undergoes a major phenotypic change at labour likely involving modifications to key regulatory proteins. In some cases, the myometrium fails to activate normally and medical intervention is required to induce labour. In this study, 2‐D DIGE was used to examine changes in the myometrial proteome at the time of spontaneous (SL) and induced labour (IL). Proteomic profiles of nonlabouring term myometria (NL, n = 6) were quantitatively compared to SL (n = 6) and prostaglandin/oxytocin‐IL term myometria (n = 6). In SL samples, 23 differentially expressed protein spots were detected (9 increased/14 decreased compared to NL, p<0.05). In IL samples, 59 differentially expressed spots were observed (13 increased/46 decreased compared to NL). Comparison of SL and IL proteomes revealed 69 differentially expressed proteins (7 increased/62 decreased). Two proteins consistently decreased in SL and IL samples were identified as transgelin (1.98‐ and 1.97‐fold decrease in SL and IL, respectively) and αB‐crystallin (3.27‐ and 2.49‐fold decrease). Levels of desmin and cytosolic phospholipase A2 β were decreased 2.9‐ and 2.65‐fold, respectively only in IL samples. Our results show human labour is accompanied by general downregulation of specific myometrial proteins. Differences exist between SL and IL myometrial proteomes indicating divergence of underlying processes and highlighting the importance of distinguishing these groups in future studies of parturition. Our findings underscore the utility of discovery approaches in investigations of organ‐wide protein changes that underlie discrete physiological events including human labour.
Dynamic urinary proteomic analysis reveals stable proteins to be potential biomarkers
Authors: Sun Wei , Chen Yong , Li Fuxin , Zhang Ling , Yang Ruifeng , Zhang Zhi , Zheng Dexian , Gao Youhe 
Published: February 2009

AbstractHuman urinary proteome analysis is a convenient and efficient approach for understanding disease processes affecting the kidney and urogenital tract. Many potential biomarkers have been identified in previous differential analyses; however, dynamic variations of the urinary proteome have not been intensively studied, and it is difficult to conclude that potential biomarkers are genuinely associated with disease rather then simply being physiological proteome variations. In this paper, pooled and individual urine samples were used to analyze dynamic variations in the urinary proteome. Five types of pooled samples (first morning void, second morning void, excessive water‐drinking void, random void, and 24 h void) collected in 1 day from six volunteers were used to analyze intra‐day variations. Six pairs of first morning voids collected a week apart were used to study inter‐day, inter‐individual, and inter‐gender variations. The intra‐day, inter‐day, inter‐individual, and inter‐gender variation analyses showed that many proteins were constantly present with relatively stable abundances, and some of these had earlier been reported as potential disease biomarkers. In terms of sensitivity, the main components of the five intra‐day urinary proteomes were similar, and the second morning void is recommended for clinical proteome analysis. The advantages and disadvantages of pooling samples are also discussed. The data presented describe a pool of stable urinary proteins seen under different physiological conditions. Any significant qualitative or quantitative changes in these stable proteins may mean that such proteins could serve as potential urinary biomarkers.
Multidimensional protein identification technology analysis highlights mitoxantrone‐induced expression modulations in the primary prostate cancer cell proteome
Authors: Symes Juliane , Evangelou Andreas , Ignatchenko Alex , Fleshner Neil , Kislinger Thomas , Medin Jeffrey A. 
Published: February 2009

AbstractChemotherapeutic agents as they are used today have limited effectiveness against prostate cancer, but may potentially be used in new combinations with more efficacious results. Mitoxantrone, used for palliation of prostate cancer, has recently been found by our group to improve the susceptibility of primary prostate cancer cells to killing through the Fas‐mediated death pathway. Here we used a shotgun proteomics approach to first profile the entire prostate cancer proteome and then identify specific factors involved in this mitoxantrone response. Peptides derived from primary prostate cancer cells treated with or without 100 nM mitoxantrone were analyzed by multidimensional protein identification technology (MudPIT). Strict limits and data filtering hierarchies were applied to identify proteins with high confidence. We identified 1498 proteins belonging to the prostate cancer proteome, 83 of which were significantly upregulated and 27 of which were markedly downregulated following mitoxantrone treatment. These proteins perform diverse functions, including ceramide production, tumour suppression, and oxidative reduction. Detailed proteomic analyses of prostate cancer cells and their response to mitoxantrone will further our understanding of its mechanisms of action. Identification of proteins influenced by treatment with mitoxantrone or other compounds may lead to the development of more effective drug combinations against prostate cancer.
Evolutionary conservation in multiple faces of protein interaction
Authors: Choi Yoon Sup , Yang Jae‐Seong , Choi Yonghwan , Ryu Sung Ho , Kim Sanguk 
Published: February 2009

AbstractProtein interfaces are believed to be evolutionarily more conserved than the rest of the protein surface, but this has not been properly verified using a large protein structural set. Furthermore, recent systematic protein interaction analyses have proved that proteins interacting with many partners have multiple interfaces to connect protein interaction networks, which have never taken into account for conservation analysis of protein interface. Here, we studied the evolutionary conservation of protein interfaces using a large‐scale dataset of 2646 protein interfaces with the classification of homodimeric/heterodimeric and obligatory/transient interactions, considering all their known multiple interfaces. We found that protein interfaces were indeed more conserved than noninterface surfaces, and the conservation level of protein interfaces increased when multiple interfaces were properly considered. These findings suggest that conservation analysis should be a good descriptor for protein interface identification and protein–protein interaction predictions. We applied this evolutionary feature to filter docking decoys and found that protein interface conservation worked remarkably well in selecting the near‐native structures from the large number of generated docking complexes. Moreover, we discovered that a strong correlation exist between protein interface size and protein interface conservation, which could be a useful filter for the prediction of protein–protein interactions. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Atomic structure of the non‐polar GaN($ \bar 2 $110) surface by cross‐sectional scanning tunneling microscopy
Authors: Krüger David , Kuhr Simon , Schmidt Thomas , Hommel Detlef , Falta Jens 
Published: February 2009

AbstractThe ($ \bar 2 $110) plane of gallium nitride, exposed by cleaving a GaN single crystal under ultra‐high vacuum conditions, has been atomically resolved for the first time, using cross‐sectional scanning tunneling microscopy. The spatial period length supports a (1 × 1) unit mesh size, i.e., the absence of a reconstruction. The contrast observed in the experimental data is well explained by the atomic arrangement expected for a truncated‐bulk structure. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Fibroblast Growth Factor-2 Overexpression in Transplanted Neural Progenitors Promotes Perivascular Cluster Formation with a Neurogenic Potential
Authors: Jenny Benoit , Kanemitsu Michiko , Tsupykov Oleg , Potter Gael , Salmon Patrick , Zgraggen Eloisa , Gascon Eduardo , Skibo Galina , Dayer Alexandre G. , Kiss Jozsef Z. 
Published: February 2009

Abstract
Stem/progenitor cell-based therapies hold promises for repairing the damaged nervous system. However, the efficiency of these approaches for neuronal replacement remains very limited. A major challenge is to develop pretransplant cell manipulations that may promote the survival, engraftment, and differentiation of transplanted cells. Here, we investigated whether overexpression of fibroblast growth factor-2 (FGF-2) in grafted neural progenitors could improve their integration in the host tissue. We show that FGF-2-transduced progenitors grafted in the early postnatal rat cortex have the distinct tendency to associate with the vasculature and establish multiple proliferative clusters in the perivascular environment. The contact with vessels appears to be critical for maintaining progenitor cells in an undifferentiated and proliferative phenotype in the intact cortex. Strikingly, perivascular clusters of FGF-2 expressing cells seem to supply immature neurons in an ischemic environment. Our data provide evidence that engineering neural progenitors to overexpress FGF-2 may be a suitable strategy to improve the integration of grafted neural progenitor cells with the host vasculature thereby generating neurovascular clusters with a neurogenic potential for brain repair.
Disclosure of potential conflicts of interest is found at the end of this article.
Integrin-Linked Kinase Is Required in Hypoxic Mesenchymal Stem Cells for Strengthening Cell Adhesion to Ischemic Myocardium
Authors: Song Suk-Won , Chang Woochul , Song Byeong-Wook , Song Heesang , Lim Soyeon , Kim Hye-Jung , Cha Min-Ji , Choi Eunju , Im Sin-Hyeog , Chang Byung-Chul , Chung Namsik , Jang Yangsoo , Hwang Ki-Chul 
Published: February 2009

Abstract
Mesenchymal stem cells (MSCs) therapy has limitations due to the poor viability of MSCs after cell transplantation. Integrin-mediated adhesion is a prerequisite for cell survival. As a novel anti-death strategy to improve cell survival in the infarcted heart, MSCs were genetically modified to overexpress integrin-linked kinase (ILK). The survival rate of ILK-transfected MSCs (ILK-MSCs) was augmented by about 1.5-fold and the phosphorylation of ERK1/2 and Akt in ILK-MSCs were increased by about three and twofold, respectively. ILK-MSCs demonstrated an increase of twofold in the ratio of Bcl-2/Bax and inhibited caspase-3 activation, compared with hypoxic MSCs. The adhesion rate of ILK-MSCs also had a 32.2% increase on the cardiac fibroblast-derived three-dimensional matrix and ILK-MSCs showed higher retention by about fourfold compared to unmodified MSCs. Six animals per group were used for the in vivo experiments analyzed at 1 week after occlusion of the left coronary artery. ILK-MSC transplanted rats had a 12.0% ± 3.1% smaller infarct size than MSC-treated rats after ligation of left anterior descending coronary artery. Transplantation of ILK-MSCs not only led to a 16.0% ± 0.4% decrease in the fibrotic heart area, but also significantly reduced the apoptotic positive index by two-thirds when compared with ligation only. The mean microvessel count per field in the infarcted myocardium of ILK-MSCs group was increased relative to the sham group and MSCs group. In conclusion, the ILK gene transduction of MSCs further assisted cell survival and adhesion, and improved myocardial damage when compared with MSC only after transplantation.
Disclosure of potential conflicts of interest is found at the end of this article.