bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuro‐fuzzy structural classification of proteins for improved protein secondary structure prediction
Authors: Hering Joachim A. , Innocent Peter R. , Haris Parvez I. 
Published: August 2003

AbstractFourier transform infrared (FTIR) spectroscopy is a very flexible technique for characterization of protein secondary structure. Measurements can be carried out rapidly in a number of different environments based on only small quantities of proteins. For this technique to become more widely used for protein secondary structure characterization, however, further developments in methods to accurately quantify protein secondary structure are necessary. Here we propose a structural classification of proteins (SCOP) class specialized neural networks architecture combining an adaptive neuro‐fuzzy inference system (ANFIS) with SCOP class specialized backpropagation neural networks for improved protein secondary structure prediction. Our study shows that proteins can be accurately classified into two main classes “all alpha proteins” and “all beta proteins” merely based on the amide I band maximum position of their FTIR spectra. ANFIS is employed to perform the classification task to demonstrate the potential of this architecture with moderately complex problems. Based on studies using a reference set of 17 proteins and an evaluation set of 4 proteins, improved predictions were achieved compared to a conventional neural network approach, where structure specialized neural networks are trained based on protein spectra of both “all alpha” and “all beta” proteins. The standard errors of prediction (SEPs) in % structure were improved by 4.05% for helix structure, by 5.91% for sheet structure, by 2.68% for turn structure, and by 2.15% for bend structure. For other structure, an increase of SEP by 2.43% was observed. Those results were confirmed by a “leave‐one‐out” run with the combined set of 21 FTIR spectra of proteins.
The role of bioinformatics in two‐dimensional gel electrophoresis
Authors: Dowsey Andrew W. , Dunn Michael J. , Yang Guang‐Zhong 
Published: August 2003

AbstractOver the last two decades, two‐dimensional electrophoresis (2‐DE) gel has established itself as thede factoapproach to separating proteins from cell and tissue samples. Due to the sheer volume of data and its experimental geometric and expression uncertainties, quantitative analysis of these data with image processing and modelling has become an actively pursued research topic. The results of these analyses include accurate protein quantification, isoelectric point and relative molecular mass estimation, and the detection of differential expression between samples run on different gels. Systematic errors such as current leakage and regional expression inhomogeneities are corrected for, followed by each protein spot in the gel being segmented and modelled for quantification. To assess differential expression of protein spots in different samples run on a series of two‐dimensional gels, a number of image registration techniques for correcting geometric distortion have been proposed. This paper provides a comprehensive review of the computation techniques used in the analysis of 2‐DE gels, together with a discussion of current and future trends in large scale analysis. We examine the pitfalls of existing techniques and highlight some of the key areas that need to be developed in the coming years, especially those related to statistical approaches based on multiple gel runs and image mining techniques through the use of parallel processing based on cluster computing and the grid technology.
Proteomic changes in renal cancer and co‐ordinate demonstration of both the glycolytic and mitochondrial aspects of the Warburg effect
Authors: Unwin Richard D. , Craven Rachel A. , Harnden Patricia , Hanrahan Sarah , Totty Nick , Knowles Margaret , Eardley Ian , Selby Peter J. , Banks Rosamonde E. 
Published: August 2003

AbstractRenal cell carcinoma (RCC) is the tenth most common cancer although the incidence is increasing. The main clinical problems stem from the relatively late presentation of many patients due to the often asymptomatic nature of the illness, and the relative insensitivity of metastatic disease to conventional chemotherapy and radiotherapy. Despite increasing knowledge of some of the genetic changes underlying sporadic renal cancer such as those involving the Von Hippel Lindau (VHL) gene, many of the underlying pathophysiological changes are ill‐defined and there remains a need for the identification of disease markers for use in diagnosis and prognosis or as potential therapeutic targets. This study has used a proteomic approach, based on two‐dimensional gel electrophoresis and mass spectrometry, to compare the protein profiles of conventional RCC tissue with patient‐matched normal kidney cortex. Sequencing of 32 protein spots with significantly increased expression in RCC samples (≥ 4/6 patients) and 41 proteins whose levels decreased (6/6 patients) confirmed several previously known RCC‐associated changes such as increases in Mn‐superoxide dismutase, lactate dehydrogenase‐A, aldolase A and C, pyruvate kinase M2, and thymidine phosphorylase. Additionally, several previously unknown changes were identified, including increased expression of three members of the annexin family and increased levels of the actin depolymerisation factor cofilin. The Warburg effect was also demonstrated with the identification of increases in proteins involved in the majority of steps in the glycolytic pathway and decreases in the gluconeogenic reactions, together with a parallel decrease in several mitochondrial enzymes. A number of the alterations seen were further confirmed in additional samples by immunohistochemistry, Western blotting, and laser capture microdissection.
Sample preparation for two‐dimensional gel electrophoresis
Authors: Shaw Margaret M. , Riederer Beat M. 
Published: August 2003

AbstractThe choice of sample preparation protocol is a critical influential factor for isoelectric focusing which in turn affects the two‐dimensional gel result in terms of quality and protein species distribution. The optimal protocol varies depending on the nature of the sample for analysis and the properties of the constituent protein species (hydrophobicity, tendency to form aggregates, copy number) intended for resolution. This review explains the standard sample buffer constituents and illustrates a series of protocols for processing diverse samples for two‐dimensional gel electrophoresis, including hydrophobic membrane proteins. Current methods for concentrating lower abundance proteins, by removal of high abundance proteins, are also outlined. Finally, since protein staining is becoming increasingly incorporated into the sample preparation procedure, we describe the principles and applications of current (and future) pre‐electrophoretic labelling methods.
Use of proteomics and physiological characteristics to elucidate ecotoxic effects of methyl tert‐butyl ether in Pseudomonas putida KT2440
Authors: Krayl Martin , Benndorf Dirk , Loffhagen Norbert , Babel Wolfgang 
Published: August 2003

AbstractWe monitored rates of growth, ATP‐synthesis, respiration, and death to assess the sensitivity of the model organism Pseudomonas putida KT2440 to methyl tert‐butyl ether (MTBE), and its degree of toxicity. The physiological data obtained suggested that the energy conservation system was the most sensitive site. However, with the help of proteomic analysis we obtained further information and deeper insight into the molecular mechanisms involved. This analysis indicated that sensitivity involves oxidative stress since alkylhydroperoxide reductase C (AhpC) and two superoxide dismutases (SodM, SodF) were amplified in the presence of MTBE. Thus, proteomics has major advantages in ecotoxicological investigations where the aims include elucidation of the molecular mechanisms as well as characterization of the ecostress and the potency of the stressor(s).
A potential cerebrospinal fluid and plasmatic marker for the diagnosis of Creutzfeldt‐Jakob disease
Authors: Guillaume Elisabeth , Zimmermann Catherine , Burkhard Pierre R. , Hochstrasser Denis F. , Sanchez Jean‐Charles 
Published: August 2003

AbstractThe recent occurrence of the new variant of Creutzfeldt‐Jakob disease (CJD), probably transmitted to humans by cattle affected by the bovine form of spongiform encephalopathy, has generated renewed interest in the clinical issues related to human spongiform encephalopathies. Using the current set of diagnostic tools, these rare but devastating conditions may be difficult to diagnose with accuracy before death. The objective of the present communication is to describe the discovery of a potential cerebrospinal fluid (CSF) and plasmatic marker of human transmissible spongiform encephalopathies. A preliminary two‐dimensional electrophoresis approach highlighted a potential neurodegenerative disorder marker called the fatty acid binding protein, FABP. Its heart form, H‐FABP, was investigated in a small group of CJD affected patients (n = 8 ) by an immunoassay approach. The amount of FABP appeared to be significantly (p≤ 0.05) increased in all tested samples. H‐FABP detection could therefore be helpful as a blood screening test for a pre‐mortem diagnosis of the disease and also to prevent the risk of iatrogenic transmission of CJD through blood transfusion.
Defining the protein repertoire of microneme secretory organelles in the apicomplexan parasite Eimeria tenella
Authors: Bromley Elizabeth , Leeds Nicola , Clark Julie , McGregor Emma , Ward Malcolm , Dunn Michael J. , Tomley Fiona 
Published: August 2003

AbstractThe apicomplexan pathogen Eimeria causes coccidiosis, an intestinal disease of chickens, which has a major welfare and economic impact on the poultry industry. There is an urgent need to identify molecules that are rational targets for drug design and novel vaccines against coccidiosis. Apicomplexan secretory organelles, including micronemes and rhoptries, are essential for invasion of the host intestinal epithelium and establishment of parasitism. However, relatively little is known about the precise molecular function of these organelles, partly because few organelle proteins have been characterized. In this study, proteomics tools have been harnessed to define the protein repertoire of micronemes. Purified microneme proteins from Eimeria tenella sporozoites were excised from two‐dimensional (2‐D) gels and analyzed using matrix‐assisted laser desorption/ionization‐time of flight‐mass spectrometry (MALDI‐TOF‐MS) and chemically assisted fragmentation (CAF)‐MALDI with de novo sequencing. Peptide mass profiles were searched against the NCBI non‐redundant (nr) database and against Eimeria‐specific databases using the Mascot search algorithm, resulting in the identification of 37 of 96 spots excised from the 2‐D gels. In addition, we have found CAF‐MALDI to be a useful adjunct for identifying proteins, without the need for tandem MS. This global approach to protein characterization will be vital to gain greater understanding of the processes involved in apicomplexan host cell invasion.
Ethical and regulatory issues arising from proteomic research and technology
Authors: Reymond Marc A. , Steinert Ralf , Eder Frank , Lippert Hans 
Published: August 2003

AbstractOver the last two decades, medical research has begun to make extensive use of products of human origin in therapeutics, oncology, and most recently, in genetic diseases. This has raised many ethical issues involving patient rights, including issues of consent. Besides informed consent, researchers should address several topics when designing studies using human tissues. Reward for the patient should be kept minimal. Sample transfer should be organized along non‐profit lines, at least in Europe. Sampling procedures should be at no risk for human volunteers, and at minimal risk for patients. Biosafety aspects should be addressed, in particular when international collaborations are intended or when collaboration is existing between academia and industry. Regulations on importation and exportation of human tissues should be observed. Data acquisition and storage should be addressed in accordance with national data protection regulations, in particular when using computerized databases. If follow‐up information is to be taken, the authorization for such information should be requested. The right for patient’s information (or for no information) on the research results should also be addressed. The issues of validation and patenting should be also solved, usually by informing the patient that he/she will have no commercial rights on potential research results. The patient should be told if the samples are transferred to another research laboratory or private company. Samples and related data should be destroyed on request at any time point during the course of the study. If possible, traceability of the donor should be ensured.
High resolution proteome analysis of cryoglobulins using Fourier transform‐ion cyclotron resonance mass spectrometry
Authors: Damoc Eugen , Youhnovski Nikolay , Crettaz David , Tissot Jean‐Daniel , Przybylski Michael 
Published: August 2003

AbstractCryoglobulins are cold‐precipitable serum immunoglobulins associated with a number of infectious, autoimmune and neoplastic disorders such as hepatitis C, Waldenström's macroglobulinemia, multiple myeloma, chronic lymphocytic leukemia, and rheumatoid arthritis. The mechanism(s) of cryoprecipitation has remained obscure hitherto, which has prompted recent intensive efforts on the identification of cryoglobulin components. In the present study, two‐dimensional gel electrophoresis (2‐DE) combined with high resolution Fourier transform‐ion cyclotron resonance (FT‐ICR) mass spectrometry has been applied as a powerful approach for the analysis of cryoglobulins. While FT‐ICR mass spectrometry has been shown to enable the high resolution identification and structure analysis of biopolymers using both electrospray (ESI) and matrix‐assisted laser desorption ionization (MALDI), the recently developed MALDI‐FT‐ICR source is shown here to provide high (sub‐ppm) mass determination accuracy and isotopic fine structure as particular advantages in the identification of proteins. The main protein components in a serum cryoprecipitate from a patient with hepatitis C virus (HCV) infection and presenting type II cryogobulinemia are immunoglobulin (Ig)M and IgG which were identified by MALDI‐FT‐ICR MS analysis after separation by 2‐DE as μ‐ and γ‐heavy chains, κ‐ and λ‐light chains, and J‐chains. Furthermore, complementarity determining regions CDR1 and CDR2 from monoclonal IgM‐RF variable region (V)L were directly identified using accurate mass determinations by FT‐ICR‐MS. The presence of Spα was ascertained as an IgM‐associated protein in the serum cryoprecipitate from a patient with HCV infection.
The Make 2D‐DB II package: Conversion of federated two‐dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases
Authors: Mostaguir Khaled , Hoogland Christine , Binz Pierre‐Alain , Appel Ron D. 
Published: August 2003

AbstractThe Make 2D‐DB tool has been previously developed to help build federated two‐dimensional gel electrophoresis (2‐DE) databases on one’s own web site. The purpose of our work is to extend the strength of the first package and to build a more efficient environment. Such an environment should be able to fulfill the different needs and requirements arising from both the growing use of 2‐DE techniques and the increasing amount of distributed experimental data.
Effect of rosiglitazone on the differential expression of obesity and insulin resistance associated proteins in lep/lep mice
Authors: Sanchez Jean‐Charles , Converset Véronique , Nolan Anna , Schmid Gerhard , Wang Steven , Heller Manfred , Sennitt Matthew V. , Hochstrasser Denis F. , Cawthorne Michael A. 
Published: August 2003

AbstractPeroxisome proliferator‐activated receptors (PPARs) participate in the molecular mechanism of pathologies with altered lipid homeostasis such as type 2 diabetes or obesity. The insulin sensitizer drug, rosiglitazone, has been shown to bind and activate PPAR‐γ1 in adipocytes and PPAR‐γ2 in hepatocytes. The identification of new molecular targets associated with fatty acid oxidation and PPAR‐γ nuclear receptor regulation in insulin resistance tissues is a key research goal. In the present study, we have used a proteomic approach to identify such targets. Lean and obese C57 Bl/6J lep/lep mice were given BRL49653, rosiglitazone, 10 mg/kg diet, by dietary admixture for 7 days. Rosiglitazone normalized the impaired glucose tolerance and dyslipidemia in lep/lep mice but had no significant effect in the lean mice. Samples of liver, white and brown adipose tissue, and muscle proteins were obtained and 100 μg of proteins was arrayed by two‐dimensional gel electrophoresis. Thirty‐four polypeptides were differentially expressed (p < 0.05) between lep/lep and lean mice and eleven were significantly (p < 0.05) modulated by rosiglitazone treatment of the obese mice. None of the proteins was modulated by rosiglitazone treatment of the lean mice. The identity of these differentially expressed proteins was made using tandem mass spectrometric analysis and revealed components of fatty acid and carbohydrate metabolism as well as proteins with unknown function.
Proteomic analysis of the larval stage of the parasite Echinococcus granulosus: Causative agent of cystic hydatid disease
Authors: Chemale Gustavo , van Rossum Arjan J. , Jefferies James R. , Barrett John , Brophy Peter M. , Ferreira Henrique B. , Zaha Arnaldo 
Published: August 2003

AbstractWe describe the preparation of Echinococcus granulosus metacestode protein extracts for two‐dimensional electrophoresis (2‐DE). Protoscoleces and hydatid fluid were prepared by precipitation using trichloroacetic acid (TCA) to remove nonprotein contaminants. Compared to the untreated control, TCA precipitation improved the 2‐DE gel profile of the protoscoleces proteins. Comparison of 2‐DE gels from insoluble and soluble fractions of the protoscoleces protein extract showed that most proteins are insoluble after lysis by sonication. Host serum proteins, especially albumin and globulins, caused horizontal streaking problems on the hydatid fluid 2‐DE gels due to their high content in this sample. Even after the preparation of a hydatid fluid parasite enriched fraction, the high amount of bovine serum albumin and globulins made parasite‐specific proteins difficult to detect by 2‐DE. Despite the absence of an E. granulosus genome sequencing or expressed sequence tag (EST) projects, it was possible to identify 15 prominent protein spots from a whole protein protoscoleces 2‐DE gel by peptide mass fingerprinting. These include actins, tropomyosin, paramyosin, thioredoxin reductase, antigen P‐29, cyclophilin, and the heat shock proteins hsp70 and hsp20. This work demonstrates that 2‐DE and PMF are important tools to identify proteins from the hydatid fluid and protoscoleces and for the comparative analysis of cysts from different hosts or between active and resting cysts.
Tissue Molecular Anatomy Project (TMAP): An expression database for comparative cancer proteomics
Authors: Medjahed Djamel , Luke Brian T. , Tontesh Tawady S. , Smythers Gary W. , Munroe David J. , Lemkin Peter F. 
Published: August 2003

AbstractBy mining publicly accessible databases, we have developed a collection of tissue‐specific predictive protein expression maps as a function of cancer histological state. Data analysis is applied to the differential expression of gene products in pooled libraries from the normal to the altered state(s). We wish to report the initial results of our survey across different tissues and explore the extent to which this comparative approach may help uncover panels of potential biomarkers of tumorigenesis which would warrant further examination in the laboratory.
Improved peptide charge state assignment
Authors: Colinge Jacques , Magnin Jérôme , Dessingy Thierry , Giron Marc , Masselot Alexandre 
Published: August 2003

AbstractWe present a new approach capable of assigning charge states to peptides based on both their intact mass spectrum and their fragmentation mass spectrum. More specifically, our approach aims at fully exploiting available information to improve correct charge assignment rate. This is achieved by using information provided by the fragmentation spectrum extensively. For low‐resolution spectra, charge assignment based on fragmentation mass spectrum is better than charge assignment based on intact peptide signal only. We introduce two methods that allow to integrate information contributing to successful peptide charge state assignment. We demonstrate the performance of our algorithms on large ion trap data sets. The application of these algorithms to large‐scale proteomics projects can save significant computation time and have a positive impact on identification false positive rates.
Correlation between the tensile properties and network draw ratio of CO2‐laser‐heated drawn poly(ethylene terephthalate) fibers
Authors: Okumura W. , Ohkoshi Y. , Gotoh Y. , Nagura M. 
Published: August 2003

AbstractLow‐orientation and amorphous poly(ethylene terephthalate) fibers were drawn continuously with heating by carbon dioxide (CO2) laser radiation. The tensile properties were examined in terms of the birefringence and network draw ratio, which was estimated from the strain shift of true stress–strain curves. Two drawing forms, neck drawing with a draw efficiency (the ratio of the network draw ratio to the actual draw ratio) of about unity and flow drawing with a draw efficiency of about zero, were found to be stable in the continuous drawing process. Meanwhile, any draw‐efficiency value between zero and unity could be obtained in the batch‐drawing process. The object whose orientation was estimated by the network draw ratio differed from that estimated by birefringence. Two linear relationships were found, between the network draw ratio and tensile strength and between the birefringence and initial modulus. The true stress at breaking increased with the network draw ratio of the CO2‐laser‐heated drawn fibers, and when the draw ratio exceeded 5.0, it became higher than that for batch‐drawn fibers. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2322–2331, 2003
Generic crack patterns in rubber‐modified polymers under biaxial stress states
Authors: Ramaswamy S. , Lesser Alan J. 
Published: August 2003

AbstractThe damage mechanisms in three different systems, namely, acrylonitrile‐butadiene‐styrene, methacrylate‐butadiene‐styrene modified poly(vinyl chloride), and styrene‐butadiene‐styrene have been investigated. The damage was analyzed over a range of biaxial stress states with confocal microscopy and scanning electron microscopy. The macroscopic yield followed a linear behavior for all the systems in an octahedral shear stress versus mean stress plot, whereas popular models for this class of materials predicted a nonlinear response. Over a certain range of biaxial stress states, a damage pattern generic to all the systems was observed. The damage pattern consisted of an array of cracks propagating perpendicular to the direction of the maximum tensile principal stress and arranged itself in a more or less periodic fashion. There was also self‐similarity in the patterns at various length scales. Similar patterns have also occurred in several other polymeric systems. The interaction in the ensemble of cracks created seems to lead to stress reduction at the crack tips, thereby limiting the crack sizes. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2248–2256, 2003