bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of naturally processed peptides bound to the class I MHC molecule H‐2Kd of normal and TAP‐deficient cells
Authors: Suri Anish , Walters James J. , Levisetti Matteo G. , Gross Michael L. , Unanue Emil R. 
Published: February 2006

AbstractThis report details the biochemical features of natural peptides selected by the H‐2Kd class I MHC molecule. In normal cell lines, the length of the naturally processed peptides ranged from 8 to 18 amino acids, although the majority were 9‐mers (16% were longer than nine residues). The binding motif for the 9‐mer peptides was dominated by the presence of a tyrosine at P2 and an isoleucine/leucine at the P9 position. The P2 residue contributed most towards binding; and the short peptides bound better and formed longer‐lived cell surface complexes than the long peptides, which bound poorly and dissociated rapidly. The longer peptides did not exhibit this strictly defined motif. Trimming the long peptides to their shorter forms did not enhance binding and conversely, extending the 9‐mer peptides did not decrease binding. The long peptides were present on the cell‐surface bound to H‐2Kd (Kd) and were not intermediate products of the class I MHC processing pathway. Finally, in two different TAP‐deficient cells the long peptides were the dominant species, which suggested that TAP‐independent pathways selected for long peptides by class I MHC molecules.
α‐melanocyte‐stimulating hormone down‐regulates CXC receptors through activation of neutrophil elastase
Authors: Manna Sunil K. , Sarkar Abira , Sreenivasan Yashin 
Published: February 2006

AbstractConsidering the role of interleukin‐8 (IL‐8) in a large number of acute and chronic inflammatory diseases, the regulation of IL‐8‐mediated biological responses is important. Alpha‐melanocyte‐stimulating hormone (α‐MSH), a tridecapeptide, inhibits most forms of inflammation by an unknown mechanism. In the present study, we have found that α‐MSH interacts predominantly with melanocortin‐1 receptors and inhibits several IL‐8‐induced biological responses in macrophages and neutrophils. It down‐regulated receptors for IL‐8 but not for TNF, IL‐4, IL‐13 or TNF‐related apoptosis‐inducing ligand (TRAIL) in neutrophils. It down‐regulated CXCR type 1 and 2 but not mRNA levels. α‐MSH did not inhibit IL‐8 binding in purified cell membrane or affinity‐purified CXCR. IL‐8 or anti‐CXCR Ab protected against α‐MSH‐mediated inhibition of IL‐8 binding. The level of neutrophil elastase, a specific serine protease, but not cathepsin G or proteinase 3 increased in α‐MSH‐treated cells, and restoration of CXCR by specific neutrophil elastase or serine protease inhibitors indicates the involvement of elastase in α‐MSH‐induced down‐regulation of CXCR. These studies suggest that α‐MSH inhibits IL‐8‐mediated biological responses by down‐regulating CXCR through induction of serine protease and that α‐MSH acts as a potent immunomodulator in neutrophil‐driven inflammatory distress.
Epstein‐Barr virus (EBV) latent membrane protein‐1‐specific cytotoxic T lymphocytes targeting EBV‐carrying natural killer cell malignancies
Authors: Demachi‐Okamura Ayako , Ito Yoshinori , Akatsuka Yoshiki , Tsujimura Kunio , Morishima Yasuo , Takahashi Toshitada , Kuzushima Kiyotaka 
Published: February 2006

AbstractEpstein‐Barr virus (EBV)‐encoded latent membrane protein (LMP) 1 is a potential target for immunotherapy of some proportion of Hodgkin's disease cases, nasopharyngeal carcinomas, EBV‐associated natural killer (NK)/T lymphomas, and chronic active EBV infection (CAEBV). Since it is unknown whether EBV‐infected NK/T cells are susceptible to lysis by LMP1‐specific cytotoxic T lymphohcytes (CTL), we here tested the ability of mRNA‐transduced antigen‐presenting cells (APC) to stimulate rare LMP1‐specific CTL. A 43‐amino acid N‐terminal deletion mutant LMP1 (ΔLMP1) could be efficiently expressed in dendritic cells and CD40‐activated B cells upon mRNA electroporation. ΔLMP1‐expressing APC were found to stimulate LMP1‐specific CTL from a healthy donor and a CTL clone recognized a peptide, IIIILIIFI, presented by HLA‐A*0206 molecules. Processing and presentation of the antigenic peptide proved dependent on expression of an immunoproteasome subunit, low‐molecular‐weight protein‐7, as confirmed by RNA interference gene silencing. Furthermore, an EBV‐infected NK cell line derived from a patient with CAEBV, and another from an NK lymphoma with enforced HLA‐A*0206 expression, were specifically lysed by the CTL. Overall, these data suggest that immunotherapy targeting LMP1 in EBV‐associated NK lymphomas and CAEBV might serve as an alternative treatment modality.
Suppressive effect of alkyl ferulate on the oxidation of microencapsulated linoleic acid
Authors: Fang Xu , Kikuchi Sho , Shima Motohiro , Kadata Megumi , Tsuno Takuo , Adachi Shuji 
Published: February 2006

AbstractThe oxidation processes of linoleic acid mixed with ferulic acid or the 1‐pentyl, 1‐hexyl and 1‐heptyl ferulates, encapsulated with gum arabic or maltodextrin, were studied. The alkyl ferulates had a higher antioxidative effect than ferulic acid, but there was no significant difference among the three alkyl ferulates. Suppression of the oxidation by 1‐hexyl ferulate or ferulic acid was more effective at the higher molar ratios of the additive to linoleic acid. The processes were analyzed using the Weibull equation to evaluate the rate constant, k, and the shape constant, n. Although the k values for linoleic acid encapsulated with gum arabic were lower than that with maltodextrin, the suppressive effect of the alkyl ferulates was more remarkable for linoleic acid encapsulated with maltodextrin than with gum arabic because of the non‐antioxidative ability of maltodextrin. Because the partition coefficient of the alkyl ferulates was much greater than that of ferulic acid, most of the alkyl ferulates would be located in the linoleic acid phase of the microcapsules and effectively suppress the oxidation of linoleic acid.
Effect of filtration on virgin olive oil stability during storage
Authors: Fregapane Giuseppe , Lavelli Vera , León Sonia , Kapuralin Jasenka , Desamparados Salvador M. 
Published: February 2006

AbstractThe effect of filtration and dehydration on the stability and quality of virgin olive oil during storage at room temperature (25 °C) and under accelerated conditions (40 °C) was studied. Different types of monovarietal olive oil, namely unfiltered (UF), filtered (F) and filtered‐dehydrated (FD), were obtained from Arbequina, Colombaia, Cornicabra, Picual and Taggiasca cultivars. Results showed that filtration and dehydration decreased the rate of hydrolysis of the triacylglycerol matrix, especially at the higher temperature and in oils with a higher initial free acidity (e.g. free acidity of 0.82% and 0.63% in UF and FD Colombaia samples, respectively, after 8 months of storage), and delayed the appearance of rancid defects (e.g. UF and FD Arbequina samples lost extra‐virgin grade after 10 and 12 months of storage, respectively). The formation of simple phenols due to the hydrolysis rate of their secoiridoid derivatives was also greater in unfiltered olive oils (e.g. 174 μmol/kg and 137 μmol/kg in UF and FD Picual samples, respectively, after 8 months of storage). Thus, filtration and especially dehydration could help to prolong the shelf life of high‐quality and less stable olive oils like those obtained from the Arbequina and Colombaia varieties.
Runge–Kutta time‐stepping schemes with TVD central differencing for the water hammer equations
Authors: Wahba E. M. 
Published: February 2006

AbstractIn the present study, Runge–Kutta schemes are used to simulate unsteady flow in elastic pipes due to sudden valve closure. The spatial derivatives are discretized using a central difference scheme. Second‐order dissipative terms are added in regions of high gradients while they are switched off in smooth flow regions using a total variation diminishing (TVD) switch. The method is applied to both one‐ and two‐dimensional water hammer formulations. Both laminar and turbulent flow cases are simulated. Different turbulence models are tested including the Baldwin–Lomax and Cebeci–Smith models. The results of the present method are in good agreement with analytical results and with experimental data available in the literature. The two‐dimensional model is shown to predict more accurately the frictional damping of the pressure transient. Moreover, through order of magnitude and dimensional analysis, a non‐dimensional parameter is identified that controls the damping of pressure transients in elastic pipes. Copyright © 2006 John Wiley & Sons, Ltd.
Playing with bone and fat
Authors: Gimble Jeffrey M. , Zvonic Sanjin , Floyd Z. Elizabeth , Kassem Moustapha , Nuttall Mark E. 
Published: February 2006

AbstractThe relationship between bone and fat formation within the bone marrow microenvironment is complex and remains an area of active investigation. Classical in vitro and in vivo studies strongly support an inverse relationship between the commitment of bone marrow‐derived mesenchymal stem cells or stromal cells to the adipoctye and osteoblast lineage pathways. In this review, we focus on the recent literature exploring the mechanisms underlying these differentiation events and discuss their implications relevant to osteoporosis and regenerative medicine. J. Cell. Biochem. 98: 251–266, 2006. © 2006 Wiley‐Liss, Inc.
Claw‐decompositions and tutte‐orientations
Authors: Barát János , Thomassen Carsten 
Published: February 2006

AbstractWe conjecture that, for each tree T, there exists a natural number kT such that the following holds: If G is a kT‐edge‐connected graph such that |E(T)| divides |E(G)|, then the edges of G can be divided into parts, each of which is isomorphic to T. We prove that for T = K1,3 (the claw), this holds if and only if there exists a (smallest) natural number kt such that every kt‐edge‐connected graph has an orientation for which the indegree of each vertex equals its outdegree modulo 3. Tutte's 3‐flow conjecture says that kt = 4. We prove the weaker statement that every 4$\lceil$ log n$\rceil$‐edge‐connected graph with n vertices has an edge‐decomposition into claws provided its number of edges is divisible by 3. We also prove that every triangulation of a surface has an edge‐decomposition into claws. © 2006 Wiley Periodicals, Inc. J Graph Theory 52: 135–146, 2006
Detailed analysis of coupling constants and isotope effects in NMR spectra of isotopomers of 12C6813C2
Authors: Anklin Clemens , Alemany Lawrence B. 
Published: February 2006

AbstractA preliminary study of the long‐range (i.e. two‐bond or longer) 13C13C coupling constants in natural abundance C70 shows, consistent with recent theoretical calculations by Peralta et al. that the largest long‐range JCC values for the polar and equatorial sites are clearly smaller than the largest long‐range JCC values for the other three sites. The unusually large size of the 2JCC couplings between inequivalent carbons in a nonpolar pentagon in C70 has no analog among 2JCC data reported for planar aromatic compounds. No long‐range JCC values appear to have been reported for any curved aromatic compounds. In addition, much more precise 1JCC values were obtained for C70 than was possible about 15 years ago. Comparing the chemical shifts for each of the five isotopomers of C70 containing only one 13C nucleus and the frequencies of the satellites for each of the four isotopomers containing two adjacent and inequivalent 13C nuclei indicates that replacing 12C with 13C shields the adjacent 13C nucleus by 15 to 23 ppb, consistent with the limited 1Δ13C(13/12C) isotope effect data available on a few small aromatic molecules. Such measurements become possible with natural abundance C70 only by using a 13C cryoprobe and a high‐field spectrometer (700 MHz). The additional information that could be obtained from a spectrum obtained under ultrahigh resolution conditions is discussed. Secure identification of the singlets arising from the four 12C6813C2 isotopomers with equivalent adjacent 13C nuclei is necessary to allow the largest long‐range JCC values to be precisely determined. The presence of numerous isotopomers containing two or more 13C nuclei would present a great challenge in interpreting the various signals in a spectrum obtained under ultrahigh resolution conditions. Copyright © 2006 John Wiley & Sons, Ltd.
Chemical shift imaging (CSI) by precise object displacement
Authors: Leclerc Sebastien , Trausch Gregory , Cordier Benoit , Grandclaude Denis , Retournard Alain , Fraissard Jacques , Canet Daniel 
Published: February 2006

AbstractA mechanical device (NMR lift) has been built to displace vertically an object (typically an NMR sample tube) inside the NMR probe with an accuracy of 1 µm. A series of single pulse experiments are performed for incremented vertical positions of the sample. With a sufficiently spatially selective radio‐frequency (r.f.) field, one obtains chemical shift information along the displacement direction (one‐dimensional chemical shift imaging (CSI)). Knowing the vertical r.f. field profile (the amplitude of the r.f. field along the vertical direction), one can reconstruct the spectrum associated with all the slices corresponding to consecutive sample positions and improve the spatial resolution, which is simply related to the accuracy of the displacement device. Beside tests performed on phantoms, the method has been applied to solvent penetration in polymers and to benzene diffusion in a heterogeneous zeolite medium. Copyright © 2006 John Wiley & Sons, Ltd.
1H relaxation times of metabolites in biological samples obtained with nondestructive ex‐vivo slow‐MAS NMR
Authors: Hu Jian Zhi , Wind Robert A. , Rommereim Donald N. 
Published: February 2006

AbstractMethods suitable for measuring 1H relaxation times such as T1, T2 and T1ρ of metabolites in small, intact biological objects including live cells, excised organs and tissues, oil seeds etc. are developed in this work. This was achieved by combining inversion‐recovery, spin‐echo, or a spin‐lock segment with the phase‐adjusted spinning sideband (PASS) technique, which was applied at low sample‐spinning rates. Here, PASS was used to produce high‐resolution 1H spectra in a nondestructive way so that the relaxation parameters of individual metabolite could be determined. The methodologies were demonstrated by measuring 1H T1, T2, and T1ρ of metabolites in excised rat liver at a spinning rate of 40 Hz. Copyright © 2006 John Wiley & Sons, Ltd.
On the use of pseudocontact shifts in the structure determination of metalloproteins
Authors: Jensen Malene Ringkjøbing , Hansen D. Flemming , Ayna Umit , Dagil Robert , Hass Mathias A. S. , Christensen Hans E. M. , Led Jens J. 
Published: February 2006

AbstractThe utility of pseudocontact shifts in the structure refinement of metalloproteins has been evaluated using a native, paramagnetic Cu2+ metalloprotein, plastocyanin from Anabaena variabilis (A.v.), as a model protein. First, the possibility of detecting signals of nuclei spatially close to the paramagnetic metal ion is investigated using the WEFT pulse sequence in combination with the conventional TOCSY and 1H–15N HSQC sequences. Second, the importance of the electrical charge of the metal ion for the determination of correct pseudocontact shifts from the obtained chemical shifts is evaluated. Thus, using both the Cu+ plastocyanin and Cd2+‐substituted plastocyanin as the diamagnetic references, it is found that the Cd2+‐substituted protein with the same electrical charge of the metal ion as the paramagnetic Cu2+ plastocyanin provides the most appropriate diamagnetic reference signals. Third, it is found that reliable pseudocontact shifts cannot be obtained from the chemical shifts of the 15N nuclei in plastocyanin, most likely because these shifts are highly dependent on even minor differences in the structure of the paramagnetic and diamagnetic proteins. Finally, the quality of the obtained 1H pseudocontact shifts, as well as the possibility of improving the accuracy of the obtained structure, is demonstrated by incorporating the shifts as restraints in a refinement of the solution structure of A.v. plastocyanin. It is found that incorporation of the pseudocontact shifts enhances the precision of the structure in regions with only few NOE restraints and improves the accuracy of the overall structure. Copyright © 2006 John Wiley & Sons, Ltd.
High‐resolution magic‐angle spinning 13C spectroscopy of brain tissue at natural abundance
Authors: Yang YongXia , Chen Lei , Gao HongChang , Zeng DanLin , Yue Yong , Liu MaiLi , Lei Hao , Deng Feng , Ye ChaoHui 
Published: February 2006

AbstractHigh‐resolution magic‐angle spinning (MAS) 1H and 13C magnetic resonance spectroscopy (MRS) has recently been applied to study the metabolism in intact biological tissue samples. Because of the low natural abundance and the low gyromagnetic ratio of the 13C nuclei, signal enhancement techniques such as cross‐polarization (CP) and distortionless enhancement by polarization transfer (DEPT) are often employed in MAS 13C MRS to improve the detection sensitivity. In this study, several sensitivity enhancement techniques commonly used in liquid‐ and solid‐state NMR, including CP, DEPT and nuclear Overhauser enhancement (NOE), were combined with MAS to acquire high‐resolution 13C spectra on intact rat brain tissue at natural abundance, and were compared for their performances. The results showed that different signal enhancement techniques are sensitive to different classes of molecules/metabolites, depending on their molecular weights and mobility. DEPT was found to enhance the signals of low–molecular weight metabolites exclusively, while the signals of lipids, which often are associated with membranes and have relatively lower mobility, were highly sensitive to CP enhancement. Copyright © 2006 John Wiley & Sons, Ltd.
Quantitative glutamate spectroscopic imaging of the human hippocampus
Authors: Pan J. W. , Venkatraman T. , Vives K. , Spencer D. D. 
Published: February 2006

AbstractWe have evaluated a three‐dimensional localized spectroscopic imaging sequence that uses two pairs of adiabatic full‐passage pulses, which optimizes the detection of glutamate resonances at moderate echo times. This sequence provides excellent volume localization while simultaneously reducing J‐modulation losses of glutamate. We have simulated the performance of this sequence for glutamate and used it to quantitatively measure glutamate in the human hippocampus using a linear components model. Using tissue segmentation and regression analysis, we measured a glutamate concentration of 8.8 ± 2.1 mM in hippocampal and temporal gray matter and 3.7 ± 1.1 mM in temporal white matter (95% CI). We have used this approach in a small group of patients (n = 5) with unilateral hippocampal epilepsy. Copyright © 2006 John Wiley & Sons, Ltd.
Relative and absolute quantitative expression profiling of cytochromes P450 using isotope‐coded affinity tags
Authors: Jenkins Rosalind E. , Kitteringham Neil R. , Hunter Christie L. , Webb Sally , Hunt Tony J. , Elsby Robert , Watson Rod B. , Williams Dominic , Penningtonand Stephen R. , Park B. Kevin 
Published: February 2006

AbstractThe development of a novel method for absolute quantification of proteins based on isotope‐coded affinity tagging using ICAT® reagents is described. The method exploits synthetic peptide standards to determine protein content at the femtomole level in biological samples. The approach is generally applicable to any subset of proteins, but is particularly appropriate for quantitative analysis of multiple, closely related isoforms, and for hydrophobic proteins that are poorly represented in 2‐D gels. Relative and absolute quantification techniques are applied to an important group of microsomal metabolic enzymes, the cytochromes P450 (P450), which are critical in determining the disposition, safety and efficacy of drugs in man. Measurement of the P450 induction profile in response to chemicals is a fundamental aspect of drug safety evaluation and is currently achieved by low‐throughput methods employing poorly discriminatory antibodies or substrates. Tagging technology is shown to supersede conventional methods for P450 profiling in terms of discriminatory power and throughput, exemplified by the simultaneous detection of distinct induction profiles for cyp2c subfamily members in response to phenobarbitone: cyp2c29 expression, but not cyp2c40 or cyp2c50, was induced threefold by treatment. This technology should abbreviate the drug development pathway, and provide a widely applicable, rapid means of quantifying proteins.
Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: Identification of new proteins at the DNA replication factory
Authors: Meile Jean‐Christophe , Wu Ling Juan , Ehrlich S. Dusko , Errington Jeff , Noirot Philippe 
Published: February 2006

AbstractConstruction and microscopic imaging of protein fusions to green fluorescent protein (GFP) have revolutionised our understanding of bacterial structure and function. We have undertaken a systematic study of the localisation of over 100 Bacillus subtilis proteins, following the development of high‐throughput construction and analysis procedures. We focused on proteins linked in various ways to the DNA replication machinery, as well as on proteins exemplifying a range of other cellular functions and structures. The results validate the approach as a way of obtaining systematic protein localisation information. They also provide a range of novel biological insights, particularly through the identification of a number of proteins not previously known to be associated with the DNA replication factory.
Synthesis, crystallization kinetics, and spherulitic growth of linear and star‐shaped poly(L‐lactide)s with different numbers of arms
Authors: Wang Lu , Dong Chang‐Ming 
Published: February 2006

AbstractWell‐defined linear poly(L‐lactide)s with one or two arms (LPLLA and 2LPLLA, respectively) and star‐shaped poly(L‐lactide)s with four or six arms (4sPLLA and 6sPLLA, respectively) were synthesized and then used for the investigation of the thermal properties, isothermal crystallization kinetics, and spherulitic growth. The maximal melting temperature, the cold‐crystallization temperature, and the degree of crystallinity of these poly(L‐lactide) polymers decreased with an increasing number of arms in the macromolecule. Moreover, the isothermal crystallization rate constant (K) of these poly(L‐lactide) polymers decreased in the order of KLPLLA > K2LPLLA > K4sPLLA > K6sPLLA2, which was consistent with the variation trend of the spherulitic growth rate (G). Meanwhile, both K and G of 6sPLLA slightly increased with the increasing molecular weight of the polymer. Furthermore, both LPLLA and 2LPLLA presented spherulites with good morphology and apparent Maltese cross patterns, whereas both unclear Maltese cross patterns and imperfect crystallization were observed for the star‐shaped 4sPLLA and 6sPLLA polymers. These results indicated that both the macromolecular architecture and the molecular weight of the polymer controlled K, G, and the spherulitic morphology of these poly(L‐lactide) polymers. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 2226–2236, 2006