Molecular Gradients Research Articles

Development of the intestinal microbiota in the piglet

The intestinal commensal microbiota of monogastricanimals such as humans and pigs comprise hundredsof different types of microorganisms (Conway, 1995;Savage, 1977). In the last several decades, the role ofthe intestinal commensal microbiota in a wide range ofhost’s physiological functions has been increasinglyrecognized (Cummings and Macfarlane, 1997). Colo-nization by such microbiota develops a range of thefunctions of intestine, as evidenced by the mal-devel-opment of the intestinal functions of germ-free animals(Hooper et al., 2001; Wostmann et al., 1983) whichwere made artificially so that they were free from mi-croorganisms. For example, the number of intraepithe-lial T lymphocytes, which play an important role in thehost defenses (Yoshikai, 1999), are less than one thirdthe number in both the jejunum and ileum of germ-freepigs than in conventional pigs (Rothkotter et al., 1999).Since the development of the intestinal commensal mi-crobiota interacts deeply with host physiological func-tions, studies that show how they are established inconnection with host physiology need to be performed.The information has the potential to improve the nutri-tional and immunological function of the host and thusit might improve the productivity of livestock.The development of the intestinal microbiota in thesuckling piglet has been the subject of several studies,most of which depended on culture-based techniquesfor the bacterial analysis (Melin et al., 1997; Swords etal., 1993; Uchida et al., 1965). Since culture-basedtechniques only can provide information on bacteriathat are readily cultivated (Langendijk et al., 1995;Suau et al., 1999), they may give a biased view of mi-crobial diversity. The molecular biological techniquestemperature gradient gel electrophoresis (TGGE) anddenaturing gradient gel electrophoresis (DGGE) havebeen developed in recent years, and are being usedmore frequently in microbial ecology (Muyzer et al.,1993). These methods are especially valuable formonitoring the shift in community structure that occursin response to environment perturbations such as achange in diet (Satokari et al., 2001; Simpson et al.,2000; Tannock et al., 2000). And as demonstrated inthis study, the application of the clustering method tothe results of these techniques (gel-image) allows thestatistical comparison of the differences within eachbanding profile that reflects the composition of the mi-crobiota. Although the efficiency of these methods toanalyze the pig fecal or intestinal microbiota has beendemonstrated by several studies (Konstantinov et al.,2003; Simpson et al., 1999, 2000), the change in theintestinal microbiota in suckling piglets has rarely beenanalyzed by these techniques.

In Silico Stochastic Network Models that Emulate the Molecular Sieving Characteristics of Bone

Recent studies implicate bone's extracellular matrix as a "living electrophoresis and ion exchange column" with low pass filter function at the matrix level; whereas small molecules pass through the matrix microporosity, larger molecules penetrate the tissue through the pericellular space. In this study, stochastic network modeling principles were applied, for the first time to our knowledge, to build in silico, nano- to microscale models of bone. Small volumes of bone were modeled to include hierarchical levels of porosity comprising the bone matrix microporosity and the pericellular network. Flow and transport through the network was calculated for molecules from 1,000 to 100,000 datons (Da). On the basis of this study, two contrasting effects determine the rate and direction of transport of different size molecules through the hierarchical porous network of bone. Whereas diffusivity of a given molecule decreases with increasing molecular size, the size exclusion effects of bone's low pass molecular sieve translate into increasing flow velocities for large molecular species along transport paths located in the immediate vicinity of the cells. Both phenomena are expected to have a profound effect on the formation of molecular gradients at a tissue level, providing cues for tissue generation and repair by cellular "micromachines," i.e., osteoclasts and osteoblasts.

Prediction of internal structure and properties in fluid model interfaces of binary and ternary liquid mixtures

The scope of this study is to demonstrate how density functional theory as part of the statistical mechanics of inhomogeneous fluids can contribute to a better understanding of the internal structure and interfacial properties of vapor–liquid and liquid–liquid interfaces in multicomponent liquid mixtures. Especially fluid mixtures with liquid–liquid phase separation can serve as models for liquid–liquid extraction systems. The partial density profiles in such an interface describe molecular concentration gradients which may act as a driving force for mass transfer across this interface.In the application of the density functional theory to liquid–liquid interfaces, we analyzed the influence of different approximations within the theory on the calculation of interfacial structure and thermodynamic potential properties. Especially the use of a weighed density approximation allows us to take short-range local ordering into account. It results in oscillating partial densities or concentration profiles and it yields a highly structured grand canonical potential density across the interface which demonstrates how energetically inhomogeneous a liquid interface is. For a ternary model system, the interfacial tension is calculated, capillary wave contributions are added and their influence is discussed.

Predicting axonal response to molecular gradients with a computational model of filopodial dynamics.

Axons are often guided to their targets in the developing nervous system by attractive or repulsive molecular concentration gradients. We propose a computational model for gradient sensing and directed movement of the growth cone mediated by filopodia. We show that relatively simple mechanisms are sufficient to generate realistic trajectories for both the short-term response of axons to steep gradients and the long-term response of axons to shallow gradients. The model makes testable predictions for axonal response to attractive and repulsive gradients of different concentrations and steepness, the size of the intracellular amplification of the gradient signal, and the differences in intracellular signaling required for repulsive versus attractive turning.

Fast Directed Motion of “Fakir” Droplets

In this Letter, we report on the motion of water droplets on surfaces decorated with molecular gradients comprising semifluorinated (SF) organosilanes. SF molecular gradients deposited on flat silica substrates facilitate faster motion of water droplets relative to the specimens covered with an analogous hydrocarbon gradient. Further increase in the drop speed is achieved by advancing it along porous substrates coated with the SF wettability gradients. The results of our experiments are in quantitative agreement with a simple scaling theory that describes the faster liquid motion in terms of reduced friction at the liquid/substrate interface.

Segmentation in vertebrates: clock and gradient finally joined.

The vertebral column is derived from somites formed by segmentation of presomitic mesoderm, a fundamental process of vertebrate embryogenesis. Models on the mechanism controlling this process date back some three to four decades. Access to understanding the molecular control of somitogenesis has been gained only recently by the discovery of molecular oscillators (segmentation clock) and gradients of signaling molecules, as predicted by early models. The Notch signaling pathway is linked to the oscillator and plays a decisive role in inter- and intrasomitic boundary formation. An Fgf8 signaling gradient is involved in somite size control. And the (canonical) Wnt signaling pathway, driven by Wnt3a, appears to integrate clock and gradient in a global mechanism controlling the segmentation process. In this review, we discuss recent advances in understanding the molecular mechanism controlling somitogenesis.

Evolution of Massive Stars Up to the End of Central Oxygen Burning

We present a detailed study of the evolution of massive stars of masses 15, 20, 25, and 30 M☉ assuming solar-like initial chemical composition. The stellar sequences were evolved through the advanced burning phases up to the end of core oxygen burning. We present a careful analysis of the physical characteristics of the stellar models. In particular, we investigate the effect of the still-unsettled reaction 12C(α,γ)16O on the advanced evolution by using recent compilations of this rate. We find that this rate has a significant impact on the evolution not only during the core helium burning phase but also during the late burning phases, especially the shell carbon burning. We have also considered the effect of different treatments of convective instability based on the Ledoux criterion in regions of varying molecular weight gradient during the hydrogen- and helium-burning phases. We compare our results with other investigations whenever available. Finally, our present study constitutes the basis of analyzing the nucleosynthesis processes in massive stars. In particular, we will present a detailed analysis of the s-process in a forthcoming paper.

Computational Studies of Non-Equilibrium Molecular Transport through Carbon Nanotubes

The transport of methane molecules into several open-ended carbon nanotubes is studied with classical, nonequilibrium molecular dynamics simulations. The forces in the simulations are determined using a reactive empirical bond order potential for short-ranged interactions and a Lennard-Jones potential for long-range interactions. The simulations show that until the carbon nanotubes are filled with methane molecules up to a specific cutoff molecular density, the molecules move forward and backward along the axis of nanotubes in a “bouncing” motion. This bouncing motion is observed for molecules inside both hydrogen-terminated and non-hydrogen-terminated opened nanotubes and is caused by a conflict between the molecules’ attractive interactions with the interior of the nanotube and their response to the molecular density gradient down the length of the tube. At molecular densities above the cutoff value, the molecules flow into, through, and out of the nanotubes in a linear manner. The effects of molecular density, nanotube diameter, and nanotube helical symmetry on the results are analyzed.

Understanding actin organization in cell structure through lattice based Monte Carlo simulations.

Understanding the connection between mechanics and cell structure requires the exploration of the key molecular constituents responsible for cell shape and motility. One of these molecular bridges is the cytoskeleton, which is involved with intracellular organization and mechanotransduction. In order to examine the structure in cells, we have developed a computational technique that is able to probe the self-assembly of actin filaments through a lattice based Monte Carlo method. We have modeled the polymerization of these filaments based upon the interactions of globular actin through a probabilistic model encompassing both inert and active proteins. The results show similar response to classic ordinary differential equations at low molecular concentrations, but a bi-phasic divergence at realistic concentrations for living mammalian cells. Further, by introducing localized mobility parameters, we are able to simulate molecular gradients that are observed in nonhomogeneous protein distributions in vivo. The method and results have potential applications in cell and molecular biology as well as self-assembly for organic and inorganic systems.

Exploring molecular and mechanical gradients in structural bioscaffolds.

Most organisms consist of a functionally adaptive assemblage of hard and soft tissues. Despite the obvious advantages of reinforcing soft protoplasm with a hard scaffold, such composites can lead to tremendous mechanical stresses where the two meet. Although little is known about how nature relieves these stresses, it is generally agreed that fundamental insights about molecular adaptation at hard/soft interfaces could profoundly influence how we think about biomaterials. Based on two noncellular tissues, mussel byssus and polychaete jaws, recent studies suggest that one natural strategy to minimize interfacial stresses between adjoining stiff and soft tissue appears to be the creation of a "fuzzy" boundary, which avoids abrupt changes in mechanical properties. Instead there is a gradual mechanical change that accompanies the transcendence from stiff to soft and vice versa. In byssal threads, the biochemical medium for achieving such a gradual mechanical change involves the elegant use of collagen-based self-assembling block copolymers. There are three distinct diblock copolymer types in which one block is always collagenous, whereas the other can be either elastin-like (soft), amorphous polyglycine (intermediate), or silk-like (stiff). Gradients of these are made by an incrementally titrated expression of the three proteins in secretory cells the titration phenotype of which is linked to their location. Thus, reflecting exactly the composition of each thread, the distal cells secrete primarily the silk- and polyglycine-collagen diblocks, whereas the proximal cells secrete the elastin- and polyglycine-collagen diblocks. Those cells in between exhibit gradations of collagens with silk or elastin blocks. Spontaneous self-assembly appears to be by pH triggered metal binding by histidine (HIS)-rich sequences at both the amino and carboxy termini of the diblocks. In the polychaete jaws, HIS-rich sequences are expanded into a major block domain. Histidine predominates at over 20 mol % near the distal tip and diminishes to about 5 mol % near the proximal base. The abundance of histidine is directly correlated to transition metal content (Zn or Cu) as well as hardness determined by nanoindentation. EXAFS analyses of the jaws indicate that transition metals such as Zn are directly bound to histidine ligands and may serve as cross-linkers.

A new chemotaxis assay shows the extreme sensitivity of axons to molecular gradients.

Axonal chemotaxis is believed to be important in wiring up the developing and regenerating nervous system, but little is known about how axons actually respond to molecular gradients. We report a new quantitative assay that allows the long-term response of axons to gradients of known and controllable shape to be examined in a three-dimensional gel. Using this assay, we show that axons may be nature's most-sensitive gradient detectors, but this sensitivity exists only within a narrow range of ligand concentrations. This assay should also be applicable to other biological processes that are controlled by molecular gradients, such as cell migration and morphogenesis.

Atomic dipole moments calculated using analytical molecular second-moment gradients.

We have implemented analytical second-moment gradients for Hartree-Fock and multiconfigurational self-consistent-field wave functions. The code is used to calculate atomic dipole moments based on the generalized atomic polar tensor (GAPT) formalism [Phys. Rev. Lett. 62, 1469 (1989)], and the proposal of Dinur and Hagler (DH) for the calculation of atomic multipoles [J. Chem. Phys. 91, 2949 (1989)]. Both approaches display smooth basis-set convergence toward a well-defined basis-set limit and give reasonable electron correlation effects on the calculated atomic properties. However, the atomic charges and atomic dipole moments obtained from the GAPT partitioning scheme are unable to provide even qualitatively meaningful molecular quadrupole moments for some molecules, and thus the atomic multipole moments calculated in this scheme cannot be considered well suited for analyzing the electron density in molecules and for calculating intermolecular interaction energies. In contrast, the DH approach gives atomic charges and dipole moments that by definition exactly reproduce the molecular quadrupole moments. The approach of DH is, however, restricted to planar molecules and thus suffers from not being applicable to molecules of arbitrary shape. Both the GAPT and DH approaches give rather poor results for octupole and hexadecapole moments, indicating that at least atomic quadrupole moments are required for an accurate representation of the molecular charge distribution in terms of atomic electric moments.

Pollen Tube Guidance: The Role of Adhesion and Chemotropic Molecules

Publisher Summary In many reproductive systems, adhesion and guidance are essential components of fertilization. In animals, sperm cells are motile and when guided to the egg cell, the sperm penetrates through the extracellular matrix (ECM) and adheres to the egg plasma membrane. Sperm cells in marine animals and algae are released into the open sea and must be guided to the egg. Marine invertebrates provide excellent material for the study of fertilization and information about the basic biology of the interaction between cell surfaces, as well as discoveries of the few molecules known to be involved in sperm–egg interaction. Motile sperm cells are also present in the lower divisions of land plants and in some seed plants. In ferns, sperm cells are released from the male gametophyte (gamete producing haploid phase of the life cycle) and swim, usually through rainwater, to the nearby female gametophyte, which bears archegonia with eggs enclosed. In both animals and plants, guidance cues from the female tissues are critical to accomplish fertilization. One of the most extensively studied guidance mechanisms is chemotaxis, defined as the movement of a cell up a molecular gradient; chemotropism refers to the growth of a cell up a molecular gradient. Adhesion molecules have been implicated in guidance in both reproduction and in embryonic cell movements in animal development, including neuron guidance. In plants, adhesion molecules are involved in reproduction, both in guidance and in the fertilization event, of gamete fusion. It is not unusual to find the same molecules involved in both adhesion and chemotropism in animals. However, in plants only a few such molecules have been reported. Recently, molecules involved in both pollen tube adhesion and guidance have been isolated from the flowering plant stigma and style transmitting tract tissues. This chapter discusses adhesion and chemotropism and looks at a chemotropic peptide in the lily stigma.

Spatial Analysis of 3′ Phosphoinositide Signaling in Living Fibroblasts: I. Uniform Stimulation Model and Bounds on Dimensionless Groups

Fluorescent protein probes now permit spatial distributions of specific intracellular signaling molecules to be observed in real time. Mathematical models have been used to simulate molecular gradients and other spatial patterns within cells, and the output of such models may be compared directly with experiments if the binding of the fluorescent probe and the physics of the imaging technique are each incorporated. Here we present a comprehensive model describing the dynamics of 3′ phosphoinositides (PIs), lipid second messengers produced in the plasma membrane in response to stimulation of the PI 3-kinase signaling pathway, as monitored in the cell-substratum contact area using total internal reflection fluorescence microscopy. With this technique it was previously shown that uniform stimulation of fibroblasts with platelet-derived growth factor elicits the formation of axisymmetric 3′ PI gradients, which we now characterize in the context of our model. We find that upper and lower bounds on the relevant dimensionless model parameter values for an individual cell can be calculated from four well-defined fluorescence measurements. Based on our analysis, we expect that the key dimensionless group, the ratio of 3′ PI turnover and diffusion rates, can be estimated within ∼20% or less.

Mapping Surface Chemistry and Molecular Orientation with Combinatorial Near‐Edge X‐Ray Absorption Fine Structure Spectroscopy

AbstractSummary: Mapping the bond chemistry and molecular orientation of self‐assembled monolayer gradients on flat surfaces and reaction intermediates in catalyst arrays is made possible using combinatorial near‐edge X‐ray absorption fine structure (NEXAFS) spectroscopy. These spatially resolved NEXAFS maps have been made by utilizing synchrotron‐based NEXAFS spectroscopy in conjunction with a computer controlled precision sample manipulator. The NEXAFS maps reveal bond concentration, rehybridization, and orientation of the surface‐bound molecules with sub‐millimeter planar spatial resolution and sub‐monolayer molecular sensitivity. The wide applicability of the combinatorial NEXAFS method is illustrated by mapping: (1) the concentration and molecular orientation of semifluorinated molecules in molecular gradients; (2) the concentration of amino groups in molecular gradients used for nanoparticle templating, and (3) the rehybridization of propylene intermediates on zeolite catalyst arrays used for measuring solid‐state acidity and catalyst activity.The principle of “combinatorial” NEXAFS. The molecular gradient is indicated pictorially by the shading on the specimen.magnified imageThe principle of “combinatorial” NEXAFS. The molecular gradient is indicated pictorially by the shading on the specimen.

Why Does a Helium-Filled Balloon "Rise"?

The article is a lighthearted, conversational exploration of the microscopic basis for Archimedes’principle. The principle is discussed in terms of molecular collisions and density gradients in a gravitational field.

Fabricating Two‐Dimensional Molecular Gradients via Asymmetric Deformation of Uniformly‐Coated Elastomer Sheets

Molecular gradients comprising two‐dimensional in‐plane variation of density of substrate‐grafted molecules (see Figure, darker regions in the plot denote regions with higher substrate density) have been fabricated. This is achieved by utilizing the technology of “mechanically assembled monolayers” in conjunction with in‐plane asymmetric stretching of elastomeric substrates uniformly‐coated with organosilane precursors.

Molecular relativistic electric field gradient calculations suggest revision of the value of the nuclear electric quadrupole moment of 127I

Relativistic ab initio methods are used to compute the electric field gradient at the iodine nucleus in nine different closed-shell diatomic molecules. Combining these theoretical electric field gradients with experimental nuclear quadrupole coupling constants gives a consistent value of the nuclear quadrupole moment of 127I of—696(12)millibarn. We argue that this value is more precise than the current standard value of the nuclear quadrupole moment of 127I and recommend adjusting the reference value accordingly. The precision of this determination is still determined by technical limitations in the theoretical work, in particular the neglect of the two-electron Gaunt interaction in the Hamiltonian and correlation contributions beyond those described at the CCSD(T) level of theory, but the errors are reduced relative to the theoretical work that underlies the current standard value of this nuclear quadrupole moment. As a secondary study we also considered the calculation of the small electric field gradient at the gold nucleus in the AuI molecule and conclude that this computation remains a challenge for theoreticians.

Molecular gradients for the second-order generalized Van Vleck variant of multireference perturbation theory

Recently, a revised second-order generalized Van Vleck perturbation theory (GVVPT2) for the description of molecular electronic structure has been reported [J. Chem. Phys. 117, 4133 (2002)] that is both state selective and of the “perturb-then-diagonalize” type of multireference perturbation theory (MRPT). Herein, formulas for analytic derivatives of the GVVPT2 energy with respect to nuclear perturbations are presented, as are illustrative calculations on model problems. Specifically, it is shown that the modification of the energy denominator, which addresses the so-called intruder-state problem of MRPT, is analytically differentiable with respect to nuclear perturbation and only requires use of matrices available, or directly obtainable, from the underlying multiconfigurational self-consistent field calculation. The developed formalism takes full advantage of the theoretical and computational characteristics of the GVVPT2 energy. In particular, the calculations are performed directly in a spin-adapted basis and utilize the recently introduced concept of macroconfigurations. Moreover, the full flexibility of the energy calculations with respect to arbitrariness of reference—i.e., no restriction to complete active space self-consistent field—is retained. Test calculations on N2 and O3 comparing the analytic derivatives with the results of finite-difference calculations corroborate the formulas and implementation.

Formation and Properties of Anchored Polymers with a Gradual Variation of Grafting Densities on Flat Substrates

We show that assemblies comprising anchored polymers with a gradual variation of grafting densities on solid substrates can be generated by first covering the substrate with a molecular gradient of the polymerization initiator, followed by polymerization from the substrate-bound initiator centers (“grafting from”). We apply this technique to prepare grafting density gradients of poly(acrylamide) (PAAm) on flat silica substrates. We demonstrate that using the grafting density gradient geometry, the mushroom-to-brush transition can be accessed on a single sample. This transition is detected by monitoring the dependence of the thickness of the grafted PAAm in a good solvent using variable angle spectroscopic ellipsometry. Wettability experiments performed on the gradient PAAm substrate provide complementary information about the nature of the mushroom-to-brush transition.