bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased molecular damage and heterogeneity as the basis of aging
Authors: Rattan Suresh I.S. 
Published: January 2008

Abstract
Aging at the molecular level is characterized by the progressive accumulation of molecular damage. The sources of damage act randomly through environmental and metabolically generated free radicals, through spontaneous errors in biochemical reactions, and through nutritional components. However, damage to a macromolecule may depend on its structure, localization and interactions with other macromolecules. Damage to the maintenance and repair pathways comprising homeodynamic machinery leads to age-related failure of homeodynamics, increased molecular heterogeneity, altered cellular functioning, reduced stress tolerance, diseases and ultimate death. Novel approaches for testing and developing effective means of intervention, prevention and modulation of aging involve means to minimize the occurrence and accumulation of molecular damage. Mild stress-induced hormesis by physical, biological and nutritional methods, including hormetins, represents a promising strategy for achieving healthy aging and for preventing age-related diseases.
Cellular responses to reactive oxygen species-induced DNA damage and aging
Authors: Bertram Catharina , Hass Ralf 
Published: January 2008

AbstractOxidative stress in cells and tissues can occur during pathophysiological developments, e.g., during inflammatory and allergic diseases or during ischemic or toxic and hyperglycemic conditions via the generation of reactive oxygen species (ROS). Moreover, ROS can be generated by radiation (UV, X-rays) and pharmacologically, e.g., by anthracyclins as chemotherapeutic compounds for treatment of a variety of tumors to induce ‘stress or aberrant signaling-inducing senescence’ (STASIS). Although STASIS is distinguished from intracellular replicative senescence, a variety of cellular mechanisms appear similar in both aging pathways. It is generally accepted that oxidative stress and ROS eventually cause DNA damage, whereby insufficient cellular repair mechanisms may contribute to premature aging and apoptosis. Conversely, ROS-induced imbalances of the signaling pathways for metabolic protein turnover may also result in opposite effects to recruit malfunctioning aberrant proteins and compounds that trigger tumorigenic processes. Consequently, DNA damage plays a role in the development of carcinogenesis, but is also associated with an aging process in cells and organisms.
Smurf1 directly targets hPEM-2, a GEF for Cdc42, via a novel combination of protein interaction modules in the ubiquitin-proteasome pathway
Authors: Yamaguchi Kei , Ohara Osamu , Ando Akikazu , Nagase Takahiro 
Published: January 2008

Abstract
Smurf1, a member of HECT-type E3 ubiquitin ligases, regulates cell polarity and protrusive activity by inducing ubiquitination and subsequent proteasomal degradation of the small GTPase RhoA. We report here that hPEM-2, a guanine nucleotide exchange factor for the small GTPase Cdc42, is a novel target of Smurf1. Pulse-chase labeling and a ubiquitination experiment using MG132, a proteasomal inhibitor, indicate that Smurf1 induces proteasomal degradation of hPEM-2 in cells. GST pull-down assays with heterologously expressed firefly luciferase-fusion proteins that include partial sequences of hPEM-2 reveal that part of the PH domain (residues 318–343) of hPEM-2 is sufficient for binding to Smurf1. In contrast, the hPEM-2 binding domain in Smurf1 was mapped to the C2 domain. Although it has been reported that the binding activities of some C2 domains to target proteins are regulated by Ca2+, Smurf1 interacts with hPEM-2 in a Ca2+-independent manner. Our discovery that hPEM-2 is, in addition to RhoA, a target protein of Smurf1 suggests that Smurf1 plays a crucial role in the spatio-temporal regulation of Rho GTPase family members.
Purification and characterization of natural Ara h 8, the Bet v 1 homologous allergen from peanut, provides a novel isoform
Authors: Riecken Susanne , Lindner Buko , Petersen Arnd , Jappe Uta , Becker Wolf-Meinhard 
Published: January 2008

Abstract
The peanut allergen Ara h 8 is an important allergen for birch pollen allergic patients because of the cross-reactivity to the homologous Bet v 1. As the existence of Ara h 8 has been shown at the cDNA level so far (AY328088) and the allergen has indirectly been detected as natural protein, it was the aim of our study to identify natural Ara h 8 in peanut extract and to develop a purification strategy. This was achieved using a unique combination of purification steps, including optimized extraction conditions, size exclusion and ion exchange chromatography and treatment of the interfering contaminants with iodo-acetic acid. A characterization of the protein by microsequencing showed discrepancies to the deduced amino acid sequence of AY328088. For this reason, we cloned and expressed a new Ara h 8 isoform from cDNA (EU046325). This IgE-reactive protein corresponds to the results of microsequencing, ESI-FTICR-MS and trypsin fingerprinting analysis of the authentic and purified nAra h 8. Apart from the ultimate use of recombinant allergens for diagnostic procedures, there is also a scientific need for the natural counterpart, as it represents an excellent reference point by which to compare protein characteristics and to standardize diagnostic and therapeutic allergens.
p53-dependent repression of the human MCL-1 gene encoding an anti-apoptotic member of the BCL-2 family: the role of Sp1 and of basic transcription factor binding sites in the MCL-1 promoter
Authors: Pietrzak Maciej , Puzianowska-Kuznicka Monika 
Published: January 2008

Abstract
p53 regulates transcription of one anti-apoptotic and four pro-apoptotic members of the BCL-2 family, but nothing is known about the regulation of MCL-1, another anti-apoptotic member of this family, by p53. Confocal microscopic analysis of COS1, HEK 293 and HeLa cells transfected with a p53 expression plasmid demonstrated a decrease in the signal of endogenous MCL-1 compared to neighboring non-transfected cells. Transcription regulation assays showed that the 1826 bp human MCL-1 promoter fragment was repressed up to 30-fold by wild-type p53 in a dose-dependent manner. As shown by electrophoretic mobility shift assays, Sp1 binding to the sites located in the -295 to +16 MCL-1 promoter fragment was decreased in the presence of p53. However, the MCL-1 promoter devoid of all Sp1 binding sites was still repressed by p53, albeit 2-fold weaker than the wild-type promoter. Overexpression of Sp1 reduced p53-dependent repression of the MCL-1 promoter only up to 2.2-fold. Transcription regulation assays performed with MCL-1 promoter deletion mutants showed that most of the p53 inhibitory effect was mediated by the -41 to +16 bp promoter fragment containing binding sites only for TATA-binding protein and other basal transcription factors. We propose a novel, promoter-based mechanism by which p53 down-regulates expression of the anti-apoptotic MCL-1 protein.
Disentanglement of protease substrate repertoires
Authors: Van Damme Petra , Vandekerckhove Joel , Gevaert Kris 
Published: January 2008

Abstract
Identification of protease substrates and detailed characterization of processed sites are essential for understanding the biological function of proteases. Because of inherent complexity reasons, this however remains a formidable analytical challenge, illustrated by the fact that the majority of the more than 500 human proteases are uncharacterized to date. Recently, in addition to conventional genetic and biochemical approaches, diverse quantitative peptide-centric proteomics approaches, some of which selectively recover N-terminal peptides, have emerged. These latter proteomic technologies in particular allow the identification of natural protease substrates and delineation of cleavage sites in a complex, natural background of thousands of different proteins. We here review current biochemical, genetic and proteomic methods for global analysis of substrates of proteases and discuss selected applications.
Die Bilirubinbestimmung – Eine aktuelle Übersicht / Bilirubin measurement – An updated survey
Authors: Thaler Markus , Luppa Peter B. , Schlebusch Harald 
Published: January 2008

Zusammenfassung
Die präzise, richtige und spezifische Bestimmung des Bilirubins und seiner Fraktionen im Serum ist im klinisch-chemischen Laboratorium trotz einer Vielzahl unterschiedlicher Methoden immer noch nicht problemlos möglich. Neben den klassischen fotometrischen Diazo-Verfahren etablierten sich trockenchemische Methoden, direkte Spektrofotometrie in Serum und Vollblut und für wissenschaftliche Zwecke Trennungen mittels HPLC. Auch für das Point-of-Care-Testing stehen neuerdings mehrere Verfahren zur Verfügung. Die vorliegende Arbeit gibt einen Überblick über die wichtigsten Methoden und beschreibt ihre jeweiligen Vor- und Nachteile.
Diagnostik und Resistenztestung bei Pneumocystis jirovecii / Diagnostic features and resistance testing of Pneumocystis jirovecii
Authors: Riebold D. , Löbermann M. , Reisinger E.C. 
Published: January 2008

Zusammenfassung
Die durch den Pilz Pneumocystis jirovecii (P. jirovecii) ausgelöste Pneumocystis Pneumonie (PCP) ist vor allem bei HIV-Infizierten bekannt. In den letzten Jahren sind jedoch vermehrt Patienten nach Organtransplantationen und andere Immunsupprimierte betroffen. Die Labordiagnostik der PCP wird oft mit klassischen Färbemethoden durchgeführt, die wenig sensitiv sind. Ein Nachweis von P. jirovecii mit molekularbiologischen Methoden (PCR) erreicht eine Sensitivität von über 95% und kann – je nach untersuchtem Gen – auch für die Resistenztestung und Aufklärung von Infektionsketten herangezogen werden.
Effects of retrieval practice on conceptual explicit and implicit consumer memory
Authors: Parker Andrew , Dagnall Neil 
Published: January 2008

AbstractTwo experiments are reported that investigate the effects of retrieval practice on explicit and implicit memory for brand names. In Experiment 1, participants were exposed to a set of brand names pertaining to a range of product categories. Following this, participants practiced retrieving a subset of the brands before taking an explicit or implicit test for the brands. The explicit test, required recall of the brands in response to product category cues. The implicit test required the generation of the first brand names that came to mind. In both tests, prior retrieval produced retrieval‐induced forgetting of the non‐practiced brands. Experiment 2 replicated this effect under conditions designed to reduce explicit contamination. In addition, Experiment 2 found that increasing the amount of retrieval practice also increased the magnitude of retrieval‐induced forgetting on the explicit but not the implicit test. Implications for advertising and marketing are considered. Copyright © 2008 John Wiley & Sons, Ltd.
Visualization of quality parameters for classification of spectra in shooting crimes
Authors: Knauthe Björn , Steffen Sylvia , Barth Martin , Niewoehner Ludwig , Otto Matthias 
Published: January 2008

AbstractX‐ray emission spectra from gunshot residues (GSR) are evaluated in order to assign them to a certain ammunition brand. Classification is based on regularized discriminant analysis (RDA) providing class information as well as additional parameters for judging the quality of an assignment. For visualization of measures such as the posterior probability, distance to centre or inverse Mahalanobis distances different approaches are explored and their common interpretation is evaluated. Copyright © 2008 John Wiley & Sons, Ltd.
Molecular and Electronic Structures of One‐Electron Oxidized NiII–(Dithiosalicylidenediamine) Complexes: NiIII–Thiolate versus NiII–Thiyl Radical States
Authors: Stenson Philip A. , Board Ashley , Marin‐Becerra Armando , Blake Alexander J. , Davies E. Stephen , Wilson Claire , McMaster Jonathan , Schröder Martin 
Published: January 2008

AbstractThe dithiosalicylidenediamine NiII complexes [Ni(L)] (R=tBu, R′=CH2C(CH3)2CH2 1, R′=C6H4 2; R=H, R′=CH2C(CH3)2CH2 3, R′=C6H4 4) have been prepared by transmetallation of the tetrahedral complexes [Zn(L)] (R=tBu, R′=CH2C(CH3)2CH2 7, R′=C6H4 8; R=H, R′=CH2C(CH3)2CH2 9, R′=C6H4 10) formed by condensation of 2,4‐di‐R‐thiosalicylaldehyde with diamines H2N‐R′‐NH2 in the presence of ZnII salts. The diamagnetic mononuclear complexes [Ni(L)] show a distorted square‐planar N2S2 coordination environment and have been characterized by 1H‐ and 13C NMR and UV/Vis spectroscopies and by single‐crystal X‐ray crystallography. Cyclic voltammetry and coulombic measurements have established that complexes 1 and 2, incorporating tBu functionalities on the thiophenolate ligands, undergo reversible one‐electron oxidation processes, whereas the analogous redox processes for complexes 3 and 4 are not reversible. The one‐electron oxidized species, 1+ and 2+, can be generated quantitatively either electrochemically or chemically with 70 % HClO4. EPR and UV/Vis spectroscopic studies and supporting DFT calculations suggest that the SOMOs of 1+ and 2+ possess thiyl radical character, whereas those of 1(py)2+ and 2(py)2+ possess formal NiIII centers. Species 2+ dimerizes at low temperature, and an X‐ray crystallographic determination of the dimer [(2)2](ClO4)2⋅2 CH2Cl2 confirms that this dimerization involves the formation of a SS bond (S⋅⋅⋅S=2.202(5) Å).
Positive‐ion ESI mass spectrometry of regioisomeric nonreducing oligosaccharide fatty acid monoesters: In‐source fragmentation of sodium adducts
Authors: Pérez‐Victoria Ignacio , Zafra Alberto , Morales Juan Carlos 
Published: January 2008

AbstractStructural characterization and differentiation of a novel group of regioisomeric monolaurate esters of the nonreducing trisaccharides raffinose and melezitose, and the nonreducing tetrasaccharide stachyose has been obtained using positive electrospray ionization (ESI) mass spectrometry with in‐source fragmentation. The surfactant nature and high polarity of these compounds make them appropriate analytes for being studied by conventional ESI‐MS. The position of the acyl chain in each particular regioisomer has been used as a reporter group that allows unambiguous rationalization of the fragmentation routes of the corresponding natriated molecular ions [M + Na]+. In all cases, the main fragment ions were produced through cleavage of the glycosidic bond involving two anomeric carbons, the C‐1′ and C‐2″ of the α‐D‐Glcp‐(1–2)‐β‐D‐Fruf bond, and it was observed that sodium cation retention occurred on the heavier mass fragment of the two formed fragments, (e.g. di‐ or trisaccharide type vs monosaccharide type). Our results may help to better understand the fragmentation behavior of nonreducing oligosaccharides (as sodium adducts) in positive ESI mass spectrometry. Copyright © 2008 John Wiley & Sons, Ltd.
On‐target derivatization of keratan sulfate oligosaccharides with pyrenebutyric acid hydrazide for MALDI‐TOF/TOF‐MS
Authors: Zhang Yuntao , Iwamoto Takeo , Radke Gary , Kariya Yutaka , Suzuki Kiyoshi , Conrad Abigail H. , Tomich John M. , Conrad Gary W. 
Published: January 2008

AbstractIn the present work, a rapid and novel method of on‐target plate derivatization of keratan sulfate (KS) oligosaccharides for subsequent analysis by matrix‐assisted laser desorption and ionization (MALDI) mass spectrometry is described. MALDI‐(time‐of‐flight)‐TOF spectra of labeled KS oligosaccharides revealed that significantly improved ionization can be accomplished through derivatization with pyrenebutyric acid hydrazide (PBH), and the most abundant peak in each spectrum corresponds to the singly charged molecular ion [M − H]− or [M + (n − 1)Na − nH]−, where n = the number of sulfates (n = 1, 2, 3…). The high‐energy collision‐induced dissociation (heCID) spectra of labeled KS oligosaccharides displayed fragments of compounds similar to those observed with laser‐induced dissociation (LID) analysis, suggesting that both heCID and LID fragmentations can be used to analyze KS oligosaccharides. Moreover, fragmentation analysis of all labeled KS oligosaccharides was performed by MALDI‐TOF/TOF‐MS. With LID mode, sodium adducts showed fragmentation of glycosidic linkages with mainly Y/B/C ions, as well as various cross‐ring cleavages providing exact information for the positions of sulfate groups along the KS oligosaccharide chains. This one‐step on‐target derivatization method makes MALDI‐TOF/TOF‐MS identification of KS fast, simple and highly throughput for trace amounts of biological samples. Copyright © 2008 John Wiley & Sons, Ltd.
Structural and dynamical properties of glucose aqueous solutions by depolarized Rayleigh scattering
Authors: Paolantoni Marco , Comez Lucia , Fioretto Daniele , Gallina Maria Elena , Morresi Assunta , Sassi Paola , Scarponi Filippo 
Published: January 2008

AbstractDepolarized Rayleigh scattering (DRS) spectra of glucose aqueous solutions measured from 0.01 to 1000 cm−1 reveal the presence of two distinct relaxation processes, in addition to the intermolecular Raman modes of the water network. The slow relaxation process with a characteristic time of tens of picoseconds is due to the glucose rotational diffusion and is spectrally separated from the fast relaxation process at picosecond time scales commonly attributed to the hydrogen‐bond lifetime; this latter time clearly increases with increase in glucose concentration. This suggests the formation of stable sugar hydration shells where the water dynamics is slower than the bulk. The destructuring effect on the tetrahedral hydrogen bonding of water induced by the sugar is also clearly evidenced when comparing the intermolecular Raman spectra at different molar ratios. Copyright © 2008 John Wiley & Sons, Ltd.
Matrix‐assisted laser desorption/ionization‐MS‐based relative quantification of peptides and proteins using iodoacetamide and N‐methyliodoacetamide as labeling reagents
Authors: Sun Mei‐Chuan , Chen Cheng‐Dong , Huang Yu‐Shan , Wu Zhong‐Siang , Ho Yen‐Peng 
Published: January 2008

AbstractThe use of iodoacetamide (IAA) and N‐methyliodoacetamide (MIAA) as labeling agents for the relative measurements of proteins using MALDI‐MS is described herein. These reagents, which alkylate the thiol groups of cysteine residues in proteins, were introduced during the alkylation step of a common protein denaturation and digestion process. This approach is simpler and cheaper than those involving isotope labeling agents. The labeling agents described herein displayed good dynamic ranges and correlation coefficients for protein quantification analyses when the proteins were treated through either in‐solution or in‐gel digestion. The best dynamic ranges (in the molar ratio) for proteins lysozyme, transferrin, and BSA (in‐solution digestion) are 0.1–10, 0.1–8, and 0.1–8, respectively. The corresponding correlation coefficients are greater than 0.99. The IAA/MIAA labeling is a useful method for the relative quantification of peptides and digested proteins when the chromatographic isotope effect is not a major concern.
Separating stereoisomers of di‐, tri‐, and tetrapeptides using capillary electrophoresis with contactless conductivity detection
Authors: Gong Xiao Yang , Dobrunz Dominik , Kümin Michael , Wiesner Markus , Revell Jefferson D. , Wennemers Helma , Hauser Peter C. 
Published: January 2008

AbstractThe separation and detection of small oligopeptides in CE with contactless conductivity detection were demonstrated. A strongly acidic separation buffer (0.5 M acetic acid) was employed in order to render the species cationic. Separation of the stereoisomers was achieved in typically 10–15 min by using either dimethyl‐β‐CD (DM‐β‐CD), (+)‐(18‐crown‐6)‐2,3,11,12‐tetracarboxylic acid (18C6H4), a combination of the two substances, or of histidine, as buffer additives. Calibration curves were determined for isomers of Gly‐Asp and H‐Pro‐Asp‐NH2, in the range of 0.05–0.5 mM and 0.1–1 mM, respectively, and were found to be linear. LODs were determined to be in the order of 1.0 μM. The determination of isomeric impurities down to about 1% was found possible. Species showing good separation could also be successfully determined on an electrophoretic lab‐on‐chip device, with analysis times of a few minutes.
Malondialdehyde tagging improves the analysis of arginine oligomers and arginine‐containing dendrimers by HPLC‐MS
Authors: Onofrejova Lucia , Leitner Alexander , Lindner Wolfgang 
Published: January 2008

AbstractThe selective modification of arginine residues by malondialdehyde (MDA) was used to improve the mass spectrometric analysis of arginine oligomers (Argx, x = 4, 6, 7, 8, 9) and an arginine‐containing dendrimeric peptide. MDA tagging significantly increased the hydrophobicity of the arginine side‐chain and resulted in improved retention in RP HPLC of the oligoarginines using formic acid as mobile phase additive. This avoided the use of TFA to generate sufficient retention, as TFA was shown to lead to a dramatically reduced sensitivity (up to ten‐fold for Arg8 and Arg9) as a result of the strong signal suppression by ion pairing with multiple basic residues. MDA modification of Arg oligomers not only resulted in improved detection sensitivity for most of the peptides studied (e. g., more than six‐fold for Arg7), but also greatly enhanced the quality of MS/MS spectra, in line with previous results for other peptides. Furthermore, MDA modification helped to identify major side products in a sample of a dendrimeric peptide, a class of peptides that is typically difficult to analyze by MS.
Atom Transfer Radical Polymerization of Styrene Using Multifunctional Iniferter Reagents as Initiators
Authors: Zhang Wei , Wang Chengchao , Li Daoguang , Song Qing , Cheng Zhenping , Zhu Xiulin 
Published: January 2008

AbstractSummary: Two multifunctional iniferters, 1,4‐bis‐(α‐N,N‐diethyldithiocarbamyl‐isobutyryloxy)‐benzene (BDCIB) and 1,3,5‐tris‐(α‐N,N‐diethyldithiocarbamyl‐isobutyryloxy)‐benzene (TDCIB), were successfully synthesized and used as initiators to initiate the polymerization of styrene in the presence of a CuBr/PMDETA complex. The polymerization results demonstrated that the kinetic plots in all cases were first‐order to the monomer, the molecular weight of the polymers increased linearly with the monomer conversion; meanwhile, the molecular weight distribution of the polymer was kept to a very low value (Mw/Mn ≤ 1.35). Furthermore, the measured molecular weights were very close to the calculated values, which indicated the high efficiency of the initiator for the polymerization of styrene. The effect of catalyst concentration and initiator concentration was not obvious and the influence of polymerization temperature was apparent, and the polymerization rate increased with the polymerization temperature. The results of chain‐extension and 1H NMR analysis proved that the polymer obtained was capped with diethylthiocarbamoylthiy (DC) group.