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Potential Functions (potential + function)
Selected AbstractsObstacle Avoidance for Spatial Hyper-Redundant Manipulators Using Harmonic Potential Functions and the Mode Shape TechniqueJOURNAL OF FIELD ROBOTICS (FORMERLY JOURNAL OF ROBOTIC SYSTEMS), Issue 1 2003F. Fahimi This paper deals with the obstacle avoidance problem for spatial hyper-redundant manipulators in known environments. The manipulator is divided into two sections, a proximal section that has not entered the space among the obstacles and a distal section among the obstacles. Harmonic potential functions are employed to achieve obstacle avoidance for the distal section in three-dimensional space in order to avoid local minima in cluttered environments. A modified panel method is used to generate the potential of any arbitrary shaped obstacle in three-dimensional space. An alternative backbone curve concept and an efficient fitting method are introduced to control the trajectory of proximal links. The fitting method is recursive and avoids the complications involved with solving large systems of nonlinear algebraic equations. The combination of a three-dimensional safe path derived from the harmonic potential field and the backbone curve concept leads to an elegant kinematic control strategy that guarantees obstacle avoidance. © 2003 Wiley Periodicals, Inc. [source] Solid-State Structure and Tautomerism of 2-Aminotroponimines Studied by X-ray Crystallography and Multinuclear NMR SpectroscopyEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 21 2004Rosa M. Claramunt Abstract Structural studies in the solid state by X-ray crystallography and by 13C and 15N CPMAS NMR spectroscopy carried out on a series of 2-aminotroponimine derivatives 2,5 has allowed to establish the existence of hydrogen bonding and to determine the most stable tautomer. Almost all the structures reflect the classical double-well potential function for the N,H···N hydrogen bonds. Only in the case of the compound N -(pyrrol-1-yl)-2-(pyrrol-1-ylamino)troponimine (5) the crystal structure shows two independent molecules, one with a classical hydrogen bond and another with either a single-well or a low-barrier hydrogen bond. The structure of this compound is discussed with the use of the solid-state NMR spectroscopic data. 2-Aminotropones, as intermediates to the 2-aminotroponimines, show the oxo-tautomer as the stable form. B3LYP/6-31G* calculations are used to rationalise the experimental results. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Analytical Methods for Transient Flow to a Well in a Confined-Unconfined AquiferGROUND WATER, Issue 4 2008Li-Tang Hu Concurrent existence of confined and unconfined zones of an aquifer can arise owing to ground water withdrawal by pumping. Using Girinskii's potential function, Chen (1974, 1983) developed an approximate analytical solution to analyze transient ground water flow to a pumping well in an aquifer that changes from an initially confined system to a system with both unconfined and confined regimes. This article presents the details of the Chen model and then compares it with the analytical model developed by Moench and Prickett (1972) for the same problem. Hypothetical pumping test examples in which the aquifer undergoes conversion from confined to water table conditions are solved by the two analytical models and also a numerical model based on MODFLOW. Comparison of the results suggests that the solutions of the Chen model give better results than the Moench and Prickett model except when the radial distance is very large or aquifer thickness is large compared with drawdown. [source] Analysis of Steady Ground Water Flow Toward Wells in a Confined-Unconfined AquiferGROUND WATER, Issue 4 2006Chen Chong-Xi A confined aquifer may become unconfined near the pumping wells when the water level falls below the confining unit in the case where the pumping rate is great and the excess hydraulic head over the top of the aquifer is small. Girinskii's potential function is applied to analyze the steady ground water flow induced by pumping wells with a constant-head boundary in a mixed confined-unconfined aquifer. The solution of the single-well problem is derived, and the critical radial distance at which the flow changes from confined to unconfined condition is obtained. Using image wells and the superposition method, an analytic solution is presented to study steady ground water flow induced by a group of pumping wells in an aquifer bounded by a river with constant head. A dimensionless function is introduced to determine whether a water table condition exists or not near the pumping wells. An example with three pumping wells is used to demonstrate the patterns of potentiometric surface and development of water table around the wells. [source] Can a physics-based, all-atom potential find a protein's native structure among misfolded structures?JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2007Abstract Recent work has shown that physics-based, all-atom energy functions (AMBER, CHARMM, OPLS-AA) and local minimization, when used in scoring, are able to discriminate among native and decoy structures. Yet, there have been only few instances reported of the successful use of physics based potentials in the actual refinement of protein models from a starting conformation to one that ends in structures, which are closer to the native state. An energy function that has a global minimum energy in the protein's native state and a good correlation between energy and native-likeness should be able to drive model structures closer to their native structure during a conformational search. Here, the possible reasons for the discrepancy between the scoring and refinement results for the case of AMBER potential are examined. When the conformational search via molecular dynamics is driven by the AMBER potential for a large set of 150 nonhomologous proteins and their associated decoys, often the native minimum does not appear to be the lowest free energy state. Ways of correcting the potential function in order to make it more suitable for protein model refinement are proposed. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Quantum chemical geometry optimizations in proteins using crystallographic raw dataJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2002Ulf Ryde Abstract A method is developed for the combination of quantum chemical geometry optimizations and crystallographic structure refinement. The method is implemented by integrating the quantum chemical software Turbomole with the crystallographic software Crystallography and NMR System (CNS), using three small procedures transferring information between the two programs. The program (COMQUM-X)is used to study the binding of the inhibitor N -methylmesoporphyrin to ferrochelatase, and we show that the method behaves properly and leads to an improvement of the structure of the inhibitor. It allows us to directly quantify in energy terms how much the protein distort the structure of the bound inhibitor compared to the optimum vacuum structure (4,6 kJ/mol). The approach improves the standard combined quantum chemical and molecular mechanics (QC/MM) approach by guaranteeing that the final structure is in accordance with experimental data (the reflections) and avoiding the risk of propagating errors in the crystal coordinates. The program can also be seen as an improvement of standard crystallographic refinement, providing an accurate empirical potential function for any group of interest. The results can be directly interpreted in standard crystallographic terms (e.g., R factors or electron density maps). The method can be used to interpret crystal structures (e.g., the protonation status of metal-bound water molecules) and even to locally improve them. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1058,1070, 2002 [source] Variational treatment of the vibrational Hamiltonian for NH3 and H2NOJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2002Philippe Marsal Abstract The full vibrational Hamiltonian for the inversion of NH3 and H2NO has been diagonalized in a basis set that is the direct product of functions of the inversion coordinate and of harmonic vibrational functions independent of this inversion coordinate. The kinetic part of the Hamiltonian matrix is constructed with the use of the closure relation for these vibrational functions. The method is tested with the potential function which is supposed to be harmonic for the vibrations orthogonal to the inversion coordinate: the first computed levels are in good agreement with experimental levels for NH3. For higher levels, anharmonic terms should be included. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 541,547, 2002; DOI 10.1002/jcc.10033 [source] A Class of Transpose Jacobian-based NPID Regulators for Robot Manipulators with an Uncertain KinematicsJOURNAL OF FIELD ROBOTICS (FORMERLY JOURNAL OF ROBOTIC SYSTEMS), Issue 11 2002C. Q. Huang Transpose Jacobian-based controllers present an attractive approach to robot set-point control in Cartesian space that derive the end-effector posture to a specified desired position and orientation with neither solving the inverse kinematics nor computing the inverse Jacobian. By a Lyapunov function with virtual artificial potential energy, a class of complete transpose Jacobian-based Nonlinear proportional-integral-derivative regulators is proposed in this paper for robot manipulators with uncertain kinematics on the basis of the set of all continuous differentiable increasing functions. It shows globally asymptotic stability for the result closed-loop system on the condition of suitable feedback gains and suitable parameter selection for the corresponding function set as well as artificial potential function, and only upper bound on Jacobian matrix error and Cartesian dynamics parameters are needed. The existing linear PID (LPID) regulators are the special cases of it. Nevertheless, in the case of LPID regulators, only locally asymptotic stability is guaranteed if the corresponding conditions are satisfied. Simulations demonstrate the result and robustness of transpose Jacobian-based NPID regulators. © 2002 Wiley Periodicals, Inc. [source] Building and navigating a network of local minimaJOURNAL OF FIELD ROBOTICS (FORMERLY JOURNAL OF ROBOTIC SYSTEMS), Issue 8 2001Seung-Woo Kim We present a novel method that constructs and navigates a network of local minima of potential fields defined over multidimensional spaces. Though motivated by problems of motion planning for robotic manipulators, similar techniques have been proposed for use in other domains such as molecular chemistry and drug design. The method is based on building a roadmap of paths connecting local minima of a potential function. The novel approach consists of an up-hill search strategy used to climb out of local minima and find new nearby local minima, without doubling back on previous local minima. With this up-hill search strategy, one can find local minima otherwise difficult to encounter, and one can focus the search to specific local minima and specific directions from those local minima. The construction of the roadmap can be done in parallel with very little communication. We present extensive simulation results. © 2001 John Wiley & Sons, Inc. [source] BDNF activated TrkB/IRR receptor chimera promotes survival of sympathetic neurons through Ras and PI-3 kinase signalingJOURNAL OF NEUROSCIENCE RESEARCH, Issue 2 2002Karen S. Kelly-Spratt Insulin receptor-related receptor (IRR) expression is tightly coupled to the nerve growth factor (NGF) receptor, TrkA, throughout development. Expression of both receptors is primarily localized to neural crest derived sensory and sympathetic neurons. In contrast to TrkA, however, the physiological ligand for IRR is unknown. To analyze the intracellular signaling and potential function of the orphan IRR in neurons, an adenovirus expressing a TrkB/IRR chimeric receptor was used to infect cultured mouse superior cervical ganglion neurons that normally require NGF for survival. Brain derived neurotrophic factor (BDNF)-activated TrkB/IRR induced neuronal survival. We utilized numerous receptor mutants in order to identify the intracellular domains of IRR necessary for signaling and neuron survival. Finally, we employed adenovirus encoding dominant negative forms of the extracellular signal-regulated kinase (ERK) signaling cascade to demonstrate that IRR, like TrkA, requires ras activation to promote neuron survival. Therefore, by use of the chimeric TrkB/IRR receptor, we have demonstrated the ability of IRR to elicit activation of signaling cascades resulting in a biological response in superior cervical ganglion (SCG) neurons. © 2002 Wiley-Liss, Inc. [source] Positive solutions and multiple solutions for periodic problems driven by scalar p -LaplacianMATHEMATISCHE NACHRICHTEN, Issue 12 2006Shouchuan Hu Abstract In this paper we study a nonlinear second order periodic problem driven by a scalar p -Laplacian and with a nonsmooth, locally Lipschitz potential function. Using a variational approach based on the nonsmooth critical point theory for locally Lipschitz functions, we first prove the existence of nontrivial positive solutions and then establish the existence of a second distinct solution (multiplicity theorem) by strengthening further the hypotheses. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] A projected-steepest-descent potential-reduction algorithm for convex programming problemsNUMERICAL LINEAR ALGEBRA WITH APPLICATIONS, Issue 10 2004Yixun Shi Abstract A recent work of Shi (Numer. Linear Algebra Appl. 2002; 9: 195,203) proposed a hybrid algorithm which combines a primal-dual potential reduction algorithm with the use of the steepest descent direction of the potential function. The complexity of the potential reduction algorithm remains valid but the overall computational cost can be reduced. In this paper, we make efforts to further reduce the computational costs. We notice that in order to obtain the steepest descent direction of the potential function, the Hessian matrix of second order partial derivatives of the objective function needs to be computed. To avoid this, we in this paper propose another hybrid algorithm which uses a projected steepest descent direction of the objective function instead of the steepest descent direction of the potential function. The complexity of the original potential reduction algorithm still remains valid but the overall computational cost is further reduced. Our numerical experiments are also reported. Copyright © 2004 John Wiley & Sons, Ltd. [source] Configurational-bias sampling technique for predicting side-chain conformations in proteinsPROTEIN SCIENCE, Issue 9 2006Tushar Jain Abstract Prediction of side-chain conformations is an important component of several biological modeling applications. In this work, we have developed and tested an advanced Monte Carlo sampling strategy for predicting side-chain conformations. Our method is based on a cooperative rearrangement of atoms that belong to a group of neighboring side-chains. This rearrangement is accomplished by deleting groups of atoms from the side-chains in a particular region, and regrowing them with the generation of trial positions that depends on both a rotamer library and a molecular mechanics potential function. This method allows us to incorporate flexibility about the rotamers in the library and explore phase space in a continuous fashion about the primary rotamers. We have tested our algorithm on a set of 76 proteins using the all-atom AMBER99 force field and electrostatics that are governed by a distance-dependent dielectric function. When the tolerance for correct prediction of the dihedral angles is a <20° deviation from the native state, our prediction accuracies for ,1 are 83.3% and for ,1 and ,2 are 65.4%. The accuracies of our predictions are comparable to the best results in the literature that often used Hamiltonians that have been specifically optimized for side-chain packing. We believe that the continuous exploration of phase space enables our method to overcome limitations inherent with using discrete rotamers as trials. [source] Protein,protein docking with multiple residue conformations and residue substitutionsPROTEIN SCIENCE, Issue 6 2002David M. Lorber Abstract The protein docking problem has two major aspects: sampling conformations and orientations, and scoring them for fit. To investigate the extent to which the protein docking problem may be attributed to the sampling of ligand side-chain conformations, multiple conformations of multiple residues were calculated for the uncomplexed (unbound) structures of protein ligands. These ligand conformations were docked into both the complexed (bound) and unbound conformations of the cognate receptors, and their energies were evaluated using an atomistic potential function. The following questions were considered: (1) does the ensemble of precalculated ligand conformations contain a structure similar to the bound form of the ligand? (2) Can the large number of conformations that are calculated be efficiently docked into the receptors? (3) Can near-native complexes be distinguished from non-native complexes? Results from seven test systems suggest that the precalculated ensembles do include side-chain conformations similar to those adopted in the experimental complexes. By assuming additivity among the side chains, the ensemble can be docked in less than 12 h on a desktop computer. These multiconformer dockings produce near-native complexes and also non-native complexes. When docked against the bound conformations of the receptors, the near-native complexes of the unbound ligand were always distinguishable from the non-native complexes. When docked against the unbound conformations of the receptors, the near-native dockings could usually, but not always, be distinguished from the non-native complexes. In every case, docking the unbound ligands with flexible side chains led to better energies and a better distinction between near-native and non-native fits. An extension of this algorithm allowed for docking multiple residue substitutions (mutants) in addition to multiple conformations. The rankings of the docked mutant proteins correlated with experimental binding affinities. These results suggest that sampling multiple residue conformations and residue substitutions of the unbound ligand contributes to, but does not fully provide, a solution to the protein docking problem. Conformational sampling allows a classical atomistic scoring function to be used; such a function may contribute to better selectivity between near-native and non-native complexes. Allowing for receptor flexibility may further extend these results. [source] Versican expression during skeletal/joint morphogenesis and patterning of muscle and nerve in the embryonic mouse limbTHE ANATOMICAL RECORD : ADVANCES IN INTEGRATIVE ANATOMY AND EVOLUTIONARY BIOLOGY, Issue 2 2005Holly E. Snow Abstract Versican, an extracellular matrix proteoglycan, has been implicated in limb development and is expressed in precartilage mesenchymal condensations. However, studies have lacked precise spatial and temporal investigation of versican localization during skeletogenesis and its relationship to patterning of muscle and nerve during mammalian limb development. The transgenic mouse line hdf (heart defect), which bears a lacZ reporter construct disrupting Cspg2 encoding versican, allowed ready detection of hdf transgene expression through histochemical analysis. Hdf transgene expression in whole mount heterozygous embryos and localization of versican relative to cartilage, muscle, and nerve tissues in paraffin-embedded limb sections of wild-type embryos from 10.5,14 days postcoitum were evaluated by lacZ histochemistry, immunohistochemistry, and in situ hybridization. Versican was localized within precartilage condensations and nascent cartilages with expression diminishing during maturation of the cartilage model at later time points. Interestingly, versican remained highly expressed in developing synovial joint interzones, suggesting potential function for versican in joint morphogenesis. Isolated myoblasts, incipient skeletal muscle masses, and neurites were not present in areas of strong versican expression within the developing limb. Versican-expressing tissues may reserve space for the future limb skeleton and developing joints and may aid in patterning of muscle and nerve by deterring muscle migration and innervation into these regions. © 2005 Wiley-Liss, Inc. [source] Non-redundant inhibitor of differentiation (Id) gene expression and function in human prostate epithelial cellsTHE PROSTATE, Issue 9 2006Ananthi J. Asirvatham Abstract BACKGROUND The four Id (inhibitor of differentiation) proteins (Id1, Id2, Id3, and Id4) dimerize and neutralize the transcriptional activity of basic helix-loop-helix (bHLH) proteins. The Id proteins negatively regulate differentiation and promote proliferation hence the expression of specific subsets of Id proteins is high in many different types of cancers. However, the expression of all the Id isoforms and their potential function in specific cancer cell types is not known. In this study, the expression and function of all four Id isoforms in prostate cancer cell lines was investigated to gain a better understanding of the role of each Id isoform in normal prostate epithelial and prostate cancer cells. METHODS Id gene and protein expression was evaluated in the context of androgen response. The cellular function of Id isoforms was evaluated by targeted loss of function of Id genes. RESULTS The four Id isoforms are differentially expressed and regulated in normal human prostate epithelial cells versus prostate cancer cell lines DU145 and LNCaP. Id4 is present only in AR positive cells (normal and LNCaP) and its expression regulated by androgens. Loss of Id1 and Id3 expression by siRNA results in loss of proliferation. Loss of Id2 had no effect on proliferation but increased apoptosis. CONCLUSIONS A complex equilibrium between Id isoforms determines the cell fate. Id1 and Id3 target cellular proliferation, Id2 targets apoptosis, and Id4 may act as a potential tumor suppressor in prostate epithelial cells. Prostate 66: 921,935, 2006. © 2006 Wiley-Liss, Inc. [source] Genomic structure, chromosomal localization and expression profile of a porcine long non-coding RNA isolated from long SAGE librariesANIMAL GENETICS, Issue 4 2009H. Ren Summary Long non-coding RNA (long ncRNA) is a novel class of ncRNA that may be involved in critical cellular processes. A considerable number of mammalian long ncRNAs have now been isolated but only a small number of these nucleic acids have been functionally well characterized. In this study, to determine the structure, regulation and function of long ncRNA in pigs, TncRNA was isolated from this mammal and its potential function during pig foetus development was identified. We anticipated that this would provide new insights into functional genomic studies in the pig. Using LongSAGE libraries generated from Chinese indigenous Tongcheng and Landrace pigs at three prenatal stages, a novel porcine long ncRNA was identified, TncRNA, which was found to be differentially expressed during myogenesis. The full-length cDNA for this gene is 3409 bp, and it harbours a typical polyadenylation signal sequence located 18 bp upstream from the 3, poly (A) tail. Genomic sequence analysis showed that pig TncRNA is alternatively spliced and several transcripts were detected. Using the INRA,University of Minnesota porcine radiation hybrid panel, TncRNA was assigned to SSC2 and found to be closely linked to the microsatellite marker SW256. Porcine TncRNA was found to be expressed in all tissues examined but in variable amounts. Comparisons between the expression profiles of TncRNA at different development stages in Tongcheng and Landrace pigs revealed up-regulation of this molecule in prenatal skeletal muscle, and differential expression in 90-day-old foetal skeletal muscle between these two pig breeds. This is the first report to describe a long ncRNA in pig. Moreover, the distinct expression pattern and structure of porcine TncRNA suggest that it performs complex and critical functions during foetal development. [source] Defining the glycophenotype of squamous epithelia using plant and mammalian lectins.APMIS, Issue 12 20023-linked N-acetylneuraminic acid in squamous epithelia, Differentiation-dependent expression of, carcinomas, its differential effect on binding of the endogenous lectins galectins- A thorough characterization of the properties of squamous epithelial cells is necessary in order to improve our understanding of the functional aspects of normal development and malignant aberrations. Up to now, studies have focused almost exclusively on monitoring distinct protein markers. With our growing awareness of the coding function of glycan chains of cellular glycoconjugates and their interaction with receptors (lectins) in situ, defining the glycophenotype of these cells has become an important issue. Whereas the commonly applied plant lectins are tools used to map the presence and localization of biochemically defined saccharide epitopes, the introduction of endogenous (mammalian) lectins to this analysis enables us to take the step from monitoring the presence of glycan to understanding the functional implications by revealing ligand properties of the detected epitope for tissue lectin. Thus, in this study we investigated a distinct aspect of glycosylation using plant and mammalian lectins, i.e. the linkage type of sialylation. We first mapped the expression profile of the type of sialylation (,2,3- or ,2,6-linked) by plant lectins. Based on the hypothesis that this factor regulates accessibility of ligands for endogenous lectins we introduced two labeled galectins to this study. Galectin-3 (but not galectin-1) binding was related to cell differentiation in normal adult and developing epithelia, cultured epidermal cells, and carcinomas derived from these epithelia. The presented data suggest that ,2,6-linked N-acetyl- D -neuraminic acid moieties could serve to mask galectin-3-reactive glycoepitopes. As a consequence, monitoring of the linkage type of sialic acid in glycans by plant lectins therefore has implications for the extent of glycan reactivity with endogenous lectins, pointing to a potential function of changes in sialylation type beyond these cell and lectin systems. [source] A new potential field method for mobile robot path planning in the dynamic environmentsASIAN JOURNAL OF CONTROL, Issue 2 2009Lu Yin Abstract A new potential field method for mobile robot path planning is proposed in this paper. At present, most potential field methods are designed to be applied in the stationary environment, and several improved potential functions have brought in the velocity factors in the dynamic circumstances. Based on the consideration that the moving trend of the robot in the dynamic environments is also necessary to produce more reasonable path, this paper defines new attractive potential function with respect to the relative position, velocity, and acceleration between the robot and the goal, as well as the repulsive potential function with respect to the relative positions, velocities, and accelerations between the robot and the obstacles. The virtual forces are calculated to make the robot plan its motion, not only with right positions, but also with suitable velocities. Furthermore, the robot will keep a similar moving trend with the goal and contrary trends with the obstacles. Finally, some methodic simulations are carried out to validate and demonstrate the effectiveness of the new potential field method. Copyright © 2009 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society [source] Neuronal FasL Induces Cell Death of Encephalitogenic T LymphocytesBRAIN PATHOLOGY, Issue 3 2000A. Flügel Apoptosis of inflammatory cells plays a crucial role in the recovery from autoimmune CNS disease. However, the underlying mechanisms of apoptosis induction are as yet ill-defined. Here we report on the neuronal expression of FasL and its potential function in inducing T-cell apoptosis. Using a combination of facial nerve axotomy and passive transfer encephalomyelitis, the fate of CD4+ encephalitogenic T cells engineered to express the gene for green fluorescent protein was followed. FasL gene transcripts and FasL protein were detected in neurons by in situ -hybridization and immunohistochemistry. T cells infiltrating preferentially the injured brain parenchyma were found in the immediate vicinity of FasL expressing neurons and even inside their perikarya. In contrast to neurons, T cells rapidly underwent apoptosis. In co-cultures of hippocampal nerve cells and CD4+ T lymphocytes, we confirmed expression of FasL in neurons and concomitant induction of T-cell death. Antibodies blocking neuronal FasL were shown to have a protective effect on T-cell survival. Thus, FasL expression by neurons in neuroinflammatory diseases may constitute a pivotal mechanism underlying apoptosis of encephalitogenic T cells. [source] Maternal expression and function of the Drosophila sox gene Dichaete during oogenesisDEVELOPMENTAL DYNAMICS, Issue 10 2006Ashim Mukherjee Abstract Members of the Sox family of DNA-binding HMG domain proteins have been shown to regulate gene transcription in a wide range of developmental processes, including sex determination, neurogenesis, and chondrogenesis. However, little is known about their potential functions in developing germline tissues. In Drosophila, the Sox protein Dichaete (a.k.a., Fish-hook) is a member of the SoxB subgroup whose HMG domain shares strong sequence similarity to that of vertebrate Sox2. Dichaete exhibits dynamic expression in embryonic and larval stages and has pleiotropic functions in a variety of tissues. In this study, we extend analyses of Dichaete function and show that expression of Dichaete protein is detected in the developing oocyte during early to mid stages of oogenesis. Strikingly, Dichaete exhibits cytoplasmic distribution and is not detected in the oocyte nucleus. Germline mosaic analyses revealed that the Dichaete gene has maternal functions that influence dorsal/ventral patterning of the egg chamber. Dichaete mutant eggs exhibit defects in formation of the dorsal appendages, differentiation of dorsal/anterior follicle cells, and mislocalization of Gurken protein and gurken mRNA. Dichaete protein was shown to possess RNA-binding capabilities, suggesting a direct post-transcriptional role in regulating RNA functions. Developmental Dynamics 235:2828,2835, 2006. © 2006 Wiley-Liss, Inc. [source] The spatio-temporal and subcellular expression of the candidate Down syndrome gene Mnb/Dyrk1A in the developing mouse brain suggests distinct sequential roles in neuronal developmentEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 5 2008Barbara Hämmerle Abstract It is widely accepted that the neurological alterations in Down syndrome (DS) are principally due to modifications in developmental processes. Accordingly, a large part of the research on DS in recent years has focused on chromosome 21 genes that influence brain development. MNB/DYRK1A is one of the genes on human chromosome 21 that has raised most interest, due to its relationship with the brain functions that are altered in DS. Although a number of interesting experimental mouse models for DS are being developed, we still know little about the expression of Mnb/Dyrk1A during mouse brain development. Here, we report that Mnb/Dyrk1A displays a rather dynamic spatio-temporal expression pattern during mouse central nervous system development. Our data indicate that Mnb/Dyrk1A is specifically expressed in four sequential developmental phases: transient expression in preneurogenic progenitors, cell cycle-regulated expression in neurogenic progenitors, transient expression in recently born neurones, and persistent expression in late differentiating neurones. Our results also suggest that the subcellular localization of MNB/DYRK1A, including its translocation to the nucleus, is finely regulated. Thus, the MNB/DYRK1A protein kinase could be a key element in the molecular machinery that couples sequential events in neuronal development. This rich repertoire of potential functions in the developing central nervous system is suitable to be linked to the neurological alterations in DS through the use of mouse experimental models. [source] Role of ceramide kinase in peroxisome proliferator-activated receptor beta-induced cell survival of mouse keratinocytesFEBS JOURNAL, Issue 15 2008Kiyomi Tsuji Ceramide (Cer) is known to be a lipid mediator in apoptosis and to have an important role in cell fate, via control of intracellular Cer levels. Recently, ceramide kinase (CerK) was identified as an enzyme that converts Cer to ceramide 1-phosphate (C1P). We examined potential functions of CerK in the regulation of keratinocyte survival, and the possible involvement of peroxisome proliferator-activated receptor beta (PPAR,). PPAR, is known to be a nuclear receptor acting as a ligand-inducible transcription factor and has been implicated in the control of keratinocyte survival. In the mouse keratinocyte cell line SP1, serum starvation induced cell death and the accumulation of intracellular Cer, an apoptotic event. However, apoptosis was inhibited by activation of PPAR,. Interestingly, activation of PPAR, enhanced the mRNA expression of CerK and CerK activity. Furthermore, the cell survival effect of PPAR, was greatly diminished in keratinocytes isolated from CerK-null mice. Chromatin immunoprecipitation revealed that, in vivo, PPAR, binds to the CerK gene via a sequence located in the first intron. Electrophoretic mobility-shift assays confirmed that PPAR, associates with this sequence in vitro. These findings indicated that CerK gene expression was directly regulated by PPAR,. In conclusion, our results demonstrate that PPAR,-mediated upregulation of CerK gene expression is necessary for keratinocyte survival against serum starvation-induced apoptosis. [source] Methods for retrieving hydrologically significant surface parameters from remote sensing: a review for applications to east Asia regionHYDROLOGICAL PROCESSES, Issue 4 2009Bunkei Matsushita Abstract As human populations and resource use continue to increase, water quality and water resource management will become major problems. With its advantages of large area coverage, high spatial resolution, frequent update and consistent quality, remote sensing has been widely used for hydrological studies and water resources management. This paper focuses on three potential functions of remote sensing for hydrological analysis in east Asia: (1) monitoring water quality in turbid lakes; (2) extracting impervious surface areas (ISAs) from watersheds and (3) estimating evapotranspiration in semi-arid areas. Reviewing the results of the above three topics, it becomes clear that the ability of the current remote sensing technique is still limited in terms of its use in hydrological simulations. An alternative to improving the sensors is developing effective algorithms to compensate for the limitations of current satellite sensors. Copyright © 2008 John Wiley & Sons, Ltd. [source] Two formulations for dynamic response of a cylindrical cavity in cross-anisotropic porous mediaINTERNATIONAL JOURNAL FOR NUMERICAL AND ANALYTICAL METHODS IN GEOMECHANICS, Issue 4 2010Hashem Eslami Abstract Two formulations for calculating dynamic response of a cylindrical cavity in cross-anisotropic porous media based on complex functions theory are presented. The basis of the method is the solution of Biot's consolidation equations in the complex plane. Employing two groups of potential functions for solid skeleton and pore fluid (each group includes three functions), the u,w formulation of Biot's equations are solved. Difference of these two solutions refers to use of two various potential functions. Equations for calculating stress, displacement and pore pressure fields of the medium are mentioned based on each two formulations. Copyright © 2009 John Wiley & Sons, Ltd. [source] The Reissner,Sagoci problem for a transversely isotropic half-spaceINTERNATIONAL JOURNAL FOR NUMERICAL AND ANALYTICAL METHODS IN GEOMECHANICS, Issue 11 2006Mohammad Rahimian Abstract A transversely isotropic linear elastic half-space, z,0, with the isotropy axis parallel to the z -axis is considered. The purpose of the paper is to determine displacements and stresses fields in the interior of the half-space when a rigid circular disk of radius a completely bonded to the surface of the half-space is rotated through a constant angle ,0. The region of the surface lying out with the circle r,a, is free from stresses. This problem is a type of Reissner,Sagoci mixed boundary value problems. Using cylindrical co-ordinate system and applying Hankel integral transform in the radial direction, the problem may be changed to a system of dual integral equations. The solution of the dual integral equations is obtained by an approach analogous to Sneddon's (J. Appl. Phys. 1947; 18:130,132), so that the circumferential displacement and stress fields inside the medium are obtained analytically. The same problem has already been approached by Hanson and Puja (J. Appl. Mech. 1997; 64:692,694) by the use of integrating the point force potential functions. It is analytically proved that the present solution, although of a quite different form, is equivalent to that given by Hanson and Puja. To illustrate the solution, a few plots are provided. The displacements and the stresses in a soil deposit due to a rotationally symmetric force or boundary displacement may be obtained using the results of this paper. Copyright © 2006 John Wiley & Sons, Ltd. [source] Identification of four low molecular and water-soluble proteins from grape (Vitis vinifera L.) seedsINTERNATIONAL JOURNAL OF FOOD SCIENCE & TECHNOLOGY, Issue 6 2010Ting Zhou Summary Profiles of soluble proteins isolated from mature seeds of grape (Vitis vinifera L.) pomace were studied using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) coupled with matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI,TOF,MS). Two-dimensional gels stained with Coomassie brilliant blue revealed more than fifty protein spots. Four abundant protein spots showing low molecular weight (Mr) and wide isoelectric point (pI) were analysed by MALDI,TOF,MS, resulting in their identification. Taken together, these results suggest that identified proteins may be linked to seed development and metabolism, but more instructive is that they have some potential functions for future food application. These results provide some insights into conversion of grape processing wastes into useful products or even as raw material for other industries. [source] Cloning, sequencing, and characterization of CYP1A1 cDNA from leaping mullet (Liza Saliens) liver and implications for the potential functions of its conserved amino acidsJOURNAL OF BIOCHEMICAL AND MOLECULAR TOXICOLOGY, Issue 5 2001Alaattin Sen Abstract A 2,037 bp CYP1A1 cDNA (GenBank AF072899) was cloned through screening of a ,ZipLox cDNA library constructed from the liver of a leaping mullet (Liza saliens) fish captured from Izmir Bay on the Aegean coast of Turkey using rainbow trout CYP1A1 cDNA as a probe. This clone has a 130 bp 5'-flanking region, a 1,563 bp open reading frame (ORF) encoding a 521-amino acid protein (58,972 Da), and a 344 bp 3'-untranslated region without a poly (A) tail. Alignment of the deduced amino acids of CYP1A1 cDNAs showed 58% and 69,96% identities with human and 12 other fish species, respectively. Southern blot analysis suggested that this CYP1A1 cDNA was from a single-copy gene. Based on the comparison with CYP1A1 genes reported for fish and mammals, the leaping mullet CYP1A1 gene is probably split into 7 exons. The intron insertion sites were predicted. Alignment of the CYP1A1 cDNA encoded amino acids from 13 fish and 7 mammalian species disclosed differences in highly conserved amino acids between aquatic and land vertebrates. The possible associated secondary structure; conserved motifs and substrate-binding sites were discussed. The phylogenetic relationships of CYP1A1s among 13 fish species were analyzed by a distance method. © 2001 John Wiley & Sons, Inc. J Biochem Mol Toxicol 15:243,255, 2001 [source] Broadening the mission of an RNA enzymeJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 6 2009Michael C. Marvin Abstract The "RNA World" hypothesis suggests that life developed from RNA enzymes termed ribozymes, which carry out reactions without assistance from proteins. Ribonuclease (RNase) P is one ribozyme that appears to have adapted these origins to modern cellular life by adding protein to the RNA core in order to broaden the potential functions. This RNA-protein complex plays diverse roles in processing RNA, but its best-understood reaction is pre-tRNA maturation, resulting in mature 5' ends of tRNAs. The core catalytic activity resides in the RNA subunit of almost all RNase P enzymes but broader substrate tolerance is required for recognizing not only the diverse sequences of tRNAs, but also additional cellular RNA substrates. This broader substrate tolerance is provided by the addition of protein to the RNA core and allows RNase P to selectively recognize different RNAs, and possibly ribonucleoprotein (RNP) substrates. Thus, increased protein content correlated with evolution from bacteria to eukaryotes has further enhanced substrate potential enabling the enzyme to function in a complex cellular environment. J. Cell. Biochem. 108: 1244,1251, 2009. © 2009 Wiley-Liss, Inc. [source] New angle-dependent potential energy function for backbone,backbone hydrogen bond in protein,protein interactionsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2010Hwanho Choi Abstract Backbone,backbone hydrogen bonds (BBHBs) are one of the most abundant interactions at the interface of protein,protein complex. Here, we propose an angle-dependent potential energy function for BBHB based on density functional theory (DFT) calculations and the operation of a genetic algorithm to find the optimal parameters in the potential energy function. The angular part of the energy funtion is assumed to be the product of the power series of sine and cosine functions with respect to the two angles associated with BBHB. Two radial functions are taken into account in this study: Morse and Leonard-Jones 12-10 potential functions. Of these two functions under consideration, the former is found to be more accurate than the latter in terms of predicting the binding energies obtained from DFT calculations. The new HB potential function also compares well with the knowledge-based potential derived by applying Boltzmann statistics for a variety of protein,protein complexes in protein data bank. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] | |||||||||||||||||||||||||