bluuebunny/crossref_metadata_2025_split huggingface dataset:
6‐Thioguanine in DNA as CD‐spectroscopic probe to study local structural changes upon protein binding
Authors: Repges Rudolf , Beuck Christine , Weinhold Elmar , Raabe Gerhard , Fleischhauer Jorg 
Published: February 2008

AbstractA combination of experimental and theoretical circular dichroism (CD) spectroscopy was used to study local deformations of DNA caused by binding of the base flipping DNA methyltransferase M.TaqI. To selectively study the structural changes within the DNA, we replaced single guanine residues at six different positions in duplex DNA with 6‐thioguanine (s6G), which absorbs at 342 nm where unmodified DNA and the enzyme are transparent. The shape and the transition wavelength of a CD signal around 340 nm in the spectra of the free DNA and the M.TaqI‐bound DNA were found to depend on the position of the s6G probe. Theoretical rotational strengths were calculated employing the matrix method which is frequently used to model the CD of large biomolecules. The only chromophores in these calculations were the nucleic acid bases. Comparison of the measured and the calculated CD spectra showed that the applied computational method qualitatively reproduces the dominant band observed around 340 nm in all cases. From our results we conclude that the spectral changes observed upon binding of the enzyme to the DNA are indeed predominantly due to structural changes within the DNA and not to other effects caused by the presence of the enzyme. Chirality, 2008. © 2008 Wiley‐Liss, Inc.
Fluidic communication between multiple vertically segregated microfluidic channels connected by nanocapillary array membranes
Authors: Gong Maojun , Flachsbart Bruce R. , Shannon Mark A. , Bohn Paul W. , Sweedler Jonathan V. 
Published: February 2008

AbstractHybrid microfluidic/nanofluidic devices offer unique capabilities for manipulating and analyzing minute volumes of expensive or hard‐to‐obtain samples. Here, multilayer poly‐(methyl methacrylate) microchips, with multiple spatially isolated microfluidic channels interconnected by nanocapillary array membranes (NCAMs), are fabricated using an adhesive contact printing process. The NCAMs, positioned between the microfluidic channel layers, add functionality to the inter‐microchannel fluid transfer unit operation. They do so because the transport of specific analytes through the NCAM can be controlled by adjusting the ionic strength, the polarity of the applied bias, the surface charge density, and the pore size. A simplified, floating injection technique for NCAM‐coupled nanofluidic devices is described and compared with conventional biased injection. In the floating injection approach, a voltage is applied across the injection channel and the slight electric field extension at the cross‐section is used to transfer analytes through the nanopores to the separation channel. Floating injection excels in plug reproducibility, separation resolution, and operation simplicity, although it decreases assay throughput relative to biased injection. Floating injection can avoid the uneven distribution of analytes in the microfluidic channel that sometimes results from biased injection because of the volume mismatch between NCAM nanopore transport capacity and the supply of fluid. Moreover, the pressure‐driven flow caused by the mismatch of the EOFs in the microfluidic channels connected by an NCAM must be considered when using NCAMs with pore diameters below 50 nm.
Assay of bradykinin‐related peptides in human body fluids using capillary electrophoresis with laser‐induced fluorescence detection
Authors: Chen Ying , Xu Liangjun , Lin Jinming , Chen Guonan 
Published: February 2008

AbstractA CE with LIF detection was developed for separation and determination of bradykinin (BK)‐related peptides, such as BK, kallidin (Kal), and neurokinin A (NKA). BK‐related peptides were derivatized with FITC prior to CE‐LIF analysis. Sodium borate 10 mmol/L at pH 9.5 was selected as derivatization media in order to get the high efficiency. Three peptides were baseline‐separated within 10 min by using 110 mmol/L sodium borate–sodium hydroxide solution at pH 10.0 as the running buffer. Concentration detection limits (S/N = 3) for BK, Kal, and NKA were 0.08, 0.5, and 0.2 nmol/L, respectively. Meanwhile we have also developed a simple, quick, and sensitive large‐volume sample stacking (LVSS) technique for CE‐LIF detection of BK, Kal, and NKA. By using this stacking technique, the detection limits (S/N = 3) for BK, Kal, and NKA were 0.02, 0.05, and 0.04 nmol/L, respectively. This method has been applied to the assay of human saliva and cerebrospinal fluid with satisfactory results.
Use of large‐volume sample stacking in on‐line solid‐phase extraction‐capillary electrophoresis for improved sensitivity
Authors: Puig Patricia , Tempels F. W. Alexander , Somsen Govert W. , de Jong Gerhardus J. , Borrull Francesc , Aguilar Carme , Calull Marta 
Published: February 2008

AbstractWe present a new system for the sensitive analysis of cephalosporins by CE using both on‐line SPE and large‐volume sample stacking (LVSS). Sample volumes of 250 μL were loaded onto the SPE microcolumn which was then desorbed with 426 nL of ACN. The SPE elution plug was injected into the CE system via an in‐line valve interface filling approximately 60% of the volume of the separation capillary. Subsequently, LVSS was performed by applying a voltage of −5 kV, which resulted in the simultaneous removal of the elution solvent and the preconcentration of the analytes in a narrow zone. This way the amount of analyte loaded into the capillary could be considerably increased without serious loss of CE separation efficiency. LODs for cefoperazone and ceftiofur were in the ng/L range which represents an improvement of a factor of 8450 and 11 450 when compared with direct CE injection. The cephalosporin test compounds presented a good linear response (corrected peak area) between 0.5 and 10 μg/L with correlation coefficients higher than 0.995. The final method is compared with previously reported LVSS‐CE and SPE‐CE systems for the analysis of cephalosporins.
Diversity of rice glutelin polypeptides in wild species assessed by the higher‐temperature sodium dodecyl sulfate‐polyacrylamide gel electrophoresis and subunit‐specific antibodies
Authors: Khan Nadar , Katsube‐Tanaka Tomoyuki , Iida Shuichi , Yamaguchi Takeshi , Nakano Junichi , Tsujimoto Hisashi 
Published: February 2008

AbstractIn efforts to find genetic resources with high nutritional value of rice seed, we assessed the diversity of the major storage protein glutelin in 13 wild and 2 cultivated rice species by a unique SDS‐PAGE method and subunit‐specific antibodies. Maximum separation of microheterogeneous glutelin α‐polypeptides, which is a prerequisite for the diversity evaluation, could be attained by SDS‐PAGE performed at higher temperature (45°C) than the generally employed temperatures (4–25°C). Seven antipeptide antibodies were raised against subunit‐specific epitope sequences designed at five sites from four variable regions spanning the glutelin α‐polypeptides. High specificity of each antibody was confirmed using rice glutelin mutants, and demonstrated considerable variation in amino acid sequence and accumulation level of glutelin subunit in wild species, in combination with the higher‐temperature SDS‐PAGE. The degree of the variation was, however, changed according to the site of variable regions and the type of subunit. Some wild species accumulated nutritious GluB subunits more than cultivated rice. The wild species Oryza longiglumis and O. brachyantha had glutelin with low reactivity against most antibodies examined in this study, reflecting the significant divergence. Such wild species may hopefully serve as important genetic resources for nutritional improvement of cultivated rice.
Performance of seismic‐isolated bridges with and without elastic‐gap devices in near‐fault zones
Authors: Dicleli Murat 
Published: February 2008

AbstractIn this paper, the efficiency of providing elastic‐gap devices (EGDs) to improve the performance of seismic‐isolated bridges (SIBs) in near‐fault (NF) zones is investigated. The device is primarily made of an assembly of circular rubber bearings and steel plates to provide additional elastic stiffness to the SIB upon closure of a gap. The EDG is intended to function at two performance levels under service and maximum considered design level (MCDL) NF earthquakes to reduce isolator displacements while keeping the substructure forces at reasonable levels. A parametric study, involving more than 500 nonlinear time history analyses of realistic and simplified structural models of typical SIBs, is conducted using simulated and actual NF ground motions to investigate the applicability of the proposed solution. It is found that providing EGD is beneficial for reducing the isolator displacements to manageable ranges for SIBs subjected to MCDL NF ground motions regardless of the distance from the fault and characteristics of the isolator. It is also found that providing EGD resulted in an improved performance of the isolators in terms of the reduction of heat generated by the isolators. Further analyses conducted using a realistic structural model of an existing bridge and five NF earthquakes confirmed that EGD may be used to reduce the displacement of the isolators while keeping the substructure base shear forces at reasonable ranges for SIBs located in NF zones. Copyright © 2008 John Wiley & Sons, Ltd.
Collapse simulation of a four‐story steel moment frame by a distributed online hybrid test
Authors: Wang Tao , McCormick Jason , Yoshitake Nobuya , Pan Peng , Murata Yosuke , Nakashima Masayoshi 
Published: February 2008

AbstractThe collapse of a one‐bay, four‐story steel moment frame is simulated in this study by the proposed peer‐to‐peer (P2P) Internet online hybrid test system. The typical beam hinging mechanism, which is ensured by a strong‐column, weak‐beam design, is reproduced. The plastic hinges at the column bases are taken as the experimental portions, while the superstructure is analyzed numerically by a general‐purpose finite element program. The implicit plastic rotations of the two column bases are treated as boundary displacements. In order to account for the complex behavior of the column bases, the P2P system is modified to use the secant stiffness during iterations, and the physical specimens are designed such that the plastic hinge behavior can be obtained. For this study, the three substructures are distributed to different locations. A large ground motion is repeatedly imposed until the column bases lose their capacity to sustain the gravity load. As a result, significant deterioration is observed at both column bases. The proposed P2P system is thus demonstrated to be able to accommodate multiple‐tested substructures involving unstable behavior. The results suggest that the P2P Internet online hybrid test system provides a reliable means of studying structures up to collapse. Copyright © 2008 John Wiley & Sons, Ltd.
Using neuropsychological feedback therapeutically in treatment for anorexia nervosa: two illustrative case reports
Authors: Lopez Carolina , Roberts Marion E. , Tchanturia Kate , Treasure Janet 
Published: February 2008

AbstractInformation processing in anorexia nervosa (AN) has been characterised as having a tendency to get trapped in detail, and having difficulties with set‐shifting. These characteristics can be addressed in treatment through personalised interventions targeting thinking styles and their role in the development and maintenance of an eating disorder (ED). This paper outlines a three‐session assessment and feedback module designed to identify and address these information processing biases. Two case reports are presented to illustrate the structure, content and outcome of the intervention. Both patients described the intervention as helpful in providing a structure and rationale for the steps required in recovery. The short nature and promising results of this intervention make it an attractive addition to current treatment programmes. Copyright © 2008 John Wiley & Sons, Ltd and Eating Disorders Association.
Genomewide scan of ocular refraction in African‐American families shows significant linkage to chromosome 7p15
Authors: Ciner Elise , Wojciechowski Robert , Ibay Grace , Bailey‐Wilson Joan E. , Stambolian Dwight 
Published: February 2008

AbstractRefractive development is influenced by environmental and genetic factors. Genetic studies have identified several regions of linkage to ocular refraction, but none have been carried out in African‐derived populations. We performed quantitative trait locus linkage analyses in African‐American (AA) families to identify genomic regions responsible for refraction. We recruited 493 AA individuals in 96 families to participate in the Myopia Family Study. Genotyping of 387 microsatellite markers was performed on 398 participants. The mean refraction among genotyped individuals was −2.87 D (SD=3.58) and myopia of at least 1 D was present in 267 (68%) participants. Multipoint, regression‐based, linkage analyses were carried out on a logarithmic transformation of ocular refraction using the statistical package MERLIN‐REGRESS. Empirical significance levels were determined via 4,898 whole‐genome gene‐dropping simulations. Linkage analyses were repeated after clustering families into two subgroups based on admixture proportions as determined by the software package STRUCTURE. Genomewide significant linkage was seen at 47 cM on chromosome 7 (logarithm of the odds ratio (LOD)=5.87, P=0.00005). In addition, three regions on chromosomes 2p, 3p and 10p showed suggestive evidence of linkage (LOD>2, P<0.005) for ocular refraction. We mapped the first quantitative trait locus for ocular refraction in an AA population to chr.7p15. Two previous studies in European‐derived families reported some evidence of linkage to a nearby region, suggesting that this region may contain polymorphisms that mediate refraction across populations. The genomic region under our linkage peak spans ∼17 Mb and contains ∼170 genes. Further refinement of this region will be pursued in future studies. Genet. Epidemiol. 2008. Published 2008 Wiley‐Liss, Inc.
GlialCAM, an immunoglobulin‐like cell adhesion molecule is expressed in glial cells of the central nervous system
Authors: Favre‐Kontula Linda , Rolland Alexandre , Bernasconi Lilia , Karmirantzou Maria , Power Christine , Antonsson Bruno , Boschert Ursula 
Published: February 2008

AbstractUsing structure based genome mining targeting vascular endothelial and platelet derived growth factor immunoglobulin (Ig) like folds, we have identified a sequence corresponding to a single transmembrane protein with two Ig domains, which we cloned from a human brain cDNA library. The cDNA is identical to hepatocyte cell adhesion molecule (hepaCAM), which was originally described as a tumor suppressor gene in liver. Here, we show that the protein is predominantly expressed in the mouse and human nervous system. In liver, the expression is very low in humans, and is not detected in mice. To identify the central nervous system (CNS) regions and cell types expressing the protein, we performed a LacZ reporter gene assay on heterozygous mice in which one copy of the gene encoding the novel protein had been replaced with β‐galactosidase. β‐galactosidase expression was prominent in white matter tracts of the CNS. Furthermore, expression was detected in ependymal cells of the brain ventricular zones and the central canal of the spinal cord. Double labeling experiments showed expression mainly in CNPase positive oligodendrocytes (OL). Since the protein is predominantly expressed in the CNS glial cells, we named the molecule glial cell adhesion molecule (GlialCAM). A potential role for GlialCAM in myelination was supported by its up‐regulation during postnatal mouse brain development, where it was concomitantly expressed with myelin basic protein (MBP). In addition, in vitro, GlialCAM was observed in various developmental stages of OL and in astrocytes in processes and at cell contact sites. In A2B5 positive OL, GlialCAM colocalizes with GAP43 in OL growth cone like structures. Overall, the data presented here indicate a potential function for GlialCAM in glial cell biology. © 2008 Wiley‐Liss, Inc.
Leukemia inhibitory factor signaling modulates both central nervous system demyelination and myelin repair
Authors: Marriott Mark P. , Emery Ben , Cate Holly S. , Binder Michele D. , Kemper Dennis , Wu Qizhu , Kolbe Scott , Gordon Ian R. , Wang Hong , Egan Gary , Murray Simon , Butzkueven Helmut , Kilpatrick Trevor J. 
Published: February 2008

AbstractLeukemia inhibitory factor (LIF) receptor signaling limits the severity of inflammatory demyelination in experimental autoimmune encephalomyelitis, a T‐cell dependent animal model of multiple sclerosis (MS) [Butzkueven et al. (2002) Nat Med 8:613–619]. To identify whether LIF exerts direct effects within the central nervous system to limit demyelination, we have studied the influence of LIF upon the phenotype of mice challenged with cuprizone, a copper chelator, which produces a toxic oligodendrocytopathy. We find that exogenously administered LIF limits cuprizone‐induced demyelination. Knockout mice deficient in LIF exhibit both potentiated demyelination and oligodendrocyte loss after cuprizone challenge, an effect that is ameliorated by exogenous LIF, arguing for a direct beneficial effect of endogenous LIF receptor signaling. Numbers of oligodendrocyte progenitor cells in cuprizone‐challenged mice are not influenced by either exogenous LIF or LIF deficiency, arguing for effects directed to the differentiated oligodendrocyte. Studies on the influence of LIF upon remyelination after cuprizone challenge fail to reveal any significant effect of exogenous LIF. The LIF‐knockout mice do, however, display impaired remyelination, although oligodendrocyte replenishment, previously identified to occur from the progenitor pool, is not significantly compromised. Thus endogenous LIF receptor signaling is not only protective of oligodendrocytes but can also enhance remyelination, and exogenous LIF has therapeutic potential in limiting the consequences of oligodendrocyte damage. © 2008 Wiley‐Liss, Inc.
Transforming growth factor‐activated kinase 1 induced in spinal astrocytes contributes to mechanical hypersensitivity after nerve injury
Authors: Katsura Hirokazu , Obata Koichi , Miyoshi Kan , Kondo Takashi , Yamanaka Hiroki , Kobayashi Kimiko , Dai Yi , Fukuoka Tetsuo , Sakagami Masafumi , Noguchi Koichi 
Published: February 2008

AbstractMitogen‐activated protein kinase (MAPK) plays an important role in the induction and maintenance of neuropathic pain. Transforming growth factor‐activated kinase 1 (TAK1), a member of the MAPK kinase kinase family, is indispensable for the activation of c‐Jun N‐terminal kinase (JNK) and p38 MAPK. We now show that TAK1 induced in spinal cord astrocytes is crucial for mechanical hypersensitivity after peripheral nerve injury. Nerve injury induced a striking increase in the expression of TAK1 in the ipsilateral dorsal horn, and TAK1 was increased in hyperactive astrocytes, but not in neurons or microglia. Intrathecal administration of TAK1 antisense oligodeoxynucleotide (AS‐ODN) prevented and reversed nerve injury‐induced mechanical, but not heat hypersensitivity. Furthermore, TAK1 AS‐ODN suppressed the activation of JNK1, but not p38 MAPK, in spinal astrocytes. In contrast, there was no change in TAK1 expression in primary sensory neurons, and TAK1 AS‐ODN did not attenuate the induction of transient receptor potential ion channel TRPV1 in sensory neurons. Taken together, these results demonstrate that TAK1 upregulation in spinal astrocytes has a substantial role in the development and maintenance of mechanical hypersensitivity through the JNK1 pathway. Thus, preventing the TAK1/JNK1 signaling cascade in astrocytes might provide a fruitful strategy for treating intractable neuropathic pain. © 2008 Wiley‐Liss, Inc.
Overexpression of CXCL16 and its receptor CXCR6/Bonzo promotes growth of human schwannomas
Authors: Held‐Feindt Janka , Rehmke Brigitte , Mentlein Rolf , Hattermann Kirsten , Knerlich Friederike , Hugo Heinz‐Hermann , Ludwig Andreas , Mehdorn H. Maximilian 
Published: February 2008

AbstractChemokines and their receptors play a decisive role in tumor progression and metastasis. Here, we describe the expression of the CXCL16‐CXCR6‐system in human schwannomas of different localization and in malignant peripheral nerve sheath tumors. The transmembrane chemokine CXCL16 and its receptor CXCR6/Bonzo were overexpressed on the mRNA and protein levels in all tumor samples investigated as compared with normal peripheral or 8th cranial nerve tissues. Chromogenic immunostaining and confocal laser microscopy revealed that CXCL16 and CXCR6 were localized mainly on S‐100 positive schwannoma cells. Cultured schwannoma cells responded to CXCL16‐stimulation by phosphorylation of kinases p42/44 (Erk 2/1) that could be inhibited by the MEK1/2‐inhibitor U0126 indicating an involvement of the mitogen‐activated protein kinase signal transduction pathway. As a biological response, CXCL16 increased proliferation and induced migration of schwannomas. Hence, CXCL16 appears to be a novel growth factor for schwannomas of different localization. © 2008 Wiley‐Liss, Inc.
Adsorption of benzene, fluorobenzene and meta‐di‐fluorobenzene on Cu(110): A computational study
Authors: Zotti L. A. , Teobaldi G. , Palotás K. , Ji W. , Gao H.‐J. , Hofer W. A. 
Published: February 2008

AbstractWe modelled the adsorption of benzene, fluorobenzene and meta‐di‐fluorobenzene on Cu(110) by Density Functional Theory. We found that the adsorption configuration depends on the coverage. At high coverage, benzene assumes a tilted position, while at low coverage a horizontal slightly distorted geometry is favoured. Functionalizing the benzene ring with one or two fluorine atoms weakens the bonding to the surface. A rotation is induced, which decreases the distance of the fluorine atom from the surface. STM simulations reveal that details about both, benzene adsorption geometry and fluorine position, can be only detected at short tip‐surface distances. © Crown copyright 2008. J Comput Chem 2008
Q‐Dock: Low‐resolution flexible ligand docking with pocket‐specific threading restraints
Authors: Brylinski Michal , Skolnick Jeffrey 
Published: February 2008

AbstractThe rapidly growing number of theoretically predicted protein structures requires robust methods that can utilize low‐quality receptor structures as targets for ligand docking. Typically, docking accuracy falls off dramatically when apo or modeled receptors are used in docking experiments. Low‐resolution ligand docking techniques have been developed to deal with structural inaccuracies in predicted receptor models. In this spirit, we describe the development and optimization of a knowledge‐based potential implemented in Q‐Dock, a low‐resolution flexible ligand docking approach. Self‐docking experiments using crystal structures reveals satisfactory accuracy, comparable with all‐atom docking. All‐atom models reconstructed from Q‐Dock's low‐resolution models can be further refined by even a simple all‐atom energy minimization. In decoy‐docking against distorted receptor models with a root‐mean‐square deviation, RMSD, from native of ∼3 Å, Q‐Dock recovers on average 15‐20% more specific contacts and 25–35% more binding residues than all‐atom methods. To further improve docking accuracy against low‐quality protein models, we propose a pocket‐specific protein–ligand interaction potential derived from weakly homologous threading holo‐templates. The success rate of Q‐Dock employing a pocket‐specific potential is 6.3 times higher than that previously reported for the Dolores method, another low‐resolution docking approach. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008