Interpenetration as a Mechanism for Liquid-Liquid Phase Transitions

We study simple lattice systems to demonstrate the influence of interpenetrating bond networks on phase behavior. We promote interpenetration by using a Hamiltonian with a weakly repulsive interaction with nearest neighbors and an attractive interaction with second-nearest neighbors. In this way, bond networks will form between second-nearest neighbors, allowing for two (locally) distinct networks to form. We obtain the phase behavior from analytic solution in the mean-field approximation and exact solution on the Bethe lattice. We compare these results with exact numerical results for the phase behavior from grand canonical Monte Carlo simulations on square, cubic, and tetrahedral lattices. All results show that these simple systems exhibit rich phase diagrams with two fluid-fluid critical points and three thermodynamically distinct phases. We also consider including third-nearest-neighbor interactions, which give rise to a phase diagram with four critical points and five thermodynamically distinct phases. Thus the interpenetration mechanism provides a simple route to generate multiple liquid phases in single-component systems, such as hypothesized in water and observed in several model and experimental systems. Additionally, interpenetration of many such networks appears plausible in a recently considered material made from nanoparticles functionalized by single strands of DNA.Comment: 12 pages, 9 figures, submitted to Phys. Rev.

Theoretical description of a DNA-linked nanoparticle self-assembly

Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide theoretical descriptions for the equilibrium clustering and dynamics, as well as the self-assembly kinetics of DNA-linked nanoparticles. Striking agreement is observed between the theory and molecular modeling of DNA tethered nanoparticles.Comment: Accepted for publication in Physical Review Letter

Interpenetration as a Mechanism for Liquid-Liquid Phase Transitions

We study simple lattice systems to demonstrate the influence of interpenetrating bond networks on phase behavior. We promote interpenetration by using a Hamiltonian with a weakly repulsive interaction with nearest neighbors and an attractive interaction with second-nearest neighbors. In this way, bond networks will form between second-nearest neighbors, allowing for two (locally) distinct networks to form. We obtain the phase behavior from analytic solution in the mean-field approximation and exact solution on the Bethe lattice. We compare these results with exact numerical results for the phase behavior from grand canonical Monte Carlo simulations on square, cubic, and tetrahedral lattices. All results show that these simple systems exhibit rich phase diagrams with two fluid-fluid critical points and three thermodynamically distinct phases. We also consider including third-nearest-neighbor interactions, which give rise to a phase diagram with four critical points and five thermodynamically distinct phases. Thus the interpenetration mechanism provides a simple route to generate multiple liquid phases in single-component systems, such as hypothesized in water and observed in several model and experimental systems. Additionally, interpenetration of many such networks appears plausible in a recently considered material made from nanoparticles functionalized by single strands of DNA.Comment: 12 pages, 9 figures, submitted to Phys. Rev.

Effects of lectins on calcification by vesicles isolated from aortas of cholesterol-fed rabbits

AbstractAdvanced vascular calcification in atherosclerosis weakens arterial walls, thereby imposing a serious rupturing effect. However, the mechanism of dystrophic calcification remains unknown. Although accumulating morphological and biochemical evidence reveals a role for calcifiable vesicles in plaque calcification, the mechanism of vesicle-mediated calcification has not been fully explored. To study whether vesicles’ membrane components, such as carbohydrates, may have a role in vesicle-mediated calcification, the effect of sugar-binding lectins on calcification was investigated. Atherosclerosis was developed by feeding rabbits with a diet supplemented with 0.5% cholesterol and 2% peanut oil for 4 months. Calcifiable vesicles were then isolated from thoracic aortas by collagenase digestion. The histological examination of aortas with hematoxylin counter-staining indicated abnormal formation of large plaques enriched with macrophage-derived foam cells. Fourier transform spectroscopy revealed mild calcification in aortas indicating that advanced stages of heavy calcification have yet to be reached. However, vesicles isolated from the aortas were capable of calcification in the presence of physiological levels of Ca2+, Pi, and ATP. Thus, at this stage of atherosclerosis, aortas may start to produce calcifiable vesicles, but at a level insufficient for substantial formation of mineral in aortas. The assessments by FT-IR analysis and Alizarin red staining indicated that concanavalin A (Con A) substantially increased mineral formation by isolated vesicles. Con A also exerted a marked stimulatory effect on 45Ca and 32Pi deposition in a dose-dependent fashion with a half-maximal effect at 6–10 μg/ml. Either α-methylmannoside or α-methylglucoside, but not mannitol, at 10 mM abolished the stimulation. Con A stimulation was abolished after Con A was removed from calcifying media, suggesting that covalent binding may not be involved in the effect. Galactosides appear to also be implicated in 45Ca and 32Pi deposition since Abrus precartorius agglutinin, which specifically binds galactosides, enhanced the deposition. Neither wheat-germ agglutinin that binds N-acetylglucoside nor N-acetylgalactoside-specific Helix pomatia agglutinin was effective, suggesting that the acetylated forms of carbohydrate moieties are either absent in vesicles or may not be involved in calcification. None of these lectins exerted an effect on ATPase. Thus, the effects of lectins appeared to be mediated through interactions with carbohydrate moieties of calcifiable vesicles. Whether stimulation of vesicle-calcification by lectins is of pathological significance in atherosclerotic calcification requires further investigation

Mechanisms of calcification by vesicles isolated from atherosclerotic rabbit aortas

AbstractAlthough several lines of evidence support the role of calcifiable vesicles in dystrophic vascular calcification, the mechanisms whereby vesicles promote aortic calcification remain incompletely understood. Previous reports indicate that ATP promotes in vitro vesicle calcification. Whether ATP-initiated calcification is simply mediated through increased Pi concentrations or by other unknown mechanisms related to ATP hydrolysis is unclear. To determine whether high Pi levels resulting from ATP hydrolysis may cause Ca×P ion products to surpass the threshold for calcium phosphate precipitation, 3 mM Pi instead of 1 mM ATP was added to calcifying media. The inclusion of 1 mM ATP in calcifying media with an initial serum level of Ca2+ (1.45 mM) and Pi (2.3 mM) was much more effective in promoting calcification than the addition of 3 mM Pi. The higher effectiveness of ATP over Pi in promoting calcification was consistent throughout various incubation periods and vesicle protein ranges. To minimize the effect of Ca×Pi ion products on calcification, the ion product was kept within the physiological ranges throughout the incubation period by reducing initial Pi or ATP concentrations in calcifying media. At these low levels of ion products, ATP was still more effective than Pi in promoting calcification. Both ATP- and Pi-stimulated calcifications were found to increase with increasing levels of ion products whereas greater effectiveness of ATP over Pi remained unaltered. These observations indicate that ATP hydrolysis may initiate calcification through some mechanisms other than a simple provision of Pi in order to surpass the solubility products. Concanavalin A (Con A) was found to bind to vesicles and to enhance both ATP- and Pi-promoted calcification. Taken together, these observations suggest that ATP hydrolysis, Ca×P ion products, and vesicle-associated carbohydrates are implicated in vesicle-mediated calcification

Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency

<p>Abstract</p> <p>Background</p> <p>Investigation of metagenomes provides greater insight into uncultured microbial communities. The improvement in sequencing technology, which yields a large amount of sequence data, has led to major breakthroughs in the field. However, at present, taxonomic binning tools for metagenomes discard 30-40% of Sanger sequencing data due to the stringency of BLAST cut-offs. In an attempt to provide a comprehensive overview of metagenomic data, we re-analyzed the discarded metagenomes by using less stringent cut-offs. Additionally, we introduced a new criterion, namely, the evolutionary conservation of adjacency between neighboring genes. To evaluate the feasibility of our approach, we re-analyzed discarded contigs and singletons from several environments with different levels of complexity. We also compared the consistency between our taxonomic binning and those reported in the original studies.</p> <p>Results</p> <p>Among the discarded data, we found that 23.7 ± 3.9% of singletons and 14.1 ± 1.0% of contigs were assigned to taxa. The recovery rates for singletons were higher than those for contigs. The <it>Pearson </it>correlation coefficient revealed a high degree of similarity (0.94 ± 0.03 at the phylum rank and 0.80 ± 0.11 at the family rank) between the proposed taxonomic binning approach and those reported in original studies. In addition, an evaluation using simulated data demonstrated the reliability of the proposed approach.</p> <p>Conclusions</p> <p>Our findings suggest that taking account of conserved neighboring gene adjacency improves taxonomic assignment when analyzing metagenomes using Sanger sequencing. In other words, utilizing the conserved gene order as a criterion will reduce the amount of data discarded when analyzing metagenomes.</p