bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein arrays: The current state‐of‐the‐art
Authors: Cutler Paul 
Published: January 2003

AbstractThe completion of projects for sequencing whole genomes such as those of human, Saccaromyces cerevisiae and Caenorhabditis elegans has led to a rapid increase in the availability of genetic information. The technology by which such information is acquired is having a major impact on the way we think about analysing the RNA and protein products of the gene transcription. Transcriptome analysis has, via microarray technology, managed to achieve a near genomic scale quantitative analysis of mRNA levels. Several other technologies such as quantitative reverse transcriptase polymerase chain reaction and representational differential analysis are also available for analysing gene products. Traditionally, protein analysis has been performed by assaying one particular protein at a time, with very little parallel analysis. As protein function is a direct consequence of the protein product of the gene and as mRNA levels do not always correlate well with protein, it is desirable to analyse the entire protein complement of a cell etc. on a similar scale to mRNA. Despite the clear interest in analysing the expression, structure and function of proteins at a genomic scale, they have proven less amenable to such generic, high‐throughput approaches. This review highlights the current thinking in the area of proteome analysis and considers the potential for future technology development in the area of protein arrays.
Serological and proteomic evaluation of antibody responses in the identification of tumor antigens in renal cell carcinoma
Authors: Unwin Richard D. , Harnden Patricia , Pappin Darryl , Rahman Dinah , Whelan Peter , Craven Rachel A. , Selby Peter J. , Banks Rosamonde E. 
Published: January 2003

AbstractRenal cell carcinoma (RCC) is relatively resistant to conventional chemotherapy and radiotherapy. However, reports of spontaneous regression along with promising results in clinical trials suggest that immunotherapuetic strategies may be of clinical benefit. Few RCC related antigens have been identified to date, and the technical difficulty and time constraints of current antigen identification techniques preclude the screening of large numbers of patients. A comparatively rapid strategy has been used to identify components of tumors that elicit an antibody response in the patient – the serological and proteomic evaluation of antibody responses (SPEAR) approach. This combines two‐dimensional polyarylamide gel electrophoresis of tumor and normal kidney samples with immunoblotting using autologous patient sera and protein identification by mass spectrometry. Using the SPEAR approach to screen RCC patients for naturally occurring antitumor antibody responses, a number of candidate immunogens have been identified in patients with high‐grade disease and their relative expression levels in tumor tissue compared to normal tissue have been studied. These proteins include annexins I and IV, thymidine phosphorylase (TP), carbonic anhydrase I, Mn‐superoxide dismutase and major vault protein (MVP). Downstream analysis of the tissue expression of some of these proteins shows that MVP is up‐regulated in 2/4 of RCC tumors but is also expressed in normal kidney whereas TP is up‐regulated in 100% (11/11) of RCC cases examined with no or minimal expression in normal kidney, indicating a potential use as a therapeutic target.
Antibody microarray profiling of human prostate cancer sera: Antibody screening and identification of potential biomarkers
Authors: Miller Jeremy C. , Zhou Heping , Kwekel Joshua , Cavallo Robert , Burke Jocelyn , Butler E. Brian , Teh Bin S. , Haab Brian B. 
Published: January 2003

AbstractWe developed a practical strategy for serum protein profiling using antibody microarrays and applied the method to the identification of potential biomarkers in prostate cancer serum. Protein abundances from 33 prostate cancer and 20 control serum samples were compared to abundances from a common reference pool using a two‐color fluorescence assay. Robotically spotted microarrays containing 184 unique antibodies were prepared on two different substrates: polyacrylamide based hydrogels on glass and poly‐1‐lysine coated glass with a photoreactive cross‐linking layer. The hydrogel substrate yielded an average six‐fold higher signal‐to‐noise ratio than the other substrate, and detection of protein binding was possible from a greater number of antibodies using the hydrogels. A statistical filter based on the correlation of data from “reverse‐labeled” experiment sets accurately predicted the agreement between the microarray measurements and enzyme‐linked immunosorbent assay measurements, showing that this parameter can serve to screen for antibodies that are functional on microarrays. Having defined a set of reliable microarray measurements, we identified five proteins (von Willebrand Factor, immunoglobulinM, Alpha1‐antichymotrypsin, Villin and immunoglobulinG) that had significantly different levels between the prostate cancer samples and the controls. These developments enable the immediate use of high‐density antibody and protein microarrays in biomarker discovery studies.
Proteome analysis on an early transformed human bronchial epithelial cell line, BEP2D, after α‐particle irradiation
Authors: Ying Wantao , Zhang Kaitai , Qian Xiaohong , Xie Ling , Wang Jie , Xiang Xiaoqiong , Cai Yun , Wu Dechang 
Published: January 2003

AbstractTo probe the mechanism of carcinogenesis of lung cancer at the molecular level and to find potential protein markers involved in the early phase of tumorgenesis, differential proteome analysis on primary passage cell line R15H, and early transformed cell line R15H20 derived from 238Pu α‐particle irradiation of human papillomavirus (HPV) 18‐immortalized human bronchial epithelial cell line (BEP2D), was carried out using two‐dimensional electrophoresis (2‐DE) and peptide mass fingerprinting (PMF) with matrix‐assisted laser desorption/ionisation‐time of flight mass spectrometry. Image analysis and Student's t‐test (p < 0.05) showed that three protein spots were only expressed in R15H, intensities of 43 protein spots on the gels were altered between R15H and R15H20. Two of the three spots that were only expressed in R15H were identified as high mobility group protein 1. Two proteins decreased in abundance in R15H20 were identified as maspin precursor, a tumor suppressor and aminoacylase‐1. Ornithine aminotransferase and peptidyl‐prolyl cis‐trans isomerase A that were increased in R15H20, were also identified. Relationships between these differentially expressed proteins and the carcinogenesis mechanism of lung cancer are discussed. The protein expression profile of the R15H cell line was also constructed during the study as a reference map for further comparative proteome analysis of the irradiation induced BEP2D cell line. Of the 90 spots analyzed with PMF in the 2‐DE gel of R15H cell line, 50 proteins were identified by searching the nonredundant protein database SWISS‐PROT/TrEMBL.
Vitamin E prevents oxidation of antiapoptotic proteins in neuronal cells
Authors: Choi Joungil , Conrad Craig C. , Dai Rong , Malakowsky Christina A. , Talent John M. , Carroll Christopher A. , Weintraub Susan T. , Gracy Robert W. 
Published: January 2003

AbstractOxidative damage to neuronal proteins appears to be central to the toxicity associated with a number of neuropathologies, including Alzheimer's disease. We have examined this by using oxidative stress to induce apoptosis in a mouse hippocampal neuronal cell line (HT‐22). Oxidatively modified proteins were measured by high‐resolution two‐dimensional gel electrophoresis coupled with oxidation‐specific immunostains. Under these conditions the oxidatively stressed cells undergo apoptosis, and specific proteins are oxidized. The three proteins that appeared to be most susceptible to oxidation were identified by mass spectrometry. Those oxidized proteins are heat shock protein 60 and vimentin, both believed to function as antiapoptotic proteins, and a third protein with sequence homology to hemoglobin α‐chain. When the cells were pretreated with vitamin E, these proteins were not oxidized and the cells did not undergo apoptosis.
Proteome analysis of the thermoreceptive pit membrane of the western diamondback rattlesnake Crotalus atrox
Authors: Zischka Hans , Keller Heike , Kellermann Joseph , Eckerskorn Christoph , Schuster Stephan C. 
Published: January 2003

AbstractRattlesnakes detect their prey's temperature by means of a cavern‐like structure, the pit organ. The sensory component of this organ lies within a thin membrane called the pit membrane. Proteome analysis conducted on this neurosensory tissue revealed only a relatively small number of proteins, thereby depicting its high degree of specialization. In addition to containing blood serum and structural proteins, the proteome of this membrane appears to be strikingly similar to that of isolated rattlesnake brain mitochondria. Indeed, our results show that over 80% of the detected tissue proteins are of mitochondrial origin. Fluorescence microscopy studies of these organelles indicate their dense arrangement and accumulation in structures which have been previously reported to be the terminal ends of free nerve fibers of the innervating trigeminal branches. Thus, original ultrastructural observations are paralleled by our findings at the molecular level.
Proteomic analysis of human bronchoalveolar lavage fluid: expression profiling of surfactant‐associated protein A isomers derived from human pulmonary alveolar proteinosis using immunoaffinity detection
Authors: He Chang 
Published: January 2003

AbstractHuman bronchoalveolar lavage fluid (BALF) proteins from pulmonary alveolar proteinosis (PAP) obtained by washing the epithelial lining of the lung with phosphate‐buffered saline, were separated using high resolution two‐dimensional gel electrophoresis (2‐DE) under denaturing and reducing conditions. By Western blotting, the proteins were transferred from polyacrylamide gel onto a chemical resilient membrane. The surfactant‐associated protein A (SP‐A) isomers were then identified with enhanced chemiluminescence detection (ECL) using antibody‐antigen reaction. Some of the gels were treated with silver staining after 2‐DE. The molecular masses of SP‐A isomers in BALF from PAP ranged from 20.5 to 26, 26 to 32, and 32 to 42 kDa, respectively; and isoelectric points (pI) were in pH range of 4.5–5.4 under denaturing and reducing conditions. In the mass range of 20.5–26 kDa and pI of 4.5–5.4, there were five isomers, and in mass range of 26–32 kDa and pI of 4.5 to 5.4, there were at least eight isomers on the ECL detection film. However, in the mass range of 32–42 kDa and pI of 4.5–5.4, there were three isomers separated one from another but there was also a cluster of overlapping spots on the ECL detection film. Thus, this communication describes a characteristic 2‐DE pattern of SP‐A isomers in BALF from PAP as follows. (1) The five isomers of mass 20.5–26 kDa and pI of 4.5–5.4; (2) the eight isomers of mass 26–32 kDa and pI of 4.5–5.4; and (3) the three isomers of mass 32–42 kDa and pI of 4.5–5.4.
Proteins induced by Xanthomonas axonopodis pv. passiflorae with leaf extract of the host plant (Passiflorae edulis)
Authors: Tahara Sandra T. , Mehta Angela , Rosato Yoko B. 
Published: January 2003

AbstractTwo‐dimensional gel electrophoresis was used to identify differentially displayed proteins during treatment of Xanthomonas axonopodis pv. passiflorae in media containing leaf extract of the compatible (passion fruit) and incompatible (tomato) hosts. The results showed that at different times of treatment (5, 25 and 45 h) the global expression of proteins was almost identical in cells grown in minimal medium (MM) and in medium containing leaf extract of the incompatible host (MMT). The protein patterns of cells grown in medium containing passiflorae (MMP) leaf extract and MM were also compared enabling the detection of 17 differential spots. Most of the proteins were induced at earlier times of incubation (5 h) and maintained until 45 h in MMP. By using another carrier ampholyte range, seven additional proteins were identified in MMP treated cells. Five proteins, including one constitutive, two induced and two up‐regulated in MMP were microsequenced. All sequences were found in the genome of xanthomonads sharing high level of identity (88–100%). Fructose biphosphate aldolase was expressed in all media employed. A putative membrane‐related protein and a hypothetical protein were novel proteins induced specifically by the passiflorae extract. An inorganic pyrophosphatase and a hypothetical protein that showed similarity to the yciF gene of Salmonella thyphimurium were up‐regulated in MMP.
Prediction of polymerization shrinkage using molecular modeling
Authors: Tilbrook D. A. , Pearson G. J. , Braden M. , Coveney P. V. 
Published: January 2003

AbstractGroup interaction modeling (GIM) is used to predict the changes in the volume and, therefore, shrinkage of a wide variety of commonly encountered acrylate and methacrylate monomers during polymerization. The predictions of the model are in excellent agreement with experimental data available in the literature. It is demonstrated that, given appropriate estimations of the ultimate matrix morphology, GIM can be used to give estimates of polymerization shrinkage in three‐dimensional crosslinked polymer networks that relate well to experimental data available for dental composite matrices. GIM provides a very useful framework within which the phenomenon of polymerization shrinkage can be considered. The approach challenges certain common misconceptions relating conversion to shrinkage. The limitations of this approach are discussed, and targets for future research are clearly outlined that could extend the scope of this methodology to encompass novel systems for which morphological information is not available. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 528–548, 2003
Poly(hydroxyether of phenolphthalein) and its blends with poly(ethylene oxide)
Authors: Zheng Sixun , Ai Shuping , Guo Qipeng 
Published: January 2003

AbstractPoly(hydroxyether of phenolphthalein) (PPH) was synthesized through the polycondensation of phenolphthalein with epichlorohydrin. It was characterized by Fourier transform infrared (FTIR) spectroscopy, NMR spectroscopy, and differential scanning calorimetry (DSC). The miscibility of the blends of PPH with poly(ethylene oxide) (PEO) was established on the basis of the thermal analysis results. DSC showed that the PPH/PEO blends prepared via casting fromN,N‐dimethylformamide possessed single, composition‐dependent glass‐transition temperatures. Therefore, the blends were miscible in the amorphous state for all compositions. FTIR studies indicated that there were competitive hydrogen‐bonding interactions with the addition of PEO to the system, which were involved with OH…OC〈, OH…OH, and OH vs ether oxygen atoms of PEO hydrogen bonding, that is both intramolecular and intermolecular, between PPH and PEO). Some of the hydroxyl stretching vibration bands significantly shifted to higher frequencies, whereas others shifted to lower frequencies, and this suggested the formation of hydrogen bonds between the pendant hydroxyls of PPH and ether oxygen atoms of PEO, which were stronger than the intramolecular hydrogen bonding between hydroxyls and carbonyls of PPH. The FTIR spectra in the range of carbonyl stretching vibrations showed that the hydroxyl‐associated carbonyl groups were partially set free because of the presence of the competitive hydrogen‐bonding interactions. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 466–475, 2003
Model for anomalous moisture diffusion through a polymer–clay nanocomposite
Authors: Drozdov A. D. , Christiansen J. deC. , Gupta R. K. , Shah A. P. 
Published: January 2003

AbstractExperimental data are reported on moisture diffusion and the elastoplastic response of an intercalated nanocomposite with vinyl ester resin matrix and montmorillonite clay filler at room temperature. Observations in diffusion tests showed that water transport in the neat resin is Fickian, whereas it becomes anomalous (non‐Fickian) with the growth of the clay content. This transition is attributed to immobilization of penetrant molecules on the surfaces of hydrophilic clay layers. Observations in uniaxial tensile tests demonstrate that the response of vinyl ester resin is strongly elastoplastic, whereas an increase in the clay content results in a severe decrease of plastic strains observed as a noticeable reduction in the curvatures of the stress‐strain diagrams. This is explained by slowing down the molecular mobility in the host matrix driven by confinement of chains in galleries between platelets. Constitutive equations are developed for moisture diffusion through and the elastoplastic behavior of a nanocomposite. Adjustable parameters in these relations are found by fitting the experimental data. Fair agreement is demonstrated between the observations and the results of numerical simulation. A striking similarity is revealed among changes in diffusivity, ultimate water uptake, and the rate of plastic flow with an increased clay content. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 476–492, 2003
Nucleation ability of multiwall carbon nanotubes in polypropylene composites
Authors: Assouline E. , Lustiger A. , Barber A. H. , Cooper C. A. , Klein E. , Wachtel E. , Wagner H. D. 
Published: January 2003

AbstractThe nonisothermal crystallization of multiwall carbon nanotube (MWNT)/isotactic polypropylene (iPP) nanocomposites was investigated. The results derived from the differential scanning calorimetry curves (onset temperature, melting point, supercooling, peak temperature, half‐time of crystallization, and enthalpy of crystallization) were compared with those of neat iPP. The data were also processed according to Ozawa's theory and Dobreva's approach. These results and X‐ray diffraction data showed that the MWNTs acted as α‐nucleating agents in iPP. Accordingly, MWNT/iPP was significantly different from neat iPP: A fibrillar morphology was observed instead of the usual spherulites. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 520–527, 2003
Quantitative evaluation of stress distribution in bulk polymer samples through the comparison of mechanical behaviors between giant single‐crystal and semicrystalline samples of poly(trans‐1,4‐diethyl muconate)
Authors: Nakamoto Shinsuke , Tashiro Kohji , Matsumoto Akikazu 
Published: January 2003

AbstractThe Raman shift and crystallite modulus were measured under the application of tensile force for a giant single crystal and a series of uniaxially oriented semicrystalline samples of poly(trans‐1,4‐diethyl muconate) (polyEMU). The apparent Raman shift factor αapp or a vibrational frequency shift per 1 GPa tensile stress was higher for the semicrystalline samples with lower crystallinity or lower bulk modulus. The apparent crystallite modulus E or Young's modulus along the chain axis in the crystalline region was not constant but varied remarkably between the giant single crystal and semicrystalline samples. A systematic change in αapp and E among the polyEMU samples with different preparation history could be interpreted quantitatively on the basis of a mechanical series parallel model consisting of crystalline and amorphous phases. The origin of different E and αapp was speculated to be a stress concentration on the taut‐tie chain contained as a parallel crystalline component in the mechanical model. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 444–453, 2003
Evaluation of the free‐volume theory of diffusion
Authors: Vrentas J. S. , Vrentas C. M. 
Published: January 2003

AbstractGeneral characteristics of the free‐volume theory of diffusion are discussed, and a recent data‐theory comparison involving free‐volume theory is critically evaluated. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 501–507, 2003
Molecular mobility of ultrasonically devulcanized silica‐filled poly(dimethyl siloxane)
Authors: Shim S. E. , Isayev I. , von Meerwall E. 
Published: January 2003

AbstractWe used NMR relaxation and pulsed‐gradient diffusion measurements at 70 °C in precipitated silica‐filled poly(dimethylsiloxane) (PDMS; silicone rubber) after crosslinking, after subsequent devulcanization by intense ultrasound, and after subsequent revulcanization. As in unfilled PDMS, transverse relaxation displays three distinct rate components attributed to an entangled and crosslinked network (similar in T2), light sol plus dangling network fragments, and unreactive trace oligomers. Ultrasound produces copious amounts of extractable sol. The T2 relaxation times decreased modestly with increasing filler content, but they and the components' proportions correlated mainly with the sol fraction, that is, the network degradation. In rupturing the network, devulcanization produces large diffusing fragments and dangling ends; revulcanization largely reverses these effects. The rates and amplitudes of the bimodal diffusivity distribution confirmed this conclusion. The weakness of the effects of filler suggests that ultrasound devulcanization is easily adaptable to the recycling of the preponderantly particulate‐filled industrial rubbers. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 454–465, 2003
Quantitative prediction of phase diagrams for polymer partitioning in aqueous two‐phase systems
Authors: Croll Tristan , Munro Peter D. , Winzor Donald J. , Trau Matt , Nielsen Lars K. 
Published: January 2003

AbstractPublished polymer distribution data for aqueous poly(ethylene glycol)/dextran mixtures have been reassessed to illustrate the feasibility of their quantitative characterization in terms of the Flory–Huggins theory of polymer thermodynamics. Phase diagrams predicted by this characterization procedure provide better descriptions of the experimental data than those based on an earlier, oversimplified treatment in similar terms. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 437–443, 2003
Structure, morphology, and crystallization of a random ethylene–propylene copolymer
Authors: Silvestre Clara , Cimmino Sossio , Triolo Roberto 
Published: January 2003

AbstractThe structure, morphology, and crystallization behavior of a random ethylene–propylene copolymer, containing 2 wt % ethylene sequences, are analyzed and compared with those of a plain polypropylene sample by means of optical and scanning microscopy, wide‐angle X‐ray scattering, and calorimetry. For the copolymer, different polymorphs (α, γ and smectic modifications) and morphologies can be obtained through changes in the crystallization and annealing conditions. The analysis of the structural results suggests that the γ phase of isotactic polypropylene can be generated for high molecular mass samples with drastic decreases in the undercooling. The spherulite growth rate (G) data, in conjunction with the crystallization temperatures (Tc's), are obtained with the procedure suggested by Chung and Chen and modified by Silvestre et al. The results demonstrate that the presence of ethylene sequences reduces G at a given value of Tc. It is hypothesized that at atmospheric pressure and Tc = 110–128 °C, the different polymorphs have different crystallization growth rates (Gγ < Gα < Gβ). © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 493–500, 2003