bluuebunny/crossref_metadata_2025_split huggingface dataset:
Behavior of peptides in capillary electrophoresis: Effect of peptide charge, mass and structure
Authors: Cifuentes Alejandro , Poppe Hans 
Published: May 2005

AbstractIn the last decade the large potential of capillary electrophoresis as a technique for separation and characterization of peptides has been demonstrated extensively. In this field, a large number of chemical structures has to be taken into consideration, for which very often no data or even standards are available. As a result, there has been a strong desire to relate electrophoretic behavior to molecular properties and structure of the compounds. The activities in that direction, in the area of capillary zone electrophoresis, are critically reviewed. Special attention is paid to peptide charge, mass, hydrophobicity and structure, and their influence on the selectivity of the separation. Also, some complexation phenomena are discussed.
Recent developments in capillary electrophoresis of carbohydrate species
Authors: El Rassi Ziad 
Published: May 2005

AbstractCarbohydrates are ubiquitous species involved in many life processes. Because of the multilateral roles of carbohydrates, their analysis has come to have increasing importance. As shown in this review, capillary electrophoresis in its various modes of operation has proved very useful in the analysis of carbohydrate species including mono‐ and oligosaccharides, glycoproteins, glycopeptides and glycosaminoglycans. Advances in separation approaches and applications as well as advances in detection including sensitive and selective precolumn derivatization are described. In summary, this comprehensive review is a supplement to previous reviews and covers the published work in 1996 and the first half of 1997.
Determination of metal ions by capillary electrophoresis
Authors: Macka Miroslav , Haddad Paul R. 
Published: May 2005

AbstractThe increasing use of capillary electrophoresis (CE) in all areas of analytical chemistry has been reflected in the appearance since 1990 of significant numbers of fundamental studies and applications of CE in the area of separations of metal ions. In this article all aspects of separations of metal ions by CE are reviewed and discussed, including general concepts and approaches, sample introduction, complex formation and sample stacking, separation selectivity, the role of kinetics, capillary wall chemistry, detection techniques, method validation, and applications to metal determinations in various matrices.
Membrane transport in rat liver endocytic pathways: Preparation, biochemical properties and functional roles of hepatic endosomes
Authors: Pol Albert , Enrich Carlos 
Published: May 2005

AbstractThe endocytic compartment has emerged as a major regulator of the uptake and processing of circulating ligands, and has been extensively studied during the last decade. In this work, the polypeptides of the three endosomal fractions: compartment of uncoupling receptors and ligands (CURL), multivesicular bodies (MVB) and receptor recycling compartment (RRC), isolated from livers of estradiol‐treated rats, were analyzed by two‐dimensional gel electrophoresis. Silver‐stained gels revealed that although the three endosomal fractions shared a generally similar pattern of approximately 120 components, qualitative and quantitative differences between the three endocytic fractions could be demonstrated. The polypeptide composition of the bile was also studied and compared with ligands and proteins identified in the different endosomal fractions. One‐ and two‐dimensional gel electrophoresis and Western blotting were used to investigate the protein composition of the three isolated endocytic fractions and 39 proteins were identified. The distribution of identified receptors, ligands and structural proteins among the three endosomal fractions was in agreement with their expected functionalities and with the different endocytic pathways in the hepatocyte.
Two‐dimensional gel electrophoresis analysis of endovacuolar organelles
Authors: Scianimanico Sandra , Pasquali Christian , Lavoie Jacques , Huber Lukas A. , Gorvel Jean‐Pierre , Desjardins Michel 
Published: May 2005

AbstractCells perform their multiple functions with the aid of a series of distinct membrane organelles. In the last years, many of these compartments have been isolated, purified, and extensively studied. The major roles of each organelle in the cell are well understood. However, most of the molecular basis by which they perform their functions is poorly known. The recent identification and study of a handful of proteins associated with endovacuolar compartments has had a major impact on the understanding of the molecular details of organelle functions even though two‐dimensional (2‐D) gel analysis indicates that hundreds of proteins are typically associated with a complex organelle. This shows that many details and surprises are still to come for cell biologists. In the present study, we have analyzed and compared different organelles of the endocytic and phagocytic apparatus using 2‐D gel electrophoresis.
Generation of proteoliposomes from subcellular fractions
Authors: Rojo Manuel , Budin Nicolas , Kellner Roland , Gruenberg Jean 
Published: May 2005

AbstractIntracellular membranes are highly dynamic, yet they retain their identity and functional characteristics. Integral membrane proteins, which must confer this specific membrane identity, remain poorly characterized at the biochemical level, largely because detergent‐mediated solubilization is required for purification and analysis, and several properties of integral membrane proteins can only be investigated when the molecule is properly embedded in a lipid bilayer. We present a method for the efficient reconstitution into proteoliposomes of integral membrane proteins from subcellular fractions. Integral membrane proteins were identified on high‐resolution two‐dimensional gels after selective extraction of soluble and peripheral membrane proteins; they accounted for 8% of the number of resolved polypeptides. A reconstitution procedure based on membrane solubilization with dodecyl‐octaoxyethylene (C12E8) and subsequent detergent removal with BioBeads SM‐2 resulted in the efficient reconstitution of several membrane proteins into proteoliposomes of uniform density. The generated proteoliposomes strongly resemble the starting membrane fraction in protein composition. This reconstitution allows the functional characterization of integral membrane proteins after enrichment and/or specific (immuno)depletion.
A novel epitope tag for the detection of rabGTPases
Authors: Nagelkerken Bas , Mohrmann Karin , Gerez Lisya , van Raak Marcel , Leijendekker Richtje , van der Sluijs Peter 
Published: May 2005

AbstractRab GTPases are localized on the cytoplasmic surface of most intracellular organelles where they play a role in the regulation of vesicular transport. As it has been difficult to detect endogenous rab proteins by morphological methods, their localizations were often inferred from transfection experiments using epitope‐tagged constructs. Because most of the available epitope tags are only recognitzed by mouse monoclonal antibodies they are often not suitable for double or triple label immunocytochemistry. To overcome this problem, we generated antibodies against a novel 10 amino acid X31 influenza hemagglutin epitope (NH). We here characterized these antibodies and document their utility for detecting early endosomal rab proteins N‐terminally tagged with the NH decapeptide in morphological and biochemical assays.
Make2ddb: A simple package to set up a two‐dimensional electrophoresis database for the World Wide Web
Authors: Hoogland Christine , Baujard Vincent , Sanchez Jean‐Charles , Hochstrasser Denis F. , Appel Ron D. 
Published: May 2005

AbstractTwo‐dimensional electrophoresis (2‐DE) has become a highly reproducible protein separation technique that currently serves as the main basis for proteome research and in particular for protein identification. Also, the Internet provides large utilities for exchanging data, and we can observe increased interest among scientists to build remote 2‐DE databases, since many members of the concerned community are now able to access the data. By preparing the data and programs that are required to create a federated 2‐DE database, the Make2ddb package, described here, helps to build such a database on the user own World Wide Web site.
Rapid access to biomedical knowledge with GeneCards and HotMolecBase: Implications for the electrophoretic analysis of large sets of gene products
Authors: Rebhan Michael , Prilusky Jaime 
Published: May 2005

AbstractRapid access to well‐organized information about gene products is important for many studies that simulatenously monitor large sets of those factors, for example with electrophoretic methods. HotMolecBase and GeneCards, Internet resources that may be accessed from our Bioinformatics homepage at http://bioinfo.weizmann.ac.il/, have been designed to address similar problems. GeneCards presents semi‐automatically collected information about all approved human genes and their products (with a focus on cellular functions and medical aspects), and offers a new kind of knowledge navigation guidance system that interactively guides the information‐seeking scientist to relevant information. On the other hand, HotMolecBase is a collection of more extensive hypertext fact sheets about a small set of medically interesting molecules (mainly proteins) that are regarded as especially promising targets for drug development. Together, both resources may help scientists world‐wide to find their way in the growing labyrinth of biomedical information on the World Wide Web. In the present article, we want to explain how these resources may be used by researchers who want to access information related to particular spots on two‐dimensional electrophoresis gels.
Establishment of the human reflex tear two‐dimensional polyacrylamide gel electrophoresis reference map: New proteins of potential diagnostic value
Authors: Molloy Mark P. , Bolis Shirley , Herbert Ben R. , Ou Keli , Tyler Margaret I. , van Dyk Derek D. , Willcox Mark D. P. , Gooley Andrew A. , Williams Keith L. , Morris Carol A. , Walsh Bradley J. 
Published: May 2005

AbstractTo understand the changes in protein expression associated with various physiological states as well as the development of pathological eye disease, we have begun to map the protein components of normal human reflex tears. An analytical reference map of normal human reflex tears was created using two‐dimensional polyacrylamide gel electrophoresis (2‐D PAGE) with pH 3.5–10 immobilized pH gradients (IPGs). Micropreparatively loaded gels were transferred to polyvinylidene difluoride (PVDF) and analysed by a combination of N‐terminal sequence tagging and amino acid compositional analysis. Thirty spots were sequence tagged, resulting in identification of six different proteins (lipocalin, lysozyme, lactotransferrin, zinc‐α‐2 glycoprotein, cystatin S, cystatin SN) that matched to entries in the SWISS‐PROT database. A group of N‐terminally blocked proteins was clearly identified from SWISS‐PROT by amino acid analysis, isoelectric point (pI) and molecular weight (Mr). A number of highly expressed protein components remain unidentified despite being subjected to amino acid analysis and Edman sequencing. A majority of the abundant proteins showed varying degrees of charge heterogeneity attributed to post‐translational processing such as glycosylation and N‐terminal truncation. We have identified a previously undescribed protein that we have named lacryglobin. This protein displays strong homology with mammaglobin, a protein overexpressed in breast cancer. The discovery of this homologue in tears offers the potential for disease diagnosis by screening tear fluid proteins.
Standardized characterization of gene expression in human colorectal epithelium by two‐dimensional electrophoresis
Authors: Reymond Marc A. , Sanchez Jean‐Charles , Hughes Graham J. , Günther Klaus , Riese Jutta , Tortola Silvia , Peinado Miguel A. , Kirchner Thomas , Hohenberger Werner , Hochstrasser Denis F. , Köckerling Ferdinand 
Published: May 2005

AbstractNew diagnostic and prognostic markers are needed in colorectal cancer. They can be found by differential analysis at DNA, RNA or protein level. The accuracy of phenotypic comparisons of tumor and normal tissues depends on the purity of the samples. We present an effective method to identify and isolate proteins that are differentially expressed under altered conditions, and a two‐dimensional reference protein map of the normal human colonic epithelium Normal colonic mucosa, primary tumors and liver metastases were prepared in the operating room. After washing in an ice‐cold medium containing protease inhibitors, crypts were isolated by mechanical preparation without using metalloproteinases. Epithelial cells were then selected using Ber‐EP4 Dynabeads. The samples were denaturated before processing for immobilized pH gradient two‐dimensional polyacrylamide gel electrophoresis according to SWISS‐2DPAGE standards. The samples contained more than 95% epithelial cells as confirmed by fluorescence‐activated cell sorting using pan‐anticytokeratin antibodies. Cell surfaces were not damaged, as assessed by scanning electronic microscope. A protein reference map of the normal colonic epithelium was defined. Using gel matching, N‐terminal sequencing and/or immunoblotting techniques, 60 polypeptides – including proteins specifically expressed in colorectal epithelium – have now been identified. This reproducible method of sample preparation permits the comparison of protein patterns found in various pathological states with the present reference map (http://www.expasy.ch). Some of these patterns might provide diagnostic or prognostic markers, or even molecular targets for therapy in the future.
Mitochondrial D‐loop 3′ (CA)n repeat polymorphism: Optimization of analysis and population data
Authors: Szibor Reinhard , Michael Matthias , Spitsyn Victor A. , Plate Ines , Ginter Evgeni K. , Krause Dieter 
Published: May 2005

AbstractWe report a dinucleotide repeat polymorphism in the 3′ area of the mitochondrial control region. The fragments obtained using a new primer set could be reliably separated by polyacrylamide gel electrophoresis (PAGE) using nondenaturing gels. A total of five alleles [(CA)3 to (CA)7] were detected on silver‐stained gels. The 90 bp product corresponds to allele 5. Samples from one African and three European populations were characterized. Significant differences could be demonstrated as to the incidence of single alleles and allele distributions in different populations. These differences were found between the three European and one African Bantu population. For specific forensic questions the mitochondrial CA repeat is well suited. Gene diversities in populations of Germany, Hungary, the Russian Federation and Cameroon were 0.36, 0.40, 0.34, 0.52, respectively.
Electrophoresis of DNA sequencing fragments at elevated temperature in capillaries filled with poly(N‐acryloylaminopropanol) gels
Authors: Lindberg Peter , Righetti Pier Giorgio , Gelfi Cecilia , Roeraade Johan 
Published: May 2005

AbstractThe performance of poly(N‐acryloylaminopropanol) (poly AAP) gel columns, proved to be stable during electrophoresis at elevated temperature, was investigated. The column manufacturing procedure included the preparation of a coating of the inner wall of the fused silica capillary column with linear poly(AAP). Then, a mixture of the AAP monomer, the cross‐linker dihydroxyethylenebisacrylamide (DHEBA) and linear poly(AAP) was introduced into the column and in situ polymerized (for preparation of linear gel columns, the addition of DHEBA was omitted). The poly(AAP) columns were first evaluated by electrophoresis of oligonucleotides at room temperature and at 50°C, utilizing 260 nm UV‐absorbance detection. In a further evaluation of column performance, samples of T‐terminated DNA Sanger fragments from the bacteria Moraxella were separated at 200 V/cm electrical field strength, utilizing a 488 nm argon ion laser and a confocal optical setup for laser‐induced fluorescence (LIF) detection. A temperature increase from 25°C to 50°C effectively released a compression of DNA bands. However, for cross‐linked poly(AAP) gel columns, the elevated temperature resulted in a considerable reduction of the DNA sequence reading length. When a linear poly(AAP) column was utilized, no detrimental effect of elevated temperature on the separation could be observed.
Application of capillary electrophoresis for the determination of inorganic ions in trace explosives and explosive residues
Authors: Kishi Tohru , Nakamura Jun , Arai Hiroyuki 
Published: May 2005

AbstractCapillary electrophoresis was developed for the analysis of low explosive residue, because a significant amount of inorganic anions and cations remain after deflagration. Certain high explosives, such as emulsion explosives, produce a vast quantity of inorganic ions after a blast and can readily be analyzed using capillary electrophoresis. Often, trace amounts of explosive residues may be present on physical evidence submitted in criminal cases. Trace amounts of inorganic ions such as nitrate, chlorate, and ammonium may be detected using capillary electrophoresis owing to the low detection limit of these species. The utility of capillary electrophoresis in the analysis of explosive residues is in its ability to simultaneously analyze trace explosives and ionic products present on physical evidence.
Capillary electrophoretic determination of trace metals in hair samples and its comparison with high performance liquid chromatography and atomic absorption spectrometry techniques
Authors: McClean Stephen , O'Kane Edmund , Coulter Daniel J. M. , McLean Stephen , Smyth W. Franklin 
Published: May 2005

AbstractCapillary electrophoresis (CE) is compared with high performance liquid chromatography (HPLC) and atomic absorption spectrometry (AA) for the determination of trace concentrations of selected metals in human hair. CE and HPLC methods are based upon the chelation of the metals with 2‐(5′‐bromo 2′‐pyridylazo)‐5‐diethylamino phenol (5‐Br‐PADAP) followed by ultraviolet‐visible (UV‐Vis) detection. Large volume sample stacking (LVSS)‐CE using injection times of up to 300 s is applied to the simultaneous determination of Co and Zn providing lower limits of detection (LODs) of 4.2 × 10−8 mol dm−3 and 6.0 × 10−8 mol dm−3, respectively, than can be achieved by conventional CE. The LVSS procedure could not be applied to hair samples due to a higher run current existing when the sample is introduced into the capillary. Conventional CE with cetyltrimethylammonium bromide (CTAB) present in the run buffer to retain the ligand in solution is used for the determination of metal concentrations in hair samples. Only Zn could be determined in this way as it exists at relatively high levels in hair. Co, Ni and Hg could be detected when spiked hair samples were analysed with estimated LODs of 5.0 × 10−7 mol dm−3, 1.0 × 10−6 dm−3 and 3.0 × 10−5 mol dm−3, respectively. HPLC was successfully used to determine Co and Cu in hair samples, with levels of 57.6 ppb and 17.31 ppm being found, respectively, and corresponded closely to results produced by AA. Fe also gave a signal together with unidentified coeluting species. In a separate HPLC study the determination of Ni and Hg as their complexes with hydrogen peroxide and 5‐Br‐PADAP was also investigated and LODs of 2.0 × 10−6 mol dm−3 and 5.0 × 10−6 mol dm−3, respectively, were achieved. AA was used as a reference method to determine levels of Co, Cu, Fe, Pb and Zn in hair and the results produced were in order of magnitude agreement with accepted literature values.
Application of high‐performance capillary electrophoresis to the quantitative analysis of nicotine and profiling of other alkaloids in ATF‐regulated tobacco products
Authors: Lu Giang Hoang , Ralapati Suresh 
Published: May 2005

AbstractTobacco products regulated by the Bureau of Alcohol, Tobacco and Firearms (ATF), are classified at different excise tax rates according to the Code of Federal Regulations. These include the smoking (cigars, cigarettes, pipe tobacco and roll‐your‐own) and smokeless (chewing tobacco and snuff) tobacco products. The active principal components in all tobacco products belong to a class of compounds known as alkaloids. Nicotine is the major tobacco alkaloid, comprising about 98% of the total alkaloids. It is also the primary determinant of what constitutes a tobacco product from a regulatory standpoint. Nornicotine, anabasine and anatabine constitute the minor tobacco alkaloids of importance and interest to ATF. We have previously shown capillary electrophoresis (CE) to be a powerful analytical tool for monitoring nicotine in ATF‐regulated products. Here we have extended those CE studies to (i) quantitate nicotine in ATF‐regulated tobacco products and (ii) to characterize these different tobacco products according to their alkaloid profiles. Results from these studies will be presented.
Can amphoteric substances with very small (or negative) ΔpK difference exist and what properties would their water solutions exhibit?
Authors: Stoyanov Alexander V. , Righetti Pier Giorgio 
Published: May 2005

AbstractFor calculating the buffer capacity of ampholytes an application of the stepwise and parallel dissociation models is considered. It is demonstrated that the scheme with stepwise dissociation possesses a “nonadditive” sum, i.e., the resulting buffer capacity of the system exceeds the sum of the separate contributions of the two ionogenic groups. On the other hand, the scheme of parallel dissociation is free from this disadvantage, and thus does not impose any restriction on the ΔpK parameter.
Isotachophoresis at pH extremes: Theory and experimental validation
Authors: Ermakov Sergey V. , Zhukov Michael Y. , Capelli Laura , Righetti Pier Giorgio 
Published: May 2005

AbstractThe evolution of an isotachophoresis (ITP) system in acidic or basic pH ranges can be quite different from that predicted by the existing theory. It was found theoretically and proved experimentally that the contribution of hydrogen or hydroxyl ion to conductivity of solution and/or its net charge changes the behavior of the ITP system, creating in the terminating electrolyte an additional zone close to the initial interfaces between electrolytes (leader and terminator). One boundary of the zone, being either sharp or dispersed, moves toward the leader; the other is always sharp and stationary and coincides with initial electrolytes' discontinuity. The latter can be registered in the presence of electroosmotic flow which delivers it to the detection point. In order to describe the dynamics of the ITP system at pH extremes an algorithm of analytical solution was developed, based on the revised Kohlrausch theory. Its predictions coincide well with computer simulations and experimental data. The results presented can help in a correct analysis of ITP data and explain some confusing phenomena which were considered to be artifacts.