bluuebunny/crossref_metadata_2025_split huggingface dataset:
Studies of the intermolecular DNA triplexes of C+·GC and T·AT triplets by electrospray ionization Fourier‐transform ion cyclotron resonance mass spectrometry
Authors: Wan Cuihong , Guo Xinhua , Liu Zhiqiang , Liu Shuying 
Published: September 2007

AbstractFormation and stabilities of four 14‐mer intermolecular DNA triplexes, consisting of third strands with repeating sequence CTCT, CCTT, CTT, or TTT, were studied by electrospray ionization Fourier‐transform ion cyclotron resonance mass spectrometry (ESI‐FTICR‐MS) in the gas phase. The gas‐phase stabilities of the triplexes were compared with their CD spectra and melting behaviors in solution, and parallel correlation between two phases were obtained. In the presence of 20 mM NH4+ (pH 5.5), the formation of the TTT triplex was not detected in both solution and the gas phase. Other triplexes showed the same order, CTCT > CCTT > CTT, of ion abundances in mass spectra and Tm values in solution. The more stable triplexes are those that contained higher percentage of C+·GC triplets and an alternating CT sequence. However, the CCTT with the same C+·GC triplets as the CTCT showed a higher stability than the latter during the gas‐phase dissociation. Furthermore, a biphasic triplex‐to‐duplex‐to‐single transition was detected in the gas phase, while a monophasic triplex‐to‐single dissociation was observed in solution. The present results reveal that hydrogen bonds and electrostatic interactions dominate in the gas phase, while base stacking and hydrophobic interactions dominate in solution to stabilize the triplexes. Moreover, weak acidic conditions (pH 5–6) promote the formation of the parallel triplexes. Copyright © 2007 John Wiley & Sons, Ltd.
Mechanisms of impaired mitochondrial energy metabolism in acute and chronic neurodegenerative disorders
Authors: Soane Lucian , Kahraman Sibel , Kristian Tibor , Fiskum Gary 
Published: September 2007

AbstractAltered mitochondrial energy metabolism contributes to the pathophysiology of acute brain injury caused by ischemia, trauma, and neurotoxins and by chronic neurodegenerative disorders such as Parkinson's and Huntington's diseases. Although much evidence supports that the electron transport chain dysfunction in these metabolic abnormalities has both genetic and intracellular environmental causes, alternative mechanisms are being explored. These include direct, reversible inhibition of cytochrome oxidase by nitric oxide, release of mitochondrial cytochrome c, oxidative inhibition of mitochondrial matrix dehydrogenases and adenine nucleotide transport, the availability of NAD for dehydrogenase reactions, respiratory uncoupling by activities such as that of the permeability transition pore, and altered mitochondrial structure and intracellular trafficking. This review focuses on the catabolism of neuronal NAD and the release of neuronal mitochondrial NAD as important contributors to metabolic dysfunction. In addition, the relationship between apoptotic signaling cascades and disruption of mitochondrial energy metabolism is considered in light of the fine balance between apoptotic and necrotic neural cell death. © 2007 Wiley‐Liss, Inc.
Late Quaternary speleothem pollen in the British Isles
Authors: Caseldine Christopher J. , McGarry Siobhán F. , Baker Andy , Hawkesworth Chris , Smart Peter L. 
Published: September 2007

AbstractAs with many terrestrial areas, the British Quaternary sequence is characterised by incomplete, fragmentary records, whose correlation is based on stratigraphic or biostratigraphic techniques due to the lack of radiometric ages beyond the ∼40 kyr limit of 14C dating. Speleothems (secondary cave calcite deposits) offer a significant advantage over many sources of palaeoenvironmental information; they can be dated to a high precision and accuracy by uranium‐thorium (238U‐230Th) thermal ionisation and inductively coupled plasma (ICP) mass spectrometry in the time period back to 500 kyr. They may also contain sufficient well‐preserved pollen representative of contemporary vegetation above the cave to allow palaeoenvironmental reconstruction. This study adopts the novel approach of combining pollen and thermal ionisation mass spectrometric (TIMS) U‐Th dating of British speleothems to produce well‐constrained palaeoenvironmental records. We report for the first time precisely dated records of pollen assemblages from speleothems suggesting the presence of thermophilous arboreal species in phases previously considered to have been consistently cool or cold and devoid of trees. Copyright © 2007 John Wiley & Sons, Ltd.
Quaternary tectonics in a passive margin: Marajó Island, northern Brazil
Authors: Rossetti Dilce F. , Góes Ana M. , Valeriano Márcio M. , Miranda Maria Carolina C. 
Published: September 2007

AbstractMarajó Island is located in a passive continental margin that evolved from rifting associated with the opening of the Equatorial South Atlantic Ocean in the Late Jurassic/Early Cretaceous period. This study, based on remote sensing integrated with sedimentology, as well as subsurface and seismographic data available from the literature, allows discussion of the significance of tectonics during the Quaternary history of marginal basins. Results show that eastern Marajó Island contains channels with evidence of tectonic control. Mapping of straight channels defined four main groups of lineaments (i.e. NNE–SSW, NE–SW, NW–SE and E–W) that parallel main normal and strike‐slip fault zones recorded for the Amazon region. Additionally, sedimentological studies of late Quaternary and Holocene deposits indicate numerous ductile and brittle structures within stratigraphic horizons bounded by undeformed strata, related to seismogenic deformation during or shortly after sediment deposition. This conclusion is consistent with subsurface Bouguer mapping suggestive of eastern Marajó Island being still part of the Marajó graben system, where important fault reactivation is recorded up to the Quaternary. Together with the recognition of several phases of fault reactivation, these data suggest that faults developed in association with rift basins might remain active in passive margins, imposing important control on development of depositional systems. Copyright © 2007 John Wiley & Sons, Ltd.
One step purification of flavanone glycosides from Poncirus trifoliata by centrifugal partition chromatography
Authors: Kim Chul Young , Lee Hee Ju , Lee Mi Kyeong , Ahn Mi‐Jeong , Kim Jinwoong 
Published: September 2007

AbstractFlavanone glycosides were successfully separated from the crude extract of Poncirus trifoliata by preparative centrifugal partition chromatography with a two‐phase solvent system composed of ethyl acetate–acetonitrile–water (3:2:5, v/v/v). Naringin (50.0 mg), neoponcirin (16.8 mg), and poncirin (71.9 mg) were purified from the 524 mg crude extract in only one step. The purities of the isolated compounds were determined to be over 90% by HPLC analysis and their structures were elucidated by 1H NMR, 13C NMR, and ESI‐MS.
A conditional GIS‐interpolation‐based model for mapping soil‐water erosion processes in Lebanon
Authors: Kheir R. Bou 
Published: September 2007

AbstractSoil erosion by water is a major cause of landscape degradation in Mediterranean environments, including Lebanon. This paper proposes a conditional decision‐rule interpolation‐based model to predict the distribution of multiple erosion processes (i.e. sheet, mass and linear) in a representative area of Lebanon from the measured erosion signs in the field (root exposure, earth pillars, soil etching and drift and linear channels). First, erosion proxies were derived from the structural OASIS classification of Landsat thematic mapper (TM) imageries combined with the addition of several thematic erosion maps (slope gradient, aspect and curvature, drainage density, vegetal cover, soil infiltration and erodibility and rock infiltration/movement) under a geographic information systems (GIS) environment. Second, erosion signs were measured in the field, and interpolated by the statistical moments (means and variance) in the defined erosion proxies, thus producing quantitative erosion maps (t ha−1) at a scale of 1:100 000. Seven decision rules were then generated and applied on these maps in order to produce the overall decisive erosion map reflecting all existing erosion processes, that is, equality (ER), dominance (DOR), bimodality (BR), masking (MR), aggravating (AR), dependence (DER) and independence (IR). The produced erosion maps are divided into seven classes ranging between 0 and more than 1·8 t ha−1 for sheet erosion, and 0 and more than 10·5 t ha−1 for mass and linear erosion. They are fairly matching with coincidences values equal to 43 per cent (sheet/linear), 48 per cent (sheet/mass) and 49 per cent (linear/mass). The overall accuracies of these maps were estimated to be 76 per cent (sheet erosion), 78 per cent (mass erosion) and 78·5 per cent (linear erosion). The overall decisive erosion map with 15 classes corresponds well to land management needs. The model used is relatively simple, and may also be applied to other areas. It is particularly useful when GIS database on factors influencing erosion is limited. Copyright © 2007 John Wiley & Sons, Ltd.
Acute sensory ataxic neuropathy with antibodies to GD1b and GQ1b gangliosides and prompt recovery
Authors: Notturno Francesca , Caporale Christina M. , Uncini Antonino 
Published: September 2007

AbstractThree patients developed acute pure sensory ataxic neuropathy. Two of the three patients had a recent Campylobacter jejuni infection. Patient 1 had monospecific IgG anti‐GD1b. Patients 2 and 3 had cross‐reactive IgG anti‐GQ1b and anti‐GD1b and patient 2 also had IgG anti‐GT1a. Motor nerve conduction studies were completely normal. Sensory conductions showed reduced amplitude or absent sensory nerve action potentials with normal or slightly slowed conduction velocities. In patient 2, serial electrophysiological studies showed reappearance and improvement of sensory nerve potential amplitudes in 4 weeks. All patients recovered completely in 2 months and sensory potential amplitudes normalized in 3–5 months. Our findings: (1) confirm the existence of a pure acute sensory ataxic neuropathy with cross‐reactive IgG anti‐GQ1b and anti‐GD1b as a variant of Guillain–Barré syndrome; (2) expand the clinical presentation of Guillain–Barré syndrome after C. jejuni infection and suggest that molecular mimicry is at the basis of acute sensory ataxic neuropathy; and (3) indicate that, in acute sensory ataxic neuropathy with prompt recovery, the site of the lesion is not in the primary sensory neurons and the pathophysiological mechanism may be functional in nature. Muscle Nerve, 2007
The immunocompetence of Schwann cells
Authors: Meyer Zu Hörste Gerd , Hu Wei , Hartung Hans‐Peter , Lehmann Helmar C. , Kieseier Bernd C. 
Published: September 2007

AbstractSchwann cells are the myelinating glial cells of the peripheral nervous system that support and ensheath axons with myelin to enable rapid saltatory signal propagation in the axon. Immunocompetence, however, has only recently been recognized as an important feature of Schwann cells. An autoimmune response against components of the peripheral nervous system triggers disabling inflammatory neuropathies in patients and corresponding animal models. The immune system participates in nerve damage and disease manifestation even in non‐inflammatory hereditary neuropathies. A growing body of evidence suggests that Schwann cells may modulate local immune responses by recognizing and presenting antigens and may also influence and terminate nerve inflammation by secreting cytokines. This review summarizes current knowledge on the interaction of Schwann cells with the immune system, which is involved in diseases of the peripheral nervous system. Muscle Nerve, 2007
Quasi‐static crack propagation in plane and plate structures using set‐valued traction‐separation laws
Authors: Areias Pedro M. A. , Rabczuk Timon 
Published: September 2007

AbstractWe introduce a numerical technique to model set‐valued traction‐separation laws in plate bending and also plane crack propagation problems. By using of recent developments in thin (Kirchhoff–Love) shell models and the extended finite element method, a complete and accurate algorithm for the cohesive law is presented and is used to determine the crack path. The cohesive law includes softening and unloading to origin, adhesion and contact. Pure debonding and contact are obtained as particular (degenerate) cases. A smooth root‐finding algorithm (based on the trust‐region method) is adopted. A step‐driven algorithm is described with a smoothed law which can be made arbitrarily close to the exact non‐smooth law. In the examples shown the results were found to be step‐size insensitive and accurate. In addition, the method provides the crack advance law, extracted from the cohesive law and the absence of stress singularity at the tip. Copyright © 2007 John Wiley & Sons, Ltd.
Resveratrol sensitizes androgen independent prostate cancer cells to death‐receptor mediated apoptosis through multiple mechanisms
Authors: Gill Catherine , Walsh Sinead E. , Morrissey Colm , Fitzpatrick John M. , Watson R. William G. 
Published: September 2007

AbstractBACKGROUNDA critical factor in prostate cancer development and progression is the altered expression of apoptotic regulatory proteins which renders cells resistant to both hormone‐ and chemo‐therapies. Resveratrol, a dietary component with chemopreventive properties has been reported to resensitize a variety of cancer cell types to apoptosis. In the current study, the ability of resveratrol pre‐treatment to sensitize hormone refractory prostate cancer cell lines (PC‐3 and DU145) to apoptosis and the mechanisms involved were investigated.METHODSApoptosis was assessed using several established parameters and protein expression was analyzed by Western blot and flow cytometry. IAP knockdown was achieved using RNAi while inhibition of Akt phosphorylation was achieved by pre‐incubation with the PI3‐kinase inhibitor LY294002.RESULTSPre‐treatment with resveratrol sensitized PC‐3 and DU145 cells to agents that specifically target death receptors (TRAIL, Fas, TNFα) but not agents that initiate apoptosis through other mechanisms (Etoposide, Paclitaxel, Tunicamycin, Thapsigargin). Resveratrol pre‐treatment altered the expression of IAPs and Bax, and decreased Akt phosphorylation in PC‐3 cells, leading to increased caspase activation and apoptosis. While knockdown of IAPs using siRNA did not mimic the effects of resveratrol, inhibition of Akt phosphorylation using LY294002 sensitized PC‐3 cells to TRAIL induced apoptosis but not to etoposide or tunicamycin.CONCLUSIONAltering apoptotic susceptibility in advanced androgen independent disease requires manipulation of a broad signaling pathway. Use of resveratrol or inhibition of Akt phosphorylation may represent an important therapeutic approach in combination with conventional therapies for the treatment of prostate cancer. Prostate 67: 1641–1653, 2007. © 2007 Wiley‐Liss, Inc.
Structure of aspartate racemase complexed with a dual substrate analogue, citric acid, and implications for the reaction mechanism
Authors: Ohtaki Akashi , Nakano Yohsuke , Iizuka Ryo , Arakawa Takatoshi , Yamada Kazuhiro , Odaka Masafumi , Yohda Masafumi 
Published: September 2007

AbstractPyrococcus horikoshii OT3 aspartate racemase (PhAspR) catalyzes the interconversion between L‐ and D‐aspartate. The X‐ray structure of PhAspR revealed a pseudo mirror‐symmetric distribution of the residues around its active site, which is very reasonable for its chiral substrates, L‐aspartate and D‐aspartate. In this study, we have determined the crystal structure of an inactive mutant PhAspR complexed with a citric acid (Cit) at a resolution of 2.0 Å. Cit contains the substrate analogue moieties of both L‐ and D‐aspartate and exhibits a low competitive inhibition activity against PhAspR. In the structure, Cit binds to the catalytic site of PhAspR, which induced the conformational change to close the active site. The distance between the thiolates was estimated to be 7.4 Å, representing a catalytic state and the substrate binding modes of PhAspR. Two conserved basic residues, Arg48 and Lys164, seem to be indispensable for PhAspR activity. Arg48 is thought to be responsible for recognizing carboxyl groups of the substrates L‐/D‐aspartates and stabilizing a reaction intermediate, and Lys164 is responsible for stabilizing a closed state structure. In this structure, the L‐aspartate moiety of Cit is likely to take the substrate position of the PhAspR–substrate complex, which is very similar to that of Glutamate racemase. There is also another possibility that the two substrate analogue moieties of the bound Cit reflect the binding modes of both L‐ and D‐aspartates. Based on the PhAspR–Cit complex structure, the reaction mechanism of aspartate racemase was elucidated. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Structural and enzymatic characterization of DR1281: A calcineurin‐like phosphoesterase from Deinococcus radiodurans
Authors: Shin Dong Hae , Proudfoot Michael , Lim Hyo Jin , Choi In‐Kyu , Yokota Hisao , Yakunin Alexander F. , Kim Rosalind , Kim Sung‐Hou 
Published: September 2007

AbstractWe have determined the crystal structure of DR1281 from Deinococcus radiodurans. DR1281 is a protein of unknown function with over 170 homologs found in prokaryotes and eukaryotes. To elucidate the molecular function of DR1281, its crystal structure at 2.3 Å resolution was determined and a series of biochemical screens for catalytic activity was performed. The crystal structure shows that DR1281 has two domains, a small α domain and a putative catalytic domain formed by a four‐layered structure of two β‐sheets flanked by five α‐helices on both sides. The small α domain interacts with other molecules in the asymmetric unit and contributes to the formation of oligomers. The structural comparison of the putative catalytic domain with known structures suggested its biochemical function to be a phosphatase, phosphodiesterase, nuclease, or nucleotidase. Structural analyses with its homologues also indicated that there is a dinuclear center at the interface of two domains formed by Asp8, Glu37, Asn38, Asn65, His148, His173, and His175. An absolute requirement of metal ions for activity has been proved by enzymatic assay with various divalent metal ions. A panel of general enzymatic assays of DR1281 revealed metal‐dependent catalytic activity toward model substrates for phosphatases (p‐nitrophenyl phosphate) and phosphodiesterases (bis‐p‐nitrophenyl phosphate). Subsequent secondary enzymatic screens with natural substrates demonstrated significant phosphatase activity toward phosphoenolpyruvate and phosphodiesterase activity toward 2′,3′‐cAMP. Thus, our structural and enzymatic studies have identified the biochemical function of DR1281 as a novel phosphatase/phosphodiesterase and disclosed key conserved residues involved in metal binding and catalytic activity. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Conformational flexibility in mammalian 15S‐lipoxygenase: Reinterpretation of the crystallographic data
Authors: Choi Jongkeun , Chon Jae Kyung , Kim Sangsoo , Shin Whanchul 
Published: September 2007

AbstractLipoxygenases (LOXs) are a family of nonheme iron dioxygenases that catalyze the regioselective and stereospecific hydroperoxidation of polyunsaturated fatty acids, and are involved in a variety of inflammatory diseases and cancers. The crystal structure of rabbit 15S‐LOX1 that was reported by Gillmor et al. in 1997 has played key roles for understanding the properties of mammalian LOXs. In this structure, three segments, including 12 residues in the superficial α2 helix, are absent and have usually been described as “disordered.” By reinterpreting the original crystallographic data we were able to elucidate two different conformations of the molecule, both having well ordered α2 helices. Surprisingly, one molecule contained an inhibitor and the other did not, thereby adopting a closed and an open form, respectively. They differed in the conformation of the segments that were absent in the original structure, which is highlighted by a 12 Å movement of α2. Consequently, they showed a difference in the size and shape of the substrate‐binding cavity. The new model should provide new insight into the catalytic mechanism involving induced conformational change of the binding pocket. It may also be helpful for the structure‐based design of LOX inhibitors. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Denatured state is critical in determining the properties of model proteins designed on different folds
Authors: Amatori A. , Tiana G. , Ferkinghoff‐Borg J. , Broglia R. A. 
Published: September 2007

AbstractThe thermodynamics of proteins designed on three common folds (SH3, chymotrypsin inhibitor 2 [CI2], and protein G) is studied with a simplified Cα model and compared with the thermodynamics of proteins designed on random‐generated folds. The model allows to design sequences to fold within a dRMSD ranging from 1.2 to 4.2 Å from the crystallographic native conformation and to study properties that are hard to be measured experimentally. It is found that the denatured state of all of them is not random but is, to different extents, partially structured. The degree of structure is more abundant for SH3 and protein G, giving rise to a weaker stability but a more efficient folding kinetics than CI2 and, even more, than the random‐generated folds. Consequently, the features of the unfolded state seem to be as important in the determination of the thermodynamic properties of these proteins as the features of the native state. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Context shapes: Efficient complementary shape matching for protein–protein docking
Authors: Shentu Zujun , Al Hasan Mohammad , Bystroff Christopher , Zaki Mohammed J. 
Published: September 2007

AbstractWe describe an efficient method for partial complementary shape matching for use in rigid protein–protein docking. The local shape features of a protein are represented using boolean data structures called Context Shapes. The relative orientations of the receptor and ligand surfaces are searched using precalculated lookup tables. Energetic quantities are derived from shape complementarity and buried surface area computations, using efficient boolean operations. Preliminary results indicate that our context shapes approach outperforms state‐of‐the‐art geometric shape‐based rigid‐docking algorithms. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Morphology, surface roughness, electron inelastic and quasielastic scattering in elastic peak electron spectroscopy of polymers
Authors: Lesiak B. , Kosiński A. , Nowakowski R. , Kövér L. , Tóth J. , Varga D. , Cserny I. , Sulyok A. , Gergely G. 
Published: September 2007

AbstractIn elastic peak electron spectroscopy (EPES), the nearest vicinity of elastic peak in the low kinetic energy region reflects electron inelastic and quasielastic processes. Incident electrons produce surface excitations, inducing surface plasmons, with the corresponding loss peaks separated by 1–20 eV energy from the elastic peak.In this work, X‐ray photoelectron spectroscopy (XPS) and helium pycnometry are applied for determining surface atomic composition and bulk density, whereas atomic force microscopy (AFM) is applied for determining surface morphology and roughness. The component due to electron recoil on hydrogen atoms can be observed in EPES spectra for selected primary electron energies. Simulations of EPES predict a larger contribution of the hydrogen component than observed experimentally, where hydrogen deficiency is observed. Elastic peak intensity is influenced more strongly by surface morphology (roughness and porosity) than by surface excitations and quasielastic scattering of electrons by hydrogen atoms. Copyright © 2007 John Wiley & Sons, Ltd.