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PubMed2004

Further characterization of the genetic defect of the Bent tail mouse, a mouse model for human neural tube defects.

BACKGROUND: Neural tube defects (NTDs) are congenital malformations arising mostly from incomplete neural tube closure during early embryogenesis. Most NTDs in humans have a complex etiology, with involvement of both genetic and environmental factors. More than 100 mouse models for human neural tube defects exist; Bent tail is one of them. The mouse mutant is caused by a submicroscopic deletion on Xq that completely encompasses the Zic3 gene. METHODS: We searched the ENSEMBL database for other genes/transcribed sequences in the Bent tail deletion in addition to Zic3, which we confirmed by PCR analysis. RESULTS: In our study, we show that the Bent tail deletion is at least 300 kb in size, encompassing a processed pseudogene and a number of expressed sequence tags in addition to Zic3. Although more research is needed to clarify the identity and function of the deleted transcripts, most of them are expressed during embryonic development and might therefore contribute to the phenotype of the Bent tail mouse. CONCLUSIONS: This study presents the first evidence for the fact that the Bent tail allele is not merely a Zic3 knockout allele, as has been previously suggested.

Animals↗

PubMed1993

Conformational filtering in polypeptides and proteins.

We present a method for assigning an ensemble of conformational states to each amino acid residue of a sequence. The states are defined as regions in the (phi, psi) map. The procedure is based on the use of conformational filters. In each filter we use a different set of approximations to estimate the probability of conformational states, and retain only the ones whose probability exceeds an acceptance probability. The resulting state assignment is not necessarily unique, but provides information that can be further exploited in searches for the tertiary structure. This conformational filtering approach to the de novo analysis of a sequence has a number of advantages over traditional structure prediction. First, it is possible to select acceptance probabilities such that the true conformational state is retained for up to 87% of residues, while substantially reducing the number of potential conformations. Second, in solution most linear peptides are present as ensembles of rapidly interconverting conformers, and such ensembles can be well predicted by filtering. Third, we can use Markov chains instead of a statistical mechanical (Ising) treatment, and avoid the need for estimating statistical weight matrices valid for the molecule as a whole. Markov models can use local transition matrices that are assumed to be independent of the rest of the chain, and are directly calculated from pairwise data. We show here that the locally identifiable transition matrices are transferable from the crystal structures of proteins to the solution structures of short peptides, and the ensembles of filtered conformations are in good agreement with nuclear magnetic resonance data. When applied to proteins, the filters retain several conformational states for most residues, and provide a measure of conformational variability. Small variability means that the segment is well defined by local interactions alone, and hence is likely to preserve its structure when isolated from the rest of the chain. Conversely, the structure of a segment with above-average conformational variability is likely to be significantly affected by its protein environment.

Amino Acid Sequence↗

PubMed2006

Decoding seen and attended motion directions from activity in the human visual cortex.

Functional neuroimaging has successfully identified brain areas that show greater responses to visual motion and adapted responses to repeated motion directions. However, such methods have been thought to lack the sensitivity and spatial resolution to isolate direction-selective responses to individual motion stimuli. Here, we used functional magnetic resonance imaging (fMRI) and pattern classification methods to show that ensemble activity patterns in human visual cortex contain robust direction-selective information, from which it is possible to decode seen and attended motion directions. Ensemble activity in areas V1-V4 and MT+/V5 allowed us to decode which of eight possible motion directions the subject was viewing on individual stimulus blocks. Moreover, ensemble activity evoked by single motion directions could effectively predict which of two overlapping motion directions was the focus of the subject's attention and presumably dominant in perception. Our results indicate that feature-based attention can bias direction-selective population activity in multiple visual areas, including MT+/V5 and early visual areas (V1-V4), consistent with gain-modulation models of feature-based attention and theories of early attentional selection. Our approach for measuring ensemble direction selectivity may provide new opportunities to investigate relationships between attentional selection, conscious perception, and direction-selective responses in the human brain.

Brain Mapping↗

PubMed2005

Single-molecule tracking of membrane molecules: plasma membrane compartmentalization and dynamic assembly of raft-philic signaling molecules.

Tracking single molecules in the plasma membrane in live cells is becoming a useful technique for studying the spatial-temporal control of membrane molecular processes, such as signal transduction and the formation of large molecular complexes. In this review, three topics largely based on recent single-molecule observations are described, with a special emphasis on the results that are considered to be difficult to obtain using conventional methods monitoring the ensemble-averaged behavior of molecules. First, we describe the high-speed single-molecule tracking data, mostly obtained by our group that necessitated the paradigm shift of the plasma membrane structure, from the two-dimensional continuum fluid model to the compartmentalized fluid model. Second, we try to present a synthetic view of the cell membrane, which contains raft and other microdomains as well as being partitioned into small compartments. Furthermore, we present our working hypothesis, based on the literature, how large, stabilized rafts may be formed, after ligation or crosslinking, from small/unstable "reserve" rafts present in the steady-state cells. Finally, we explain our initial application of single-molecule fluorescence imaging for studies of the creation of T-cell receptor signaling complexes (immunological synapses or SMACS), by observing the recruitment of single Lck molecules as an initial approach. This revealed that the assembly of Lck at the T-cell receptor cluster site, observed by conventional fluorescence microscopy, actually represents dynamic concentrations of Lck molecules, entering and exiting the cluster domain rapidly, with the aid of the raft domains.

Animals↗

PubMed2005

On the separation of nonadditive symmetric mixtures in nanoscopic slitlike pores: A simple model for racemic fluids.

A grand canonical ensemble Monte Carlo simulation method is used to study the adsorption of nonadditive symmetric mixtures of Lennard-Jones spherical particles in nanoscopic slitlike pores. The walls of the pore are assumed to be formed by the parallel (100) planes of the model face centered cubic crystal of adjustable corrugation potential. It is demonstrated that depending on the nonadditivity effects in the mixture and the pore width the condensed phases formed inside the pore may have different structures. In particular, it is shown that the mixture may separate into layers containing only one component each and the stacking may depend on the pore width and properties of the mixture.

Adsorption↗

PubMed2006

Solid-state phase transition induced by pressure in LiOH x H2O.

When the free energy surface of the lithium hydroxide monohydrate crystal was explored, the high-pressure solid-state phase transition was determined. The high-pressure phase has been obtained through ab initio Car-Parrinello molecular dynamics simulation in the isothermic-isobaric ensemble. The recent metadynamics method has been applied to overcome the high activation energy barriers typical of rare events, like solid-state phase transition at high pressures. In the LiOH x H2O system, there are two kinds of H bonds: water-water and hydroxyl-water. The effect of the pressure has been investigated, to give further insight into the high-pressure phase. The strengthening of the H bonds of the system produces modifications in the water and the hydroxyl ion dipole electronic environment. The infrared spectra of both phases have been calculated and compared with experiments, and the assignment of the external modes has been discussed.

Lithium Compounds↗

PubMed2004

Nanoscale colloids in a freely adsorbing polymer solution: a Monte Carlo simulation study.

A key issue in nanoscale materials and chemical processing is the need for thermodynamic and kinetic models covering colloid-polymer systems over the mesoscopic length scale (approximately 1-100 nm). We have applied Monte Carlo simulations to attractive nanoscale colloid-polymer mixtures toward developing a molecular basis for models of these complex systems. The expanded ensemble Monte Carlo simulation method is applied to calculate colloid chemical potentials (micro(c)) and polymer adsorption (gamma) in the presence of freely adsorbing Lennard-Jones (LJ) homopolymers (surface modifiers). gamma and micro(c) are studied as a function of nanoparticle diameter (sigma(c)), modifier chain length (n) and concentration, and colloid-polymer attractive strength over 0.3 < Rg/sigma(c) < 6 (Rg is the polymer radius of gyration). In the attractive regime, nanocolloid chemical potential decreases and adsorbed amount increases as sigma(c), or n is increased. The scaling of gamma with n from the simulations agrees with the theory of Aubouy and Raphael (Macromolecules 1998, 31, 4357) in the extreme limits of Rg/sigma(c). When Rg/sigma(c) is large, the "colloid" approaches a molecular size and interacts only locally with a few polymer segments and gamma approximately n. When Rg/sigma(c) is small, the system approaches the conventional colloid-polymer size regime where multiple chains interact with a single particle, and gamma approximately sigma(c)2, independent of n. In contrast, adsorption in the mesoscopic range of Rg/sigma(c) investigated here is represented well by a power law gamma approximately n(p), with 0 < p < 1 depending on concentration and LJ attractive strength. Likewise, the chemical potential from our results is fitted well with micro(c) approximately n(q)sigma(c)3, where the cubic term results from the sigma(c) dependence of particle surface area (approximately sigma(c)2) and LJ attractive magnitude (approximately sigma(c)). The q-exponent for micro(c) (micro(c) approximately n(q)) varies with composition and LJ attractive strength but is always very close to the power exponent for gamma (gamma approximately n(p)). This result leads to the conclusion that in attractive systems, polymer adsorption (and thus polymer-colloid attraction) dominates the micro(c) dependence on n, providing a molecular interpretation of the effect of adsorbed organic layers on nanoparticle stability and self-assembly.

Journal Article↗

PubMed2004

The structure of fluids confined in crystalline slitlike nanoscopic pores: bilayers.

Grand canonical and canonical ensemble Monte Carlo simulation methods are used to study the structure and phase behavior of Lennard-Jones fluids confined between the parallel (100) planes of the face centered cubic crystal. Ultra thin slit pores of the width allowing for the formation of only two adsorbate layers are considered. It is demonstrated that the structure of adsorbed phases is very sensitive to the wall-wall separation and to the strength of the fluid-wall potential. It is also shown that the structure of low temperature (solid) phases strongly depends on the fluid density. In particular, when the surface field is sufficiently strong, then the high density phases may exhibit a domain wall structure, quite the same as found in monolayer films adsorbed at a single substrate wall. On the other hand, the weakening of the surface potential leads to the regime in which only the hexagonally ordered bilayer structure is stable. The phase diagrams for a series of systems are estimated. It is shown that, depending on the pore width and the temperature, the condensation leads to the formation of the commensurate or incommensurate phases. The incommensurate phases may have the domain-wall or the hexagonal structure depending on the pore width and the strength of the fluid-wall potential.

Journal Article↗

PubMed2005

The structure of fluids confined in crystalline slitlike nanoscopic pores.

Journal Article↗

PubMed2006

Chemical reaction equilibrium in nanoporous materials: NO dimerization reaction in carbon slit nanopores.

We present a molecular-level simulation study of the effects of confinement on chemical reaction equilibrium in nanoporous materials. We use the reaction ensemble Monte Carlo (RxMC) method to investigate the effects of temperature, nanopore size, bulk pressure, and capillary condensation on the nitric oxide dimerization reaction in a model carbon slit nanopore in equilibrium with a bulk reservoir. In addition to the RxMC simulations, we also utilize the molecular-dynamics method to determine self-diffusion coefficients for confined nonreactive mixtures of nitric oxide monomers and dimers at compositions obtained from the RxMC simulations. We analyze the effects of the temperature, nanopore width, bulk pressure, and capillary condensation on the reaction equilibrium with respect to the reaction conversion, fluid structure, and self-diffusion coefficients. We show that the influence of the temperature, nanopore size, and capillary condensation on the confined reaction equilibrium is quite dramatic while the effect of the bulk pressure on the reaction equilibrium in the carbon slit nanopore is only moderate. This work is an extension of previous work by Turner et al. [J. Chem. Phys. 114, 1851 (2001)] on the confined reactive nitric oxide system.

Journal Article↗

PubMed2006

On the structure of bilayer condensed phases confined between crystalline walls of triangular symmetry.

Grand canonical ensemble Monte Carlo simulation method is used to study the structure of Lennard-Jones fluids confined between the parallel walls, formed by the (111) planes of the face centered cubic crystal. Thin slit pores with a width allowing for the formation of only two atomic layers are considered. It is shown that the structure of confined solidlike phases is very sensitive to the pore width, the misfit between the size of adsorbate atoms and the size of surface lattice, as well as the corrugation of the surface potential. In particular, when the misfit between the adsorbate atoms and the surface lattice is very small, even a weakly corrugated surface potential highly stabilizes solidlike phases of triangular symmetry. On the other hand, in the case of large misfit the packing effects become a dominating factor and lead to the appearance of solidlike phases of different structures and symmetries.

Journal Article↗

PubMed2006

Dynamical properties of the soft sticky dipole-quadrupole-octupole water model: a molecular dynamics study.

The dynamical properties of the soft sticky dipole-quadrupole-octupole (SSDQO) water model using SPC/E moments are calculated utilizing molecular dynamics simulations. This new potential for liquid water describes the water-water interactions by a Lennard-Jones term and a sticky potential, which is an approximate moment expansion with point dipole, quadrupole, and octupole moments, and reproduces radial distribution functions of pure liquid water using the moments of SPC/E [Ichiye and Tan, J. Chem. Phys. 124, 134504 (2006)]. The forces and torques of SSDQO water for the dipole-quadrupole, quadrupole-quadrupole, and dipole-octupole interactions are derived here. The simulations are carried out at 298 K in the microcanonical ensemble employing the Ewald method for the long-range dipole-dipole interactions. Here, various dynamical properties associated with translational and rotational motions of SSDQO water using the moments of SPC/E (SSDQO:SPC/E) water are compared with the results from SPC/E and also experiment. The self-diffusion coefficient of SSDQO:SPC/E water is found to be in excellent agreement with both SPC/E and experiment whereas the single particle orientational relaxation time for dipole vector is better than SPC/E water but it is somewhat smaller than experiment. The dielectric constant of SSDQO:SPC/E is essentially identical to SPC/E, and both are slightly lower than experiment. Also, molecular dynamics simulations of the SSDQO water model are found to be about twice as fast as three-site models such as SPC/E.

Computer Simulation↗

PubMed2006

Isomolar-semigrand ensemble molecular dynamics: application to vapor-liquid equilibrium of the mixture methane/ethane.

The isomolar-semigrand ensemble molecular dynamics (iSGMD) method is applied to the simulation of the binary system methane/ethane. The vapor-liquid equilibrium properties of this system at a temperature of 192.37 K are computed using the Gibbs-Duhem integration method. The iSGMD method, which resembles conventional hybrid Monte Carlo (MC) but is applicable to phase equilibrium calculations, is designed to overcome the difficulties associated with performing standard Monte Carlo-type particle transformations in liquid systems that are very dense and/or are comprised of complex molecules with many intramolecular degrees of freedom. This work shows that particle transformations using the iSGMD method for the simple system methane/ethane are at least 25 times more successful than standard MC-type transformations. The P-x-y curve for the system methane/ethane at 192.37 K computed using iSGMD simulations agrees very well with the experimental P-x-y curve as well as results of a previous MC study.

Journal Article↗

PubMed2006

Thermodynamics of water octamer in a uniform electric field.

We study the water octamer in a uniform electric field using the all-exchanges parallel tempering Monte Carlo method in the canonical ensemble. The heat capacity, quenched energy configurations, and the order parameter Q(4) are employed to understand the phase changes observed as a function of temperature and the strength of the applied electric field. At a low field strength of 0.1 V A(-1) a solidlike to liquidlike "melting" transition is detected. The corresponding heat capacity peak appears around 206 K, where Q(4) shows a significant change of slope. For E> or =0.5 V A(-1) such features are absent. However, at E=0.5 V A(-1) we find a solidlike to solidlike transition between cubic and extended structures around T approximately 25 K.

Journal Article↗

PubMed2002

On the calculation of absolute macromolecular binding free energies.

The standard framework for calculating the absolute binding free energy of a macromolecular association reaction A + B --> AB with an association constant K(AB) is to equate chemical potentials of the species on the left- and right-hand sides of this reaction and evaluate the chemical potentials from theory. This theory involves (usually hidden) assumptions about what constitutes the bound species, AB, and where the contribution of the solvent appears. We present here an alternative derivation that can be traced back to Bjerrum, in which the expectation value of K(AB) is obtained directly through the statistical mechanical method of evaluating its ensemble (Boltzmann-weighted) average. The generalized Bjerrum approach more clearly delineates: (i) the different contributions to binding; (ii) the origin of the much-discussed and somewhat controversial association entropy term; and (iii) where the solvent contribution appears. This approach also allows approximations required for practical evaluation of the binding constant in complex macromolecular systems, to be introduced in a well defined way. We provide an example, with application to test cases that illustrate a range of binding behavior.

Energy Transfer↗

PubMed2006

Systematic identification of pseudogenes through whole genome expression evidence profiling.

The identification of pseudogenes is an integral and significant part of the genome annotation because of their abundance and their impact on the experimental analysis of functional genes. Most of the computational annotation systems are not optimized for systematic pseudogene recognition, often annotating pseudogenes as functional genes, and users then propagate these errors to subsequent analyses and interpretations. In order to validate gene annotations and to identify pseudogenes that are potentially mis-annotated, we developed a novel approach based on whole genome profiling of existing transcript and protein sequences. This method has two important features: (i) equally detects both processed and non-processed pseudogenes and (ii) can identify transcribed pseudogenes. Applying this method to the human Ensembl gene predictions, we discovered that 2011 (9% of total) Ensembl genes in the categories of known and novel might be pseudogenes based on expression evidence. Of these, 1200 genes are found to have no existing evidence of transcription, and 811 genes are found with transcription evidence but contain significant translation disruption. Approximately 40% of the 2011 identified pseudogenes presented a multi-exon structure, representing non-processed pseudogenes. We have demonstrated the power of whole genome profiling of expression sequences to improve the accuracy of gene annotations.

Computational Biology↗

PubMed2001

Thermodynamics and diffusion of a lattice gas on a simple cubic lattice.

A lattice gas model with nearest neighbor attractive interactions on a simple cubic lattice is considered. The method of nonequilibrium statistical ensembles due to Zubarev is used to derive expressions for jump and chemical diffusion coefficients. For thermally activated hopping dynamics in the hydrodynamical (low frequency, long wavelength) limit, and neglecting specific memory effects, these expressions are represented in a simple form in terms of the zero concentration limit of the chemical diffusion coefficient and equilibrium characteristics, i.e., the chemical potential, and the probability for two nearest neighbor sites to be vacant. These equilibrium characteristics are calculated by means of the self-consistent diagram approximation. The equilibrium characteristics and diffusion coefficients are in a good agreement with extensive Monte Carlo simulation results.

Journal Article↗

PubMed2003

Non-Gaussian random-matrix ensembles with banded spectra.

Non-Gaussian random-matrix ensembles are important in many applications. We propose Monte Carlo and Langevin methods for generating non-Gaussian ensembles and their eigenvalue spectra. We also provide a general framework for analytic studies of the level density in these ensembles. We show that, in general, the level densities exhibit banded spectra, with important implications for mesoscopic systems and complex nuclei. The universality of energy-level fluctuations is confirmed.

Journal Article↗