bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of proanthocyanidins in fresh grapes and grape products using liquid chromatography with mass spectrometric detection
Authors: Wu Qingli , Wang Mingfu , Simon James E. 
Published: June 2005

AbstractFresh grapes and grape products, such as grape wine and grape juice, were analyzed for proanthocyanidins (PACs) using liquid chromatography with electrospray ionization mass spectrometric (MS) detection. PACs were successfully separated and analyzed on the basis of their protonated molecules, allowing the identification of PACs in different degrees of polymerization from monomers to oligomers (up to 7 units), and in various isomeric forms. Using reversed‐phase high‐performance liquid chromatography (HPLC) combined with MS detection, the PAC monomers, (+)‐catechin (C), (−)‐epicatechin (EC), (−)‐catechin gallate (CG), and (−)‐epicatechin gallate (ECG), were successfully quantified using selected ion monitoring (SIM) mode. Standard curves were fitted for each PAC ranging from 43.8 to 5600 ng/mL for C, from 42.2 to 5400 ng/mL for EC, from 36.7 to 4700 ng/mL for CG, and from 39.8 to 5100 ng/mL for ECG. Good linearity (r2 > 0.999) was achieved for each analyte. The accuracy and precision (RSD) were within 10% (n = 8) at the limit of detection. This method allows direct quantification of monomeric PACs in fresh grapes and grape‐derived products. Additionally, flow injection analysis (FIA) was applied to estimate the concentration levels of PAC oligomers by comparing their FIA‐MS peak areas, which were well correlated (r2 = 0.936) to the total concentrations of PAC monomers. Copyright © 2005 John Wiley & Sons, Ltd.
Development of a multiresidue method for analysis of major Fusarium mycotoxins in corn meal using liquid chromatography/tandem mass spectrometry
Authors: Cavaliere Chiara , Foglia Patrizia , Pastorini Elisabetta , Samperi Roberto , Laganà Aldo 
Published: June 2005

AbstractA sensitive and reliable liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI‐MS/MS) method has been developed to determine, in a single run, eight trichothecenes, three fumonisins, zearalenone and α‐zearalenol, in corn meal samples. LC and MS conditions were varied to find the best compromise in terms of sensitivity and separation. An acceptable compromise was obtained using a C18 column thermostatted at 45°C and a mobile phase gradient of methanol/water with 10 mmol/L formate buffer (pH 3.8). A multiple reaction monitoring program, in which fumonisins and trichothecenes (except nivalenol and deoxynivalenol) are acquired in positive ESI as [M+H]+ or [M+NH4]+, and all other compounds in negative ESI, was developed to match appropriate retention time windows. Sample preparation used a simple homogenization of the corn meal sample with acetonitrile/water (75:25, v/v) followed by extraction on a C18 cartridge and clean‐up on a cartridge containing graphitized carbon black. Method detection limits were in the range 2–14 ng/g, with the exception of nivalenol (27 ng/g), deoxynivalenol (40 ng/g) and 15‐acetyldeoxynivalenol (30 ng/g). Good accuracy (recoveries 81–104%) and precision (RSD 4–11%) were obtained by performing calibration using a spiked analyte‐free extract. Copyright © 2005 John Wiley & Sons, Ltd.
Proteomics of gluten: mapping of the 1Bx7 glutenin subunit in Chinese Spring cultivar by matrix‐assisted laser desorption/ionization
Authors: Alberghina Gaetano , Cozzolino Rosaria , Fisichella Salvatore , Garozzo Domenico , Savarino Anna 
Published: June 2005

AbstractThe verification of the cDNA‐deduced sequence of the high molecular weight glutenin subunit 1Bx7 in Chinese Spring cultivar was achieved by direct matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) analysis of the tryptic fragments. The published sequence of the 1Bx7 subunit contains 5 Lys and 15 Arg residues but, due to the presence of three Arg–Pro bonds, which are generally resistant to cleavage by trypsin, or cleaved to a very limited extent by trypsin, 19 peptides can be predicted. The identification of the tryptic fragments was achieved by direct MALDI‐MS analysis by using three different matrices (DHB, SA and HCCA) in combination with the most compatible sample preparation procedures in order to obtain the maximum sequence coverage. MALDI analysis of the 1Bx7 tryptic digest resulted in the identification of the expected peptides and additional fragments arising from non‐specific cleavages; the fragments that were not detected are peptides with low mass (from 147.2 to 317.4), so we obtained a sequence coverage of 98.8%. The results reported here also indicated that the sequence of the 1Bx7 subunit from cv. Chinese Spring is different from the cDNA‐deduced sequence reported in the literature; in particular, a possible insertion of the hexapeptide QPGQGQ within the sequence Gln630‐Tyr725 was suggested. Finally, it is possible to rule out glycosylation of the 1Bx7 subunit, or any other post‐translational modification, to within the detection limits of the method. Copyright © 2005 John Wiley & Sons, Ltd.
Structural characterization of 2‐aminobenzamide‐derivatized oligosaccharides using a matrix‐assisted laser desorption/ionization two‐stage time‐of‐flight tandem mass spectrometer
Authors: Morelle Willy , Slomianny Marie‐Christine , Diemer Hélène , Schaeffer Christine , Dorsselaer Alain van , Michalski Jean‐Claude 
Published: June 2005

AbstractOligosaccharides were derivatized by reductive amination using 2‐aminobenzamide (2‐AB) and analyzed by matrix‐assisted laser desorption/ionization two‐stage time‐of‐flight (MALDI‐TOF/TOF) tandem mass spectrometry (MS/MS) in the positive ion mode. The major signals were obtained under these conditions from the [M+Na]+ ions for all 2‐AB‐derivatized oligosaccharides. A systematic study was conducted on a series of 2‐AB‐derivatized oligosaccharides to allow rationalization of the fragmentation processes. The MALDI‐TOF/TOF‐MS/MS spectra of the [M+Na]+ ions of 2‐AB‐derivatized oligosaccharides were dominated by glycosidic cleavages. These fragments originating both from the reducing and the non‐reducing ends of the oligosaccharide yield information on sequence and branching. Moreover, the MALDI‐TOF/TOF‐MS/MS spectra were also characterized by abundant cross‐ring fragments which are very informative on the linkages of the monosaccharide residues constituting these oligosaccharides. MALDI‐TOF/TOF‐MS/MS analysis of 2‐AB‐derivatized oligosaccharides, by providing structural information at the low‐picomole level, appears to be a powerful tool for carbohydrate structural analysis. Copyright © 2005 John Wiley & Sons, Ltd.
Development of a low volume plasma sample precipitation procedure for liquid chromatography/tandem mass spectrometry assays used for drug discovery applications
Authors: Xu Xiaoying , Zhou Qiao , Korfmacher Walter A. 
Published: June 2005

AbstractThe demand for high sensitivity bioanalytical methods has dramatically increased in the drug discovery stage; in addition, there has been a growing trend of reducing the sample volume that is required for these assays. A sensitive high‐performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS) procedure has been developed and tested to meet these needs. The assay requires only a low plasma sample volume (10 µL) and employs a protein precipitation procedure using a 1:6 plasma/acetonitrile ratio. The supernatant is injected directly into the LC/MS/MS system using the selected reaction monitoring (SRM) procedure for detection. A generic HPLC gradient based on a methanol/water mobile phase with a flow rate set to 0.8 mL/min was used. The test method showed very good linearity between 0.1–1000 ng/mL (R2 = 0.9737), precision (%RSD = 6–9), accuracy (%RE = −2) and reproducibility (%RSD = 11). A drug discovery IV/PO study was assayed using both the new low volume method and our standard volume (50 µL) method. The correlation of the two sets of data from the two methods was excellent (R2 = 0.9287). This new assay procedure has been successfully used in our laboratory for over 100 different rat or mouse discovery PK studies. Copyright © 2005 John Wiley & Sons, Ltd.
Ipsilateral Breast Tumor Recurrence after Breast‐conserving Therapy: A Comparison of Quadrantectomy versus Lumpectomy at a Single Institution
Authors: Noh Woo Chul , Paik Nam Sun , Kim Min Suk , Yang Kwang Mo , Cho Chul Koo , Choi Dong Wook , Lee Jong Inn , Kang Sung Ku , Kim Sang Bum , Moon Nan Mo 
Published: June 2005

AbstractThe aims of study were to compare the rates of ipsilateral breast tumor recurrence (IBTR), for patients treated with either quadrantectomy or lumpectomy at a single institution, and to identify predictors of IBTR after breast‐conserving therapy (BCT). The database and medical records of 807 patients who underwent BCT for breast cancer between 1987 and 2002 were reviewed. The age of the patient, tumor size, lymph node status, extensive intraductal component (EIC), re‐excision, final margin status, and the extent of surgery were examined in reference to IBTR rates. Of the total 807 patients, 456 (56.5%) had undergone quadrantectomy and 351 patients (43.5%) had lumpectomy. Apart from the higher re‐excision rate in the lumpectomy group (p < 0.001), there were no significant differences in clinical and pathologic characteristics between the patients in the two groups. At the median follow‐up time of 72 months, 28 cases of IBTR (3.4%) and 56 cases of systemic recurrence (6.9%) had developed in 72 patients (8.9%). On multivariate analysis, young age (≤ 35) (p = 0.041), positive lymph node (p <0.001), and the presence of EIC (p = 0.004) were independent predictors of IBTR. However, we could not find a significant difference in IBTR rate between the two groups (p = 0.546). Thus, the extent of breast surgery (quadrantectomy or lumpectomy) did not make a significant difference in IBTR if adequate surgical margins could be achieved.
Identifying Plasmodium falciparum merozoite surface antigen 3 (MSP3) protein peptides that bind specifically to erythrocytes and inhibit merozoite invasion
Authors: Rodríguez Luis E. , Curtidor Hernando , Ocampo Marisol , Garcia Javier , Puentes Alvaro , Valbuena John , Vera Ricardo , López Ramses , Patarroyo Manuel E. 
Published: June 2005

AbstractReceptor–ligand interactions between synthetic peptides and normal human erythrocytes were studied to determine Plasmodium falciparum merozoite surface protein‐3 (MSP‐3) FC27 strain regions that specifically bind to membrane surface receptors on human erythrocytes. Three MSP‐3 protein high activity binding peptides (HABPs) were identified; their binding to erythrocytes became saturable, had nanomolar affinity constants, and became sensitive on being treated with neuraminidase and trypsin but were resistant to chymotrypsin treatment. All of them specifically recognized 45‐, 55‐, and 72‐kDa erythrocyte membrane proteins. They all presented α‐helix structural elements. All HABPs inhibited in vitro P. falciparum merozoite invasion of erythrocytes by ∼55%–85%, suggesting that MSP‐3 protein's role in the invasion process probably functions by using mechanisms similar to those described for other MSP family antigens.
Mycobacterium tuberculosis serine/threonine kinases PknB, PknD, PknE, and PknF phosphorylate multiple FHA domains
Authors: Grundner Christoph , Gay Laurie M. , Alber Tom 
Published: June 2005

AbstractThe physiologic roles and the substrates of the Mycobacterium tuberculosis (Mtb) serine/threonine kinases are largely unknown. Here, we report six novel interactions of PknB, PknD, PknE, and PknF with the Forkhead‐Associated (FHA) domains of Rv0020c and the putative ABC transporter Rv1747. Purified PknB and PknF kinase domains phosphorylated multiple FHA‐domain proteins in vitro. Although they remain to be verified in vivo, these reactions suggest a web of interactions between STPKs and FHA domains.
Crystallographic studies on acyl ureas, a new class of glycogen phosphorylase inhibitors, as potential antidiabetic drugs
Authors: Oikonomakos Nikos G. , Kosmopoulou Magda N. , Chrysina Evangelia D. , Leonidas Demetres D. , Kostas Ioannis D. , Wendt K. Ulrich , Klabunde Thomas , Defossa Elisabeth 
Published: June 2005

AbstractAcyl ureas were discovered as a novel class of inhibitors for glycogen phosphorylase, a molecular target to control hyperglycemia in type 2 diabetics. This series is exemplified by 6‐{2,6‐Dichloro‐ 4‐[3‐(2‐chloro‐benzoyl)‐ureido]‐phenoxy}‐hexanoic acid, which inhibits human liver glycogen phosphorylase a with an IC50 of 2.0 μM. Here we analyze four crystal structures of acyl urea derivatives in complex with rabbit muscle glycogen phosphorylase b to elucidate the mechanism of inhibition of these inhibitors. The structures were determined and refined to 2.26Å resolution and demonstrate that the inhibitors bind at the allosteric activator site, where the physiological activator AMP binds. Acyl ureas induce conformational changes in the vicinity of the allosteric site. Our findings suggest that acyl ureas inhibit glycogen phosphorylase by direct inhibition of AMP binding and by indirect inhibition of substrate binding through stabilization of the T′ state.
Design of improved membrane protein production experiments: Quantitation of the host response
Authors: Bonander Nicklas , Hedfalk Kristina , Larsson Christer , Mostad Petter , Chang Celia , Gustafsson Lena , Bill Roslyn M. 
Published: June 2005

AbstractEukaryotic membrane proteins cannot be produced in a reliable manner for structural analysis. Consequently, researchers still rely on trial‐and‐error approaches, which most often yield insufficient amounts. This means that membrane protein production is recognized by biologists as the primary bottleneck in contemporary structural genomics programs. Here, we describe a study to examine the reasons for successes and failures in recombinant membrane protein production in yeast, at the level of the host cell, by systematically quantifying cultures in high‐performance bioreactors under tightly‐defined growth regimes. Our data show that the most rapid growth conditions of those chosen are not the optimal production conditions. Furthermore, the growth phase at which the cells are harvested is critical: We show that it is crucial to grow cells under tightly‐controlled conditions and to harvest them prior to glucose exhaustion, just before the diauxic shift. The differences in membrane protein yields that we observe under different culture conditions are not reflected in corresponding changes in mRNA levels ofFPS1, but rather can be related to the differential expression of genes involved in membrane protein secretion and yeast cellular physiology.
Lessons from the design of a novel atomic potential for protein folding
Authors: Chen William W. , Shakhnovich Eugene I. 
Published: June 2005

AbstractWe investigate all‐atom potentials of mean force for estimating free energies in protein folding and fold recognition. We search through the space potentials and design novel atomic potentials with a random mixing approximation and a contact‐correlated Gaussian approximation of decoy states. We show that the two derived potentials are highly correlated, supporting the use of the random energy model as an accurate statistical description of protein conformational states. The novel atomic potentials perform well in a Z‐score and fold decoy recognition test. Furthermore, the designed atomic potential performs slightly and significantly better than atomic potentials derived under a quasi‐chemical assumption. While accounting for connectivity correlations between atom types does not improve the performance of the designed potential, we show these correlations lead to ambiguities in the distribution of energetic contributions for atoms on the same residue. Within the confines of the model then, many potentials may exist which stabilize all native folds in subtly different ways. Comparison of different protein conformations under the various atomic potentials reveals both a remarkable degree of correspondence in the estimated free energies and a remarkable degree of correspondence in the identity of the contacts types that make the dominant contributions to the estimated free energies. This consistency may be interpreted as a sign that the design procedure is extracting physically meaningful quantities.
Rv0216, a conserved hypothetical protein from Mycobacterium tuberculosis that is essential for bacterial survival during infection, has a double hotdog fold
Authors: Castell Alina , Johansson Patrik , Unge Torsten , Jones T. Alwyn , Bäckbro Kristina 
Published: June 2005

AbstractThe Mycobacterium tuberculosis genome contains about 4000 genes, of which approximately a third code for proteins of unknown function or are classified as conserved hypothetical proteins. We have determined the three‐dimensional structure of one of these, the rv0216 gene product, which has been shown to be essential for M. tuberculosis growth in vivo. The structure exhibits the greatest similarity to bacterial and eukaryotic hydratases that catalyse the R‐specific hydration of 2‐enoyl coenzyme A. However, only part of the catalytic machinery is conserved in Rv0216 and it showed no activity for the substrate crotonyl‐CoA. The structure of Rv0216 allows us to assign new functional annotations to a family of seven other M. tuberculosis proteins, a number if which are essential for bacterial survival during infection and growth.
Characterization of peptide folding nuclei by hydrogen/deuterium exchange‐mass spectrometry
Authors: Li Xue , Hood Robin J. , Wedemeyer William J. , Watson J. Throck 
Published: June 2005

AbstractCovalently linked pairs of well‐chosen peptides can be good model systems for protein folding studies because they can adopt stable secondary, side‐chain, and tertiary structure under certain conditions. We demonstrate a method for characterizing the structure in such peptide pairs by hydrogen/deuterium exchange of individual amide groups analyzed by collision‐induced dissociation tandem mass spectrometry, in concert with circular dichroism spectroscopy. We apply the method to two peptides (and their three possible pairs) from bovine pancreatic trypsin inhibitor to address specific hypotheses regarding the stabilization of local secondary structure by long‐range interactions.
TNF-α and intPLA2 genes' polymorphism in anorexia nervosa
Authors: Slopien Agnieszka , Rybakowski Filip , Dmitrzak-Weglarz Monika , Czerski Piotr , Hauser Joanna , Komorowska-Pietrzykowska Renata , Rajewski Andrzej 
Published: June 2005

Objective:The aim of this study was the assessment of −308G/A tumor necrosis factor (TNF)-α gene polymorphism and intPLA2 gene polymorphism in patients with anorexia nervosa (AN) and healthy controls.Subjects:We studied 91 non-related patients with AN and 144 healthy women (blood donors and students). The mean age of women from study group was 18.22 years (SD ± 3.13 years) and from control group was 31.71 years (SD ± 8.22).Methods:Gene polymorphisms were studied with the use of polymerase chain reaction-restriction fragment length polymorphism method. TNF-α gene polymorphism consists of G/A substitution in −308 promoter region. IntPLA2 gene polymorphism is related to intron 1, in which restrictive region is found and recognized by BanI enzyme.Results:We did not obtain statistically significant differences in the frequency of genotypes and alleles of −308G/A TNF-α polymorphism between the study and control groups (genotypes: P = 0.106, alleles: P = 0.076). We did analogous analysis in the restrictive and bulimic subgroups. We did not observe statistically relevant differences in the frequency of genotypes (P = 0.700) and alleles (P = 0.305). We did not obtain statistically relevant difference in the frequency of genotypes and alleles of intPLA2 gene between the study group and controls (genotypes: P = 0.300, alleles: P = 0.331). We did analogous analysis in both subgroups of AN. We did not observe statistically relevant differences in the frequency of genotypes (P = 0.344) and alleles (P = 0.230).Conclusions:There was no statistically relevant trend for the association between TNF-α polymorphism and AN. We did not find association between studied polymorphism of intPLA2 gene and risk of AN.
Secretory antibodies against Giardia intestinalis in lactating Nicaraguan women
Authors: Téllez A. , Palm D. , Weiland M. , Alemán J. , Winiecka‐Krusnell J. , Linder E. , Svärd S. 
Published: June 2005

SUMMARY Secretory IgA (sIgA) antibodies are important in the host defence against the intestinal protozoan parasite Giardia intestinalis. However, few antigens have been identified. In this study 100 milk and saliva samples from lactating women, living in an endemic region (León, Nicaragua), were screened for the presence of antibodies against G. intestinalis. Most milk and saliva samples contained anti‐Giardia antibodies (59% and 52%, respectively), with a mean sIgA content 50 times higher in milk than in saliva. The positive samples reacted with trophozoite membrane, flagella and cytoplasmic antigens. Western blot analysis showed that milk and saliva anti‐Giardia sIgA recognized up to 16 different Giardia proteins in the molecular weight region 20–165 kDa. Two‐dimensional Western blotting showed that the major immunoreactive proteins were the same as the immunoreactive proteins identified by serum from acute giardiasis patients in a non‐endemic country. The major difference was a stronger reactivity against the variant surface proteins (VSPs) in the milk samples. Milk sIgAs also recognized recombinant Giardia proteins such as alpha‐1 giardin, ornithine carbamoyl transferase, VSP‐4EX, arginine deaminase and alpha‐enolase. These antigens will be important targets in the development of new immunodiagnostic tools and vaccines.
Schistosoma infection inhibits cellular immune responses to core HCV peptides
Authors: Farid A. , Al‐Sherbiny M. , Osman A. , Mohamed N. , Saad A. , Shata M. T. , Lee D.‐H. , Prince A. M. , Strickland G. T. 
Published: June 2005

SUMMARY Patients coinfected with hepatitis C virus (HCV) and the trematode, Schistosoma mansoni, have an increased incidence of viral persistence and accelerated fibrosis. To investigate immunological mechanisms responsible for this more aggressive natural history of HCV, the core HCV‐specific T‐cell responses were analysed in 44 donated blood units rejected because they had antibodies to HCV (anti‐HCV). Half also had anti‐S. mansoni antibodies, evidence of past or active infection. HCV‐specific ELISPOT responses were examined using pools of 180 overlapping 9‐mer peptides with offsets of one covering the core of HCV genotype 4a. Comparison of T‐cell responses in blood units positive for both anti‐HCV and anti‐Schistosoma antibodies with blood units positive only for anti‐HCV antibodies showed a significant decrease in core‐specific T‐cell IFN‐γ (505± 46 vs. 803 ± 66 ISC/106 cells, P < 0·001), IL‐4 (2 ± 108 vs. 641 ± 131 ISC/106 cells, P < 0·001), and IL‐10 (159 ± 105 vs. 466 ± 407 ISC/106 cells, P < 0·002) responses. In contrast, there was no significant difference in cell‐mediated immune response (CMI) to PHA mitogen between these two groups. Therefore, we concluded T cells from persons with anti‐Schistosoma have reduced IFN‐γ, IL‐4, and IL‐10 secreting HCV‐specific T‐cell responses. This may explain why Schistosoma coinfection increases persistence and severity of HCV infection.