bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of capillary electrophoresis‐mass spectrometry for determining organic food contaminants and residues
Authors: Font Guillermina , Ruiz Maria José , Fernández Monica , Picó Yolanda 
Published: May 2008

AbstractFood contamination continues to be a serious problem around the world. Surveillance of chemical contaminants in foods is important not only for public health but also because of the negative economic impact of contamination. From the analytical perspective, analysis of contaminants in food is an extremely challenging area. There is a wide variety of questions, ranging from the quantification of extremely low levels of individual components to the detailed assessment and evaluation of the analytical technique possibilities. This review considers the applications of CE coupled to MS detection (CE‐MS) for the analysis of organic contaminants in food. Analytical information on sample concentration techniques, as well as on the CE separation conditions and recoveries obtained from water and food are provided. Different sections include several fields of application, such as pesticides, drug residues, or toxic formed during food processing in different matrices. A number of tables report a comprehensive listing of CE‐MS applications. As a result, this work presents an update overview on the principal application of CE‐MS together with a discussion of their main advantages and drawbacks, and an outline of future trends on analysis of organic contaminants.
Sample complexity reduction for two‐dimensional electrophoresis using solution isoelectric focusing prefractionation
Authors: Richardson Matthew R. , Liu Sean , Ringham Heather N. , Chan Victor , Witzmann Frank A. 
Published: May 2008

AbstractDespite its excellent resolving power, 2‐DE is of limited use when analyzing cellular proteomes, especially in differential expression studies. Frequently, fewer than 2000 protein spots are detected on a single 2‐D gel (a fraction of the total proteome) regardless of the gel platform, sample, or detection method used. This is due to the vast number of proteins expressed and their equally vast dynamic range. To exploit 2‐DE unique ability as both an analytical and a preparative tool, the significant sample prefractionation is necessary. We have used solution isoelectric focusing (sIEF) via the ZOOM® IEF Fractionator (Invitrogen) to generate sample fractions from complex bacterial lysates, followed by parallel 2‐DE, using narrow‐range IPG strips that bracket the sIEF fractions. The net result of this process is a significant enrichment of the bacterial proteome resolved on multiple 2‐D gels. After prefractionation, we detected 5525 spots, an approximate 3.5‐fold increase over the 1577 spots detected in an unfractionated gel. We concluded that sIEF is an effective means of prefractionation to increase depth of field and improve the analysis of low‐abundance proteins.
Lectin‐based electrophoretic analysis of the expression of the 35 kDa inter‐α‐trypsin inhibitor heavy chain H4 fragment in sera of patients with five different malignancies
Authors: Mohamed Emida , Abdul‐Rahman Puteri Shafinaz , Doustjalali Saeid Reza , Chen Yeng , Lim Boon‐Kiong , Omar Siti Zawiah , Bustam Anita Zarina , Singh Vivek Ajit , Mohd‐Taib Nur Aishah , Yip Cheng‐Har , Hashim Onn Haji 
Published: May 2008

AbstractA 35 kDa glycoprotein whose abundance was previously demonstrated to be enhanced in sera of patients with endometrial adenocarcinoma (n = 12), was isolated from pooled sera of three of the cancer patients using champedak galactose‐binding lectin affinity chromatography in the present study. Subjecting it to 2‐DE and MS/MS, the glycoprotein was identified as the O‐glycosylated fragment of inter‐α‐trypsin inhibitor heavy chain H4 (ITIH4). When compared to control sera (n = 17), expression of the 35 kDa ITIH4 cleavage fragment was demonstrated to be significantly enhanced in sera of patients with breast carcinoma (n = 10), epithelial ovarian carcinoma (n = 10), and germ cell ovarian carcinoma (n = 10) but not in patients with nasopharyngeal carcinoma (n = 13) and osteosarcoma (n = 7). The lectin‐based electrophoretic bioanalytical method adopted in the present study may be used to assess the physiological relevance of ITIH4 fragmentation and its correlation with different malignancies, their stages and progression.
Noncovalent interactions in human plasma proteins analyzed by the comparison of nondenaturing and denaturing micro‐2‐D gel electrophoresis patterns after polypeptide assignment using matrix‐assisted laser desorption/ionization‐mass spectrometry and peptide mass fingerprinting
Authors: Manabe Takashi , Jin Ya 
Published: May 2008

AbstractPreviously, we reported the analysis of human plasma proteins by 2‐DE under nondenaturing conditions (Type‐I 2‐DE) followed by the assignment of stained spots using MALDI‐MS and PMF [1]. Here, we employ 2‐DE conditions modified only in the second‐dimensional separation; SDS was added in the gradient slab gel aiming to dissociate noncovalently bound proteins/polypeptides (Type‐II 2‐DE). Totally 169 CBB‐stained spots on a micro‐2‐DE gel were numbered and subjected to polypeptide assignment using MALDI‐MS‐PMF. One hundred sixty spots out of the 169 provided significant match (p <0.05) with polypeptides in databases. Comparisons of the results of polypeptide assignment on the two 2‐DE patterns indicated that 10 polypeptides in 20 stained spots on the Type‐I 2‐DE pattern [1] shifted toward low‐molecular‐weight positions on the Type‐II 2‐DE pattern, demonstrating the presence of noncovalent interactions. Seventeen polypeptides in 38 stained spots were only assigned on the Type‐II 2‐DE gel, which could mostly be accounted for by the disruption of noncovalent protein–protein interactions in the presence of SDS, i.e., protein/polypeptide complexes which might form smear bands on the Type‐I 2‐DE gel dissociate to form clear spots on the Type‐II 2‐DE gel. The method employed here, comparisons of nondenaturing and denaturing 2‐DE maps with polypeptide assignment by MALDI‐MS‐PMF, would enable the simultaneous detection of multiple noncovalent interactions in complex protein/polypeptide systems.
Microscale characterization of the binding specificity and affinity of a monoclonal antisulfotyrosyl IgG antibody
Authors: Lassen Klaus S. , Bradbury Andrew R. M. , Rehfeld Jens F. , Heegaard Niels H. H. 
Published: May 2008

AbstractSulfation is a potentially important post‐translational modification of proteins and has been demonstrated in a number of polypeptides, notably in gastrointestinal hormones. In contrast to phosphorylation, however, the investigation of sulfation patterns in tissues and on purified proteins has been complicated by the absence of specific immunoreagents (antibodies) for this modification as well as the chemical lability of the sulfate group. Here, we investigate the properties of a novel mAb against sulfated tyrosyl groups (anti‐Tyr(SO3H) antibody) using CE and a panel of sulfated and nonsulfated peptides and proteins. The data show that the anti‐Tyr(SO3H) antibody is completely specific for compounds containing sulfated tyrosyls. Affinity electrophoresis experiments allowed us to estimate dissociation constants for sulfated hirudin fragment (56–65), gastrin‐17, and cholecystokinin octapeptide (CCK8) in the 1–3 μM range. The affinity of the antibody toward complement 4 protein that contains three sulfotyrosines was analyzed by surface plasmon resonance technology and modeled according to a bivalent‐binding model which yielded a Kd1 of 20.1 μM for the monovalent complex. The same binding was studied by CE and found to be in the micromolar scale albeit with some uncertainty due to complex separation patterns. The work illustrates the amount of information on antibody–antigen interactions that may be obtained with microelectrophoretic methods consuming minute quantities of material. Furthermore the specificity of this antibody could be confirmed in one operation using an array of sulfated and nonsulfated compounds.
Proteomics of marine bacteria
Authors: Schweder Thomas , Markert Stephanie , Hecker Michael 
Published: May 2008

AbstractLittle is known about the life of marine microorganisms under their particular environmental conditions. Genome sequencing combined with the techniques of functional genomics, especially proteome analyses, now open up revolutionary insights into the adaptation strategies marine organisms have evolved in response to the challenges of their habitat. This report summarizes the first approaches and state‐of‐the‐art in the field of proteome analysis of marine bacteria. This includes, amongst others, proteomics on culturable, free‐living marine bacteria and on uncultivable bacteria living in symbiosis with higher organisms. Finally, new approaches to determine the metaproteome of uncultured microbial consortia from marine habitats are discussed.
Preparative isolation of protein complexes and other bioparticles by elution from polyacrylamide gels
Authors: Seelert Holger , Krause Frank 
Published: May 2008

AbstractDue to its unmatched resolution, gel electrophoresis is an indispensable tool for the analysis of diverse biomolecules. By adaptation of the electrophoretic conditions, even fragile protein complexes as parts of intracellular networks migrate through the gel matrix under sustainment of their integrity. If the thickness of such native gels is significantly increased compared to the analytical version, also high sample loads can be processed. However, the cage‐like network obstructs an in‐depth analysis for deciphering structure and function of protein complexes and other species. Consequently, the biomolecules have to be removed from the gel matrix into solution. Several approaches summarized in this review tackle this problem. While passive elution relies on diffusion processes, electroelution employs an electric field to force biomolecules out of the gel. An alternative procedure requires a special electrophoresis setup, the continuous elution device. In this apparatus, molecules migrate in the electric field until they leave the gel and were collected in a buffer stream. Successful isolation of diverse protein complexes like photosystems, ATP‐dependent enzymes or active respiratory supercomplexes and some other bioparticles demonstrates the versatility of preparative electrophoresis. After liberating particles out of the gel cage, numerous applications are feasible. They include elucidation of the individual components up to high resolution structures of protein complexes. Therefore, preparative electrophoresis can complement standard purification methods and is in some cases superior to them.
Analysis of histones, histone variants, and their post‐translationally modified forms
Authors: Lindner Herbert H. 
Published: May 2008

AbstractFor many years, histones were considered passive structural components of eukaryotic chromatin. Meanwhile it has been proven that histones also participate in gene regulation and repression via post‐translational modification. The multitude of these post‐translational modifications and the existence of numerous histone variants require particular separation strategies for their analysis, a prerequisite for studying biological processes. The most widely utilized techniques for the separation of histones, namely PAGE, HPCE, RP‐HPLC, and hydrophilic Interaction LC, are reviewed here. Problems inherent to the analysis of histones owing to their unique physical and chemical properties along with advantages and shortcomings of particular methods are discussed.
Enhanced dechlorination of trichloroethylene by membrane‐supported Pd‐coated iron nanoparticles
Authors: Wu Linfeng , Ritchie Stephen M.C. 
Published: May 2008

AbstractIn this study, cellulose acetate (CA) supported iron and Pd/Fe nanoparticles were used for dechlorination of trichloroethylene (TCE) from water. Solution and microemulsion methods were used to synthesize the iron nanoparticles. Pd/Fe bimetallic particles were prepared by postcoating Pd on the prepared iron nanoparticles. These materials were then dispersed in CA solution, which was used to prepare the membrane‐supported nanoparticles. TEM imaging confirmed that the iron and Pd/Fe bimetallic nanoparticles were ∼10 nm in diameter. The results of dechlorination studies showed that the surface composition of the Pd/Fe bimetallic nanoparticles (microemulsion method) significantly affected the observed reduction rate constant. In addition, the rate constant was a nonlinear function of metal loading and initial TCE concentration. A comparative study for the Pd/Fe (Pd 1.9 wt %) nanoparticles from solution and microemulsion methods showed that the nanoparticles formed by the latter method gave superior performance for the dechlorination of TCE. © 2008 American Institute of Chemical Engineers Environ Prog, 2008
Tetraglyme coatings reduce fibrinogen and von Willebrand factor adsorption and platelet adhesion under both static and flow conditions
Authors: Zhang Min , Horbett Thomas A. 
Published: May 2008

AbstractPrevious studies have showed that radio‐frequency plasma deposited tetraglyme coatings greatly reduced fibrinogen adsorption (ΓFg) from highly diluted plasmas (0.1 and 1%) and subsequent platelet adhesion under static conditions. In this study, the protein resistant properties of tetraglyme were re‐examined with high‐concentration plasma, and subsequent platelet adhesion was measured under both static and flow conditions. The resistance of tetraglyme to vWf adsorption (ΓvWf) and the role of vWf in platelet adhesion under flow were also investigated. ΓFg and ΓvWf were measured with 125I radiolabeled proteins. Flow studies were done at shear rates of 50 or 500 s−1 by passing a platelet/red cell suspension through a GlycoTech flow chamber. When adsorbed from a series of increasing plasma concentrations, the adsorption of both proteins to tetraglyme increased steadily, and did not show a peak at intermediate dilutions, i.e., there was no Vroman effect. When plasma concentration was less than 10%, the tetraglyme surface was highly nonfouling, exhibiting ultralow ΓFg (less than 5 ng/cm2) and extremely low platelet adhesion under both static and flow conditions. However, when the adsorption was done from 100% plasma, ΓFg was much higher (∼85 ng/cm2), indicating that tetraglyme surface may not be sufficiently protein‐resistant in the physiological environment. To correlate platelet adhesion under flow with ΓFg and ΓvWf, a series of tetraglyme surfaces varying in ether content and protein adsorption was created by varying deposition power. On these surfaces, platelet adhesion at low shear rate depended only on the amount of ΓFg, but under high shear, both ΓFg and ΓvWf affected platelet adhesion. In particular, it was found that ΓvWf must be reduced to less than 0.4 ng/cm2 to achieve ultra low platelet adhesion under high shear. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009
TiO2 nanotubes on Ti: Influence of nanoscale morphology on bone cell–materials interaction
Authors: Das Kakoli , Bose Susmita , Bandyopadhyay Amit 
Published: May 2008

AbstractTi being bioinert shows poor bone cell adhesion with an intervening fibrous capsule. Ti could be made bioactive by several methods including growing in situ TiO2 layer on Ti‐surface. TiO2 nanotubes were grown on Ti surface via anodization process and the bone cell–material interactions were evaluated. Human osteoblast cell attachment and growth behavior were studied using an osteoprecursor cell line for 3, 7, and 11 days. An abundant amount of extracellular matrix (ECM) between the neighboring cells was noticed on anodized nanotube surface with filopodia extensions coming out from cells to grasp the nanoporous surface of the nanotube for anchorage. To better understand and compare cell–materials interactions, anodized nanoporous sample surfaces were etched with different patterns. Preferential cell attachment was noticed on nanotube surface compare to almost no cells in etched Ti surface. Cell adhesion with vinculin adhesive protein showed higher intensity, positive contacts on nanoporous surface and thin focal contacts on the Ti‐control. Immunochemistry study with alkaline phosphatase showed enhanced osteoblastic phenotype expressions in nanoporous surface. Osteoblast proliferation was significantly higher on anodized nanotube surface. Surface properties changed with the emergence of nanoscale morphology. Higher nanometer scale roughness, low contact angle and high surface energy in nanoporous surface enhanced the osteoblast‐material interactions. Mineralization study was done under simulated body fluid (SBF) with ion concentration nearly equal to human blood plasma to understand biomimetic apatite deposition behavior. Although apatite layer formation was noticed on nanotube surface, but it was nonuniform even after 21 days in SBF. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009
Expansion and characterization of adipose tissue‐derived stromal cells cultured with low serum medium
Authors: Hattori Hidemi , Nogami Yashiro , Tanaka Tomohiro , Amano Yoshiko , Fukuda Koichi , Kishimoto Satoko , Kanatani Yasuhiro , Nakamura Shingo , Takase Bonpei , Ishihara Masayuki 
Published: May 2008

AbstractAdipose tissue contains a population of cells that have extensive self‐renewal capacity and the ability to differentiate along multiple lineages. In addition, adipose tissue‐derived stromal cells (ATSCs) are able to differentiate into various cell types that may be useful for autologous cell transplantation for defects of bone, cartilage, adipose, and tendon, etc. Most protocols for in vitro cultures of ATSCs include fetal bovine serum (FBS) as a nutritional supplement. However, in some cell cultures, it involves multiple doses of FBS, which raises a concern over possible infections as well as immunological reactions that are caused by medium‐derived FBS proteins, sialic acid, etc. In this study, we were able to expand mouse ATSCs using low mouse serum media containing collagen type I, heparin‐carrying polystyrene, and fibroblast growth factor (FGF)‐2. These expanded mouse ATSCs maintained their multilineage potential for differentiation into adipocytes, osteoblasts, and chondrocytes. Therefore, this method, which uses autologous cells and low serum media, may be able to be utilized for clinical cell therapies. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2008
IFN‐γ regulation of vacuolar pH, cathepsin D processing and autophagy in mammary epithelial cells
Authors: Khalkhali‐Ellis Zhila , Abbott Daniel E. , Bailey Caleb M. , Goossens William , Margaryan Naira V. , Gluck Stephen L. , Reuveni Moshe , Hendrix Mary J.C. 
Published: May 2008

AbstractIn this study we examined the ability of interferon‐γ (IFN‐γ) to regulate mammary epithelial cell growth and gene expression, with particular emphasis on two genes: Maspin (a member of serine protease inhibitor superfamily), and the lysosomal aspartyl endopeptidase cathepsin D (CatD). The protein products of these genes are critically involved in regulation of multitude of biological functions in different stages of mammary tissue development and remodeling. In addition, the expression of Maspin is down‐regulated in primary breast cancer and is lost in metastatic disease, while CatD is excessively produced and aberrantly secreted by breast cancer cells. We report that IFN‐γ receptors are expressed in mammary epithelial cells, and receptor engagement by IFN‐γ transduces the IFN‐γ signal via Stat‐1 resulting in decreased vacuolar pH. This change in vacuolar pH alters CatD protein processing and secretion concurrent with increased Maspin secretion. In addition, IFN‐γ exerts a suppressive effect on cell growth and proliferation, and induces morphological changes in mammary epithelial cells. Our studies also reveal that breast cancer cells, which are devoid of Maspin, are refractory to IFN‐γ with respect to changes in vacuolar pH and CatD. However, Maspin transfection of breast cancer cells partially sensitizes the cells to IFN‐γ's effect, thus providing new therapeutic implications. J. Cell. Biochem. 105: 208–218, 2008. © 2008 Wiley‐Liss, Inc.
Hydrodynamic modeling of diffusion tensor properties of flexible molecules
Authors: Barone Vincenzo , Zerbetto Mirco , Polimeno Antonino 
Published: May 2008

AbstractWe present a computationally efficient implementation of hydrodynamic modeling for the evaluation of diffusion tensors of molecules with internal degrees of freedom, adapted to take into account information from linear scaling computations of solvent accessible surfaces implemented in the framework of last generation continuum solvent models. Torsional angles are taken also explicitly into account, while retaining correct hydrodynamic interactions. A comparison with literature data is presented to prove the effectiveness of the approach for a wide range of molecular dimensions and solvent environments. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
HIV‐1 protease cleavage site prediction based on amino acid property
Authors: Niu Bing , Lu Lin , Liu Liang , Gu Tian Hong , Feng Kai‐Yan , Lu Wen‐Cong , Cai Yu‐Dong 
Published: May 2008

AbstractKnowledge of the polyprotein cleavage sites by HIV protease will refine our understanding of its specificity, and the information thus acquired is useful for designing specific and efficient HIV protease inhibitors. Recently, several works have approached the HIV‐1 protease specificity problem by applying a number of classifier creation and combination methods. The pace in searching for the proper inhibitors of HIV protease will be greatly expedited if one can find an accurate, robust, and rapid method for predicting the cleavage sites in proteins by HIV protease. In this article, we selected HIV‐1 protease as the subject of the study. 299 oligopeptides were chosen for the training set, while the other 63 oligopeptides were taken as a test set. The peptides are represented by features constructed by AAIndex (Kawashima et al., Nucleic Acids Res 1999, 27, 368; Kawashima and Kanehisa, Nucleic Acids Res 2000, 28, 374). The mRMR method (Maximum Relevance, Minimum Redundancy; Ding and Peng, Proc Second IEEE Comput Syst Bioinformatics Conf 2003, 523; Peng et al., IEEE Trans Pattern Anal Mach Intell 2005, 27, 1226) combining with incremental feature selection (IFS) and feature forward search (FFS) are applied to find the two important cleavage sites and to select 364 important biochemistry features by jackknife test. Using KNN (K‐nearest neighbors) to combine the selected features, the prediction model obtains high accuracy rate of 91.3% for Jackknife cross‐validation test and 87.3% for independent‐set test. It is expected that our feature selection scheme can be referred to as a useful assistant technique for finding effective inhibitors of HIV protease, especially for the scientists in this field. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009