Neighbor Pairs Research Articles

Cytotoxicity of the traditional chinese medicine (TCM) plumbagin in its copper chemistry

The anticancer traditional Chinese medicine (TCM), plumbagin (PLN), was isolated from Plumbago Zeylanica. Reaction of plumbagin with Cu(II) salt, afforded [Cu(PLN)(2)].2H(2)O (1). With 2,2'-bipyridine (bipy) as a co-ligand, PLN reacts with Cu(II) to give [Cu(PLN)(bipy)(H(2)O)](2)(NO(3))(2).4H(2)O (2). 1 and 2 were characterized by elemental analysis, IR, ESI-MS spectra. Their crystal structures were determined by single crystal X-ray diffraction methods. The in vitro cytotoxicity of PLN, 1 and 2 against seven human tumour cell lines was assayed. The metal-based compounds exhibit enhanced cytotoxicity vs. that of free PLN, suggesting that these compounds display synergy in the combination of metal ions with PLN. The binding properties of PLN, 1 and 2 to DNA were investigated through UV-vis, fluorescence, CD spectra, and gel mobility shift assay, which indicated that 1 and 2 were non-covalent binding and mainly intercalated the neighboring base pairs of DNA. PLN, 1 and 2 exhibit inhibition activity to topoisomerase I (TOPO I), but 1 and 2 were more effective than PLN.

Diffusion of Li atoms in LiMn2O4 - A structural point of view -

The structure of LiMn2O4, its phase transition at around 290 K, and the diffusion mechanism of Li are discussed based on the recent synchrotron X-ray diffraction and molecular dynamics simulation studies. The high-temperature modification (cubic Fd 3m) is essentially of spinel-type containing various types of disorder; (1) the Li atoms are not located exactly at the tetrahedral 8a sites, but mainly distributed among four positions 0.14 A apart from 8a, (2) some portion of Li atoms are further displaced toward the 16c octahedral interstices with a notable accumulation at the positions 0.35 A apart from 16c, and (3) the O atoms also show a statistical distribution around their ideal 32e sites. The low-temperature modification adopts a 3 × 3 × 1 superstructure (orthorhombic Fddd) with respect to the high-temperature modification. The bond-length fluctuation has been observed along the pseudo-tetragonal Jahn-Teller distortion direction parallel to the a axis in the heterocubane Mn24O94 cluster. The four Mn2 atoms in the heterocubane presumably shares three electrons in the e-parentage low-energy-level orbitals by the double-exchange Zener mechanism. The time-averaged oxidation state for Mn2 is estimated to be +3.25. The heterocubane Zener polarons are isolated with each other and embedded in an ordered way in the charge-ordered matrix containing Mn1III, Mn3III, Mn4IV and Mn5IV. Two kinds of diffusion mechanisms for Li atoms are proposed for the high-temperature modification from the molecular dynamics simulation. One is a microscopic version of the classical picture for diffusion based on the concentration difference in diffusion species. This mechanism requires an activation energy of ca. 0.25 eV to jump over a saddle point at the bottleneck. The other mechanism is a diffusion accompanied by the local lattice distortion coupled with the 3d electron transfer between a pair of nearby Mn atoms. This requires no activation energy for Li to pass through the bottleneck. The valence exchange between +3 and +4 in the neighboring Mn pair prompts the displacement of coordinating O atoms along the pseudo-tetragonal Jahn-Teller distortion direction, which presumably plays a principal role in opening the bottleneck of oxygen triangle along the diffusion pathway.

Structural and Dynamics Study of DNA Dodecamer Duplexes That Contain Un-, Hemi-, or Fully Methylated GATC Sites

Methylation of DNA plays a regulatory role in DNA metabolism. The Escherichia coli DNA adenine methyltransferase methylates the N6 positions of adenines in the sequence 5'-GATC-3', which exists in the fully methylated state during most of the cell cycle. Just after DNA replication, however, the GATC sites transiently become hemimethylated, a condition that is indispensable for various cellular processes, such as negative modulation of replication initiation at oriC by SeqA. The lack of structural and dynamic information on DNA duplexes that contain fully methylated GATC sites makes it difficult to explain how hemimethylated GATC sites are recognized in vivo by proteins in a sea of fully methylated ones. Here, we used NMR spectroscopy to characterize the solution structure of a dodecamer DNA duplex that contained a fully methylated GATC site and the dynamics of the unmethylated, hemimethylated, and fully methylated GATC duplexes. Only the hemimethylated GATC duplex displays a unique major groove conformation, which is optimized for entrance into the cleft structure of SeqA. The apparent equilibrium constants for base-pair opening of the three differentially methylated GATC duplexes revealed that N6-methylation of the adenine residue affects the thermodynamics and kinetics of its own and neighboring base pairs. The equilibrium constants for base-pair opening of three GATC duplexes were determined using proton exchange catalyzed by TRIS. The two G.C base pairs of the hemimethylated GATC duplex displayed a faster base-pair opening rate and required less energy for the base-pair opening reaction than did those of the fully methylated one.

Relationship between triple and pair correlations in an A y B 1 − y solid solution with a planar hexagonal lattice

An analytical relationship is found between triple correlations and nearest neighbor pair correlations in an AyB1 − y solid solution with a planar hexagonal lattice (plane group p6mm). The range of variations in the triple correlation is determined as a function of the composition of the AyB1 − y solid solution and the value of the pair correlation. It is assumed that periodically ordered planar hexagonal and square island nanostructures can be considered as solid solutions A1/4□3/4 with vacancy sites □ and sites occupied by nanoparticles A. In this case, an ordered distribution of nanoparticles over the planar-lattice sites occurs because the nearest neighbor pair correlation is negative and has a maximum magnitude.

The stereochemistry of trans-4-hydroxynonenal-derived exocyclic 1,N2-2'-deoxyguanosine adducts modulates formation of interstrand cross-links in the 5'-CpG-3' sequence.

The trans-4-hydroxynonenal (HNE)-derived exocyclic 1,N2-dG adduct with (6S,8R,11S) stereochemistry forms interstrand N2-dG−N2-dG cross-links in the 5′-CpG-3′ DNA sequence context, but the corresponding adduct possessing (6R,8S,11R) stereochemistry does not. Both exist primarily as diastereomeric cyclic hemiacetals when placed into duplex DNA [Huang, H., Wang, H., Qi, N., Kozekova, A., Rizzo, C. J., and Stone, M. P. (2008) J. Am. Chem. Soc. 130, 10898−10906]. To explore the structural basis for this difference, the HNE-derived diastereomeric (6S,8R,11S) and (6R,8S,11R) cyclic hemiacetals were examined with respect to conformation when incorporated into 5′-d(GCTAGCXAGTCC)-3′·5′-d(GGACTCGCTAGC)-3′, containing the 5′-CpX-3′ sequence [X = (6S,8R,11S)- or (6R,8S,11R)-HNE−dG]. At neutral pH, both adducts exhibited minimal structural perturbations to the DNA duplex that were localized to the site of the adduction at X7·C18 and its neighboring base pair, A8·T17. Both the (6S,8R,11S) and (6R,8S,11R) cyclic hemiacetals were located within the minor groove of the duplex. However, the respective orientations of the two cyclic hemiacetals within the minor groove were dependent upon (6S) versus (6R) stereochemistry. The (6S,8R,11S) cyclic hemiacetal was oriented in the 5′-direction, while the (6R,8S,11R) cyclic hemiacetal was oriented in the 3′-direction. These cyclic hemiacetals effectively mask the reactive aldehydes necessary for initiation of interstrand cross-link formation. From the refined structures of the two cyclic hemiacetals, the conformations of the corresponding diastereomeric aldehydes were predicted, using molecular mechanics calculations. Potential energy minimizations of the duplexes containing the two diastereomeric aldehydes predicted that the (6S,8R,11S) aldehyde was oriented in the 5′-direction while the (6R,8S,11R) aldehyde was oriented in the 3′-direction. These stereochemical differences in orientation suggest a kinetic basis that explains, in part, why the (6S,8R,11S) stereoisomer forms interchain cross-links in the 5′-CpG-3′ sequence whereas the (6R,8S,11R) stereoisomer does not.

Dipolar interactions and constant dielectric loss spectra

Frequency-independent dielectric loss spectra constitute an ubiquitous phenomenon in strongly disordered materials. The degree of universality of this effect calls for a microscopic model that takes into account interactions and structural disorder, but otherwise requires only minimal assumptions. Under this point of view we review and further investigate the cooperative relaxation behaviour in an assembly of defect centres at frozen random positions. These centres carry an internal dipolar degree of freedom and interact by dipole-dipole forces. Such a description essentially amounts to studying the cooperative dynamics of interacting “asymmetric double well potential” (ADWP)-like centres, without invoking an ad hoc barrier distribution. Kinetic Monte Carlo simulations of an associated random dipolar lattice model show a transition from Debye to constant dielectric loss behaviour upon lowering the temperature. These results are interpreted with the help of analytic theories that focus on slow relaxation within strongly interacting nearest neighbour pairs of defects. Finally, a collective mode representation of the dielectric response derived from stochastic field theory is presented.

Overlapping genes in the human and mouse genomes

BackgroundIncreasing evidence suggests that overlapping genes are much more common in eukaryotic genomes than previously thought. In this study we identified and characterized the overlapping genes in a set of 13,484 pairs of human-mouse orthologous genes.ResultsAbout 10% of the genes under study are overlapping genes, the majority of which are different-strand overlaps. The majority of the same-strand overlaps are embedded forms, whereas most different-strand overlaps are not embedded and in the convergent transcription orientation. Most of the same-strand overlapping gene pairs show at least a tenfold difference in length, much larger than the length difference between non-overlapping neighboring gene pairs. The length difference between the two different-strand overlapping genes is less dramatic. Over 27% of the different-strand-overlap relationships are shared between human and mouse, compared to only ~8% conservation for same-strand-overlap relationships. More than 96% of the same-strand and different-strand overlaps that are not shared between human and mouse have both genes located on the same chromosomes in the species that does not show the overlap. We examined the causes of transition between the overlapping and non-overlapping states in the two species and found that 3' UTR change plays an important role in the transition.ConclusionOur study contributes to the understanding of the evolutionary transition between overlapping genes and non-overlapping genes and demonstrates the high rates of evolutionary changes in the un-translated regions.

Fast computation of Gröbner basis of homogenous ideals of % MathType!MTEF!2!1!+- % feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn % hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr % 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9 % vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x % fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaWefv3ySLgznf % gDOjdaryqr1ngBPrginfgDObcv39gaiuaacqWFfcVraaa!41D0! $$ \mathbb{F} $$ [x, y

This paper provides a fast algorithm for Grobner bases of homogenous ideals of $$ \mathbb{F} $$ [x, y] over a finite field $$ \mathbb{F} $$ . We show that only the S-polynomials of neighbor pairs of a strictly ordered finite homogenours generating set are needed in the computing of a Grobner base of the homogenous ideal. It reduces dramatically the number of unnecessary S-polynomials that are processed. We also show that the computational complexity of our new algorithm is O(N 2), where N is the maximum degree of the input generating polynomials. The new algorithm can be used to solve a problem of blind recognition of convolutional codes. This problem is a new generalization of the important problem of synthesis of a linear recurring sequence.

Quantum phase transitions and quantum communication in a spin star system

We consider a generalized spin star system which can be solved exactly, with the central spin- system embedded in a bath of N spin- particles. In this system, in addition to the central–outer couplings, each pair of nearest neighbours of the bath spins interacts within themselves. The general expressions of the eigenstates as well as the eigenvalues of the model are derived with the use of symmetries of the system. We then investigate the quantum phase transitions in some limiting cases and show that the occurrence of the quantum phase transitions can be obtained by varying the external control parameters. We further analyse the properties of quantum communication in this model. In the time evolution, some simple and interesting results are discovered concerning transfer fidelity, cloning fidelity, as well as entanglements created.

Generic two-phase coexistence, relaxation kinetics, and interface propagation in the quadratic contact process: Analytic studies

The quadratic contact process is implemented as an adsorption–desorption model on a two-dimensional square lattice. The model involves random adsorption at empty sites, and correlated desorption requiring diagonal pairs of empty neighbors. A simulation study of this model [D.-J. Liu, X. Guo, J.W. Evans, Phys. Rev. Lett. 98 (2007) 050601] revealed the existence of generic two-phase coexistence between a low-coverage active steady-state and a completely covered absorbing state. Here, an analytic treatment of model behavior is developed based on truncation approximations to the exact master equations. Applying this approach for spatially homogeneous states, we characterize steady-state behavior as well as the kinetics of relaxation to the steady-states. Extending consideration to spatially inhomogeneous states, we obtain discrete reaction–diffusion type equations characterizing evolution. These are employed to analyze an orientation-dependence of the propagation of planar interfaces between active and absorbing states which underlies the generic two-phase coexistence. We also describe the dynamics and critical forms of planar perturbations of the active state and of droplets of one phase embedded in the other.

Kinetic and molecular dynamics analysis of carbon diffusion in austenite

A kinetic 10-frequency model for interstitial diffusion via octahedral interstices in the fcc lattice is developed. In this model, the specific role of the transition probabilities during association and dissociation of the first nearest neighbour interstitial pairs through the second nearest neighbour sites is considered. Application of the model is made to carbon diffusion in austenite. Molecular dynamics is used to investigate carbon interstitial diffusion in austenite at low carbon contents. The assumption that carbon atoms can interact with each other only indirectly (via neighbouring iron atoms) is used. The Arrhenius parameters of interstitial carbon jump frequencies consistent with the 10-frequency model are determined. Comparison of the molecular dynamics results with experimental data at 1273 K in the context of the 10-frequency model is performed. It is shown that a small direct repulsion between carbon atoms at first nearest neighbours should be included. It is found that the initial increase (with increasing carbon content) in both the tracer and the chemical diffusion coefficients is shown to be a result of increased rates of dissociation of carbon from first and second nearest neighbour pairs to third nearest neighbour sites.

PLANT UPTAKE OF INORGANIC AND ORGANIC NITROGEN: NEIGHBOR IDENTITY MATTERS

The importance of interspecific competition as a cause of resource partitioning among species has been widely assumed but rarely tested. Using neighbor removals in combination with 15N tracer additions in the field, we examined variation among three alpine species in the uptake of 15N-NH4+, 15N-NO3-, and 15N-13C-[2]-glycine in intact neighborhoods, when paired with a specific neighbor, and when all neighbors were removed. Species varied in the capacity to take up 15N-labeled NH4+, NO3-, and glycine in intact neighborhoods and in interspecific pairs. When interspecific neighbor pairs were compared with no neighbor controls, neighbors reduced 15N uptake in target species by as much as 50%, indicating competition for N. Furthermore, neighbor identity influenced the capacity of species to take up different forms of N. Thus, competition within interspecific neighbor pairs often caused reduced uptake of a particular form of N, as well as shifts to uptake of an alternative form of N. Such shifts in resource use as a result of competition are an implicit assumption in studies of resource partitioning but have rarely been documented. Our study suggests that plasticity in the uptake of different forms of N may be a mechanism by which cooccurring plants reduce competition for N.

Generic two-phase coexistence, relaxation kinetics, and interface propagation in the quadratic contact process: Simulation studies

The quadratic contact process is formulated as an adsorption-desorption model on a two-dimensional square lattice. It involves random adsorption at empty sites and correlated desorption requiring diagonally adjacent pairs of empty neighbors. We assess the model behavior utilizing kinetic Monte Carlo simulations. One finds generic two-phase coexistence between a low-coverage active steady state and a completely covered or "poisoned" absorbing steady state; i.e., both states are stable over a finite range of adsorption rates or "pressures." This behavior is in marked contrast to that for equilibrium phase separation. For spatially homogeneous systems, we provide a comprehensive characterization of the kinetics of relaxation to the steady states. We analyze rapid poisoning for higher pressures above an effective spinodal point terminating a metastable active state, nucleation-mediated poisoning in the metastable region, the dynamics of poisoned droplets within the two-phase coexistence region, and behavior reminiscent of bootstrap percolation dynamics for lower pressures. For spatially inhomogeneous systems, we analyze the propagation of planar interfaces between active and absorbing states, fully characterizing an orientation dependence which underlies the generic two-phase coexistence.

Protein−Protein Interfaces: Properties, Preferences, and Projections

Herein, we study the interfaces of a set of 146 transient protein-protein interfaces in order to better understand the principles of their interactions. We define and generate the protein interface using tools from computational geometry and topology and then apply statistical analysis to its residue composition. In addition to counting individual occurrences, we evaluate pairing preferences, both across and as neighbors on one side of an interface. Likelihood correction emphasizes novel and unexpected pairs, such as the His-Cys pair found in most complexes of serine proteases with their diverse inhibitors and the Met-Met neighbor pair found in unrelated protein interfaces. We also present a visualization of the protein interface that allows for facile identification of residue-residue contacts and other biochemical properties.

Computer Simulations and Analysis of Structural and Energetic Features of Some Crystalline Energetic Materials

A database of 43 literature X-ray crystal structure determinations for compounds with known, or possible, energetic properties has been collected along with some sublimation enthalpies. A statistical study of these crystal structures, when compared to a sample of general organic crystals, reveals a population of anomalously short intermolecular oxygen-oxygen separations with an average crystal packing coefficient of 0.77 that differs significantly from 0.70 found for the general population. For the calculation of lattice energies, three atom-atom potential energy schemes and the semiempirical SCDS-PIXEL scheme are compared. The nature of the packing forces in these energetic materials is further analyzed by a study of the dispersive versus Coulombic contributions to overall lattice energies and to molecule-molecule energies in pairs of near neighbors in the crystals, a partitioning made possible by the unique features of the SCDS-PIXEL scheme. It is shown that dispersion forces are stronger than Coulombic forces, contrary to common belief. The low abundance of hydrogen atoms in these molecules, the close oxygen-oxygen contacts, and the high packing coefficients explain the observation that, for these energetic materials, crystal densities are anomalously high compared to those of most organic materials. However, an understanding, not to mention prediction or control, of the deeper mechanisms for the explosive power of these crystalline materials, such as the role of lattice defects, remains beyond present capabilities.

Spatial Analyses of Periodontal Data Using Conditionally Autoregressive Priors Having Two Classes of Neighbor Relations

Attachment loss, the extent of a tooth's root (in millimeters) that is no longer attached to surrounding bone by periodontal ligament, is often used to measure the current state of a patient's periodontal disease and monitor disease progression. Attachment loss data can be analyzed using a conditionally autoregressive (CAR) prior distribution that smooths fitted values toward neighboring values. However, it may be desirable to have more than one class of neighbor relation in the spatial structure, so the different classes of neighbor relations can induce different degrees of smoothing. For example, we may wish to allow smoothing of neighbor pairs bridging the gap between teeth to differ from smoothing of pairs that do not bridge such gaps. Adequately modeling the spatial structure may improve the monitoring of periodontal disease progression. This article develops a two-neighbor-relation CAR model to handle this situation and presents associated theory to help explain the sometimes unusual posterior distributions of the parameters controlling the different types of smoothing. The posterior of these smoothing parameters often has long upper tails, and its shape can change dramatically depending on the spatial structure. Like previous authors, we show that the prior distribution on these parameters has little effect on the posterior of the fixed effects but has a marked influence on the posterior of both the random effects and the smoothing parameters. Our analysis of attachment loss data also suggests that the spatial structure itself varies between individuals.

Quadratic Contact Process: Phase Separation with Interface-Orientation-Dependent Equistability

The quadratic contact process is implemented on a square lattice as a model with random adsorption and correlated desorption requiring empty pairs of diagonal neighbors. The model exhibits a discontinuous phase transition between an active state and an absorbing state, but equistability between these states depends on the orientation of the separating interface. Correspondingly, for a generalized class of models, we find phase coexistence over a finite region of their two-dimensional parameter space. This is in stark contrast to behavior in equilibrium systems.

Expression Divergence of Tandemly Arrayed Genes in Human and Mouse

Tandemly arrayed genes (TAGs) account for about one third of the duplicated genes in eukaryotic genomes, yet there has not been any systematic study of their gene expression patterns. Taking advantage of recently published large-scale microarray data sets, we studied the expression divergence of 361 two-member TAGs in human and 212 two-member TAGs in mouse and examined the effect of sequence divergence, gene orientation, and chromosomal proximity on the divergence of TAG expression patterns. Our results show that there is a weak negative correlation between sequence divergence of TAG members and their expression similarity. There is also a weak negative correlation between chromosomal proximity of TAG members and their expression similarity. We did not detect any significant relationship between gene orientation and expression similarity. We also found that downstream TAG members do not show significantly narrower expression breadth than upstream members, contrary to what we predict based on TAG expression divergence hypothesis that we propose. Finally, we show that both chromosomal proximity and expression correlation in TAGs do not differ significantly from their neighboring non-TAG gene pairs, suggesting that tandem duplication is unlikely to be the cause for the higher-than-random expression association between neighboring genes on a chromosome in human and mouse.

Linear Multilayer ICA Generating Hierarchical Edge Detectors

In this letter, a new ICA algorithm, linear multilayer ICA (LMICA), is proposed. There are two phases in each layer of LMICA. One is the mapping phase, where a two-dimensional mapping is formed by moving more highly correlated (nonindependent) signals closer with the stochastic multidimensional scaling network. Another is the local-ICA phase, where each neighbor (namely, highly correlated) pair of signals in the mapping is separated by MaxKurt algorithm. Because in LMICA only a small number of highly correlated pairs have to be separated, it can extract edge detectors efficiently from natural scenes. We conducted numerical experiments and verified that LMICA generates hierarchical edge detectors from large-size natural scenes.

Comparing the electron and hole mobilities in the α and β phases of perylene: role of π-stacking

Computational studies are carried out on α and β polymorphs of perylene molecular crystals to estimate their hole and electron mobilities (μhole and μelectron). For both the polymorphs, it is found that the LUMO bandwidhs are larger than the HOMO bandwidth resulting in larger electron conductance, as observed experimentally and which has remained unexplained until now. For a microscopic understanding, we perform quantum chemical calculations for the hole and electron transfer matrix elements (Hmnhole and Hmnelectron) on some selected unique nearest neighbour pairs of molecules in the crystal geometries. This along with calculations for the hole and electron reorganization energies (λhole and λelectron) within the embedded cluster method reveal that for both the crystals, μelectron exceeds μhole by two orders of magnitude. The electron mobility for the α-phase (μelectron = 67.2 cm2 V−1 s−1) is found to be three times that for the β-phase. The major driving force for preferential electron conductance in α-perylene is the slipped parallel π-stacking arrangement of the molecules at short intermolecular distances (d = 3.9 A) in the crystal. We suggest that experimental strategies that further enhance the percentage of such specific π-stacking dimers in molecular assemblies have the potential to further increase μelectron. The present theoretical calculations provide a unified understanding of the parameters that optimize an organic crystal for enhanced electron and hole mobilities.