Ferromagnetic resonance and SQUID magnetometry have been used to study magnetic material in the head with antennae, thorax, and abdomen of Solenopsis interrupta ants. The temperature dependence of the head with antennae using both techniques was measured. Room-temperature spectra and saturation magnetization were used to compare the magnetic material amount in the ant body parts. Both techniques show that the highest magnetic material fraction is in the head with antennae. The ordering temperature is observed at 100 ± 20 K for the ferromagnetic resonance spectra HF component. The estimated magnetic anisotropy constant K and g-values at room temperature are in good agreement with magnetite, supporting this material as the main magnetic particle constituent in the Solenopsis interrupta head with antenna. Particle diameters of 26 ± 2 nm and smaller than 14 nm were estimated. This work suggests that the head with antenna of the Solenopsis interrupta ant contains organized magnetic material and points to it as a good candidate as a magnetic sensor.
Fire ants; FMR; SQUID; Magnetic nanoparticles; Temperature transitions
Based on the ground state of counterions condensed on a DNA molecule, a model has been developed to successfully detect the process of DNA condensation. Through further investigation, the process of DNA condensation strongly depends on the correlation distance between condensed counterions on DNA molecules. Generally, there are two routes. The process of DNA condensation with the correlation distance between condensed counterions being 2 nm or 4 nm is different from the one with the correlation distance between condensed counterions being 3 nm or 5 nm. Effects of ionic strength on the diameter of toroidal condensates originate from the increase of correlation distance between condensed counterions.
DNA condensation; Monte Carlo simulation; Correlation distance between condensed counterions
The phenomena related to brain function occur as the interplay of various modules at different spatial and temporal scales. Particularly, the integration of the dynamical behavior of cells within the complex brain topology reveals a heterogeneous multi-scale problem, which has, to date, mainly been addressed by methods of statistical physics such as mean-field approximations. In contrast, the present study introduces an abstract mathematical model of a deterministic nature that provides a robust integral transformation of the microscopic activities into macroscopic spatiotemporal patterns. The existence of the transformation operator is guaranteed by the convergence of a repetitive patching of the network domain with its fundamental domains that express the local topologies of the tissue. Depending on the choice of the local connectivity function, this framework represents a computationally efficient generalization of the classical Kirchhoff’s, Hebbian, and Hopfield’s approaches. The capabilities of this multi-scale method have been evaluated within the structure of the dorsal striatum of rats, a brain region with major involvement in motor and cognitive information processing. Numerical simulations suggest the formation of characteristic spatiotemporal patterns due to the activation of cholinergic interneurons.
Multi-scale transformations; Mathematical modeling; Dorsal striatum; Rat
We present a model for transmissible diseases spreading among predators in a predator–prey system. Upon successful contact, a susceptible individual becomes infected but is not yet able to spread the disease further. After an incubation period, the diseased individual becomes infectious. We investigate the system’s equilibria by analytical and numerical means. For a suitable set of parameter values, the system shows persistent oscillations. The model also exhibits bistability of the coexistence equilibrium with the prey-only equilibrium.
Incubating diseases; Latency; Exposed; Ecoepidemiology; Ecosystems; Primary 92D30; Secondary 92D25; 92D40
The infection pathway of a virus in the cytoplasm of a living cell is studied from the viewpoint of diffusion theory, based on a phenomenon observed by single-molecule imaging. The cytoplasm plays the role of a medium for stochastic motion of a virus contained in an endosome as well as a free virus. It is experimentally known that the exponent of anomalous diffusion fluctuates in localized areas of the cytoplasm. Here, generalizing the fractional kinetic theory, such fluctuations are described in terms of the exponent locally distributed over the cytoplasm and a theoretical proposition is presented for its statistical form. The proposed fluctuations may be examined in an experiment of heterogeneous diffusion in the infection pathway.
Fluctuations; HeLa cell; Adeno-associated virus; Endosome; Infection pathway; Fractional kinetic theory
We investigate and quantify salient features of the charge distributions on viral capsids. Our analysis combines the experimentally determined capsid geometry with simple models for ionization of amino acids, thus yielding a detailed description of spatial distribution for positive and negative charges across the capsid wall. The obtained data is processed in order to extract the mean radii of distributions, surface charge densities, as well as dipole moment densities. The results are evaluated and examined in light of previously proposed models of capsid charge distributions, which are shown to have to some extent limited value when applied to real viruses.
Capsid; Virus; Electrostatics; Geometry; Icosahedron; Dipole moment
A model of osteoporosis based on induced inflammation (IMO) was applied on rabbit bones. The structural heterogeneity and molecular complexity of bone significantly affect bone mechanical properties. A tool like Fourier transform infrared spectroscopy, able to analyze both the inorganic and organic phase simultaneously, could provide compositional information regarding cortical and trabecular sections under normal and osteoporotic conditions. In this study, we assessed the mineral/matrix ratio, carbonate and phosphate content and labile (i.e., non-apatitic) species contribution to bone mineral and collagen cross-linking patterns. Clear differences were observed between cortical and trabecular bone regarding mineral and carbonate content. Induced inflammation lowers the mineral/matrix ratio and increases the overall carbonate accumulation. Elevated concentrations of labile species were detected in osteoporotic samples, especially in the trabecular sections. Collagen cross-linking patterns were indirectly observed through the 1660/1690 cm − 1 ratio in the amide I band and a positive correlation was found with the mineralization index. Principal component analysis (PCA) applied to female samples successfully clustered trabecular and osteoporotic cases. The important role played by the phosphate ions was confirmed by corresponding loadings plots. The results suggest that the application of the IMO model to rabbit bones effectively alters bone remodeling and forms an osteoporotic bone matrix with a dissimilar composition compared to the normal one.
Fourier transform infrared spectroscopy; Bone composition; Osteoporosis; Inflammation-mediated osteoporosis; Apatite; Rabbit bone; PCA analysis
Herein, we propose a modified version of the Wako-Saitô-Muñoz-Eaton (WSME) model. The proposed model introduces an empirical temperature parameter for the hypothetical structural units (i.e., foldons) in proteins to include site-dependent thermodynamic behavior. The thermodynamics for both our proposed model and the original WSME model were investigated. For a system with beta-hairpin topology, a mathematical treatment (contact-pair treatment) to facilitate the calculation of its partition function was developed. The results show that the proposed model provides better insight into the site-dependent thermodynamic behavior of the system, compared with the original WSME model. From this site-dependent point of view, the relationship between probe-dependent experimental results and model’s thermodynamic predictions can be explained. The model allows for suggesting a general principle to identify foldon behavior. We also find that the backbone hydrogen bonds may play a role of structural constraints in modulating the cooperative system. Thus, our study may contribute to the understanding of the fundamental principles for the thermodynamics of protein folding.
WSME model; Protein; Beta-hairpin; Backbone hydrogen bond; Thermodynamics; Probe-dependent thermodynamic behavior; Site-dependent behavior; Foldon
Mucin glycoproteins consist of tandem-repeating glycosylated regions flanked by non-repetitive protein domains with little glycosylation. These non-repetitive domains are involved in polymerization of mucin and play an important role in the pH-dependent gelation of gastric mucin, which is essential for protecting the stomach from autodigestion. We examine folding of the non-repetitive sequence of PGM-2X (242 amino acids) and the von Willebrand factor vWF-C1 domain (67 amino acids) at neutral and low pH using discrete molecular dynamics (DMD) in an implicit solvent combined with a four-bead peptide model. Using the same implicit solvent parameters, folding of both domains is simulated at neutral and low pH. In contrast to vWF-C1, PGM-2X folding is strongly affected by pH as indicated by changes in the contact order, radius of gyration, free-energy landscape, and the secondary structure. Whereas the free-energy landscape of vWF-C1 shows a single minimum at both neutral and low pH, the free-energy landscape of PGM-2X is characterized by multiple minima that are more numerous and shallower at low pH. Detailed structural analysis shows that PGM-2X partially unfolds at low pH. This partial unfolding is facilitated by the C-terminal region GLU236-PRO242, which loses contact with the rest of the domain due to effective “mean-field” repulsion among highly positively charged N- and C-terminal regions. Consequently, at low pH, hydrophobic amino acids are more exposed to the solvent. In vWF-C1, low pH induces some structural changes, including an increased exposure of CYS at position 67, but these changes are small compared to those found in PGM-2X. For PGM-2X, the DMD-derived average β-strand propensity increases from 0.26 ± 0.01 at neutral pH to 0.38 ± 0.01 at low pH. For vWF-C1, the DMD-derived average β-strand propensity is 0.32 ± 0.02 at neutral pH and 0.35 ± 0.02 at low pH. The DMD-derived structural information provides insight into pH-induced changes in the folding of two distinct mucin domains and suggests plausible mechanisms of the aggregation/gelation of mucin.
Electronic supplementary material The online version of this article (doi:10.1007/s10867-012-9280-x) contains supplementary material, which is available to authorized users.
Mucin; PGM-2X; vWF-C1; Mucin gelation; DMD simulation; Protein folding; Free-energy landscape; Pig gastric mucin
The main contribution of this paper is to use homogenization techniques to compute diffusion coefficients from experimental images of microbial biofilms. Our approach requires the analysis of several experimental spatial structures of biofilms in order to derive from them a Representative Volume Element (RVE). Then, we apply a suitable numerical procedure to the RVE to derive the diffusion coefficients. We show that diffusion coefficients significantly vary with the biofilm structure. These results suggest that microbial biofilm structures can favour nutrient access in some cases.
Homogenization technique; Diffusion process; Nutrient access; Bacterial biofilms
In this paper, a deterministic malaria transmission model in the presence of a drug-resistant strain is investigated. The model is studied using stability theory of differential equations, optimal control, and computer simulation. The threshold condition for disease-free equilibrium is found to be locally asymptotically stable and can only be achieved in the absence of a drug-resistant strain in the population. The existence of multiple endemic equilibria is also established. Both the Sensitivity Index (SI) of the model parameters and the Incremental Cost-Effectiveness Ratio (ICER) for all possible combinations of the disease-control measures are determined. Our results revealed among others that the most cost-effective strategy for drug-resistant malaria control is the combination of the provision of basic amenities (such as access to clean water, electricity, good roads, health care, and education) and treatment of infective individuals. Therefore, more efforts from policy-makers on the provisions of basic amenities and treatment of infectives would go a long way to combat the malaria epidemic.
Malaria; Drug-resistant strain; Stability; Optimality system; Sensitivity analysis; 92B05; 93A30; 93C15
Revealing vibration characteristics of sub-cellular structural components such as membranes and microtubules has a principal role in obtaining a deeper understanding of their biological functions. Nevertheless, limitations and challenges in biological experiments at this scale necessitates the use of mathematical and computational models as an alternative solution. As one of the three major cytoskeletal filaments, microtubules are highly anisotropic structures built from tubulin heterodimers. They are hollow cylindrical shells with a ∼ 25 nm outer diameter and are tens of microns long. In this study, a mechanical model including the effects of the viscous cytosol and surrounding filaments is developed for predicting the coupled oscillations of a single microtubule immersed in cytoplasm. The first-order shear deformation shell theory for orthotropic materials is used to model the microtubule, whereas the motion of the cytosol is analyzed by considering the Stokes flow. The viscous cytosol and the microtubule are coupled through the continuity condition across the microtubule–cytosol interface. The stress and velocity fields in the cytosol induced by vibrating microtubule are analytically determined. Finally, the influences of the dynamic viscosity of the cytosol, filament network elasticity, microtubule shear modulus, and circumferential wave-number on longitudinal, radial, and torsional modes of microtubule vibration are elucidated.
Cell mechanics; Microtubule-cytoplasm system; Coupled frequency; Orthotropic elastic shell
Endogenous circadian rhythms allow living organisms to anticipate daily variations in their natural environment. Temperature regulation and entrainment mechanisms of circadian clocks are still poorly understood. To better understand the molecular basis of these processes, we built a mathematical model based on experimental data examining temperature regulation of the circadian RNA-binding protein CHLAMY1 from the unicellular green alga Chlamydomonas reinhardtii, simulating the effect of temperature on the rates by applying the Arrhenius equation. Using numerical simulations, we demonstrate that our model is temperature-compensated and can be entrained to temperature cycles of various length and amplitude. The range of periods that allow entrainment of the model depends on the shape of the temperature cycles and is larger for sinusoidal compared to rectangular temperature curves. We show that the response to temperature of protein (de)phosphorylation rates play a key role in facilitating temperature entrainment of the oscillator in Chlamydomonas reinhardtii. We systematically investigated the response of our model to single temperature pulses to explain experimentally observed phase response curves.
Circadian oscillator; Temperature compensation; Temperature entrainment; Phase response curves; Chlamydomonas reinhardtii
Terahertz absorption spectrum (0.5–4.0 THz) of L-alanine in the solid phase was measured by terahertz time-domain spectroscopy at room temperature. Simulations utilizing gaseous-state and solid-state theory were performed to determine the origins of the observed vibrational features. Our calculations showed that the measured features in solid-state materials could be well understood by considering the crystal packing interactions in a solid-state density functional theory calculation. Furthermore, intermolecular vibrations of L-alanine are found to be the dominating contributions to these measured spectral features in the range of 0.5–4.0 THz, except that located at 3.11 THz.
THz-TDS; L-alanine; Solid-state theory
Recent studies have discovered strong differences between the dynamics of nucleic acids (RNA and DNA) and proteins, especially at low hydration and low temperatures. This difference is caused primarily by dynamics of methyl groups that are abundant in proteins, but are absent or very rare in RNA and DNA. In this paper, we present a hypothesis regarding the role of methyl groups as intrinsic plasticizers in proteins and their evolutionary selection to facilitate protein dynamics and activity. We demonstrate the profound effect methyl groups have on protein dynamics relative to nucleic acid dynamics, and note the apparent correlation of methyl group content in protein classes and their need for molecular flexibility. Moreover, we note the fastest methyl groups of some enzymes appear around dynamical centers such as hinges or active sites. Methyl groups are also of tremendous importance from a hydrophobicity/folding/entropy perspective. These significant roles, however, complement our hypothesis rather than preclude the recognition of methyl groups in the dynamics and evolution of biomolecules.
Electronic supplementary material The online version of this article (doi:10.1007/s10867-012-9268-6) contains supplementary material, which is available to authorized users.
Protein dynamics; RNA world; RNA dynamics; Nucleic acid dynamics
Double-stranded pBS plasmid DNA was irradiated with gamma rays at doses ranging from 1 to 12 kGy and electron beams from 1 to 10 kGy. Fragment-size distributions were determined by direct visualization, using atomic force microscopy with nanometer-resolution operating in non-tapping mode, combined with an improved methodology. The fragment distributions from irradiation with gamma rays revealed discrete-like patterns at all doses, suggesting that these patterns are modulated by the base pair composition of the plasmid. Irradiation with electron beams, at very high dose rates, generated continuous distributions of highly shattered DNA fragments, similar to results at much lower dose rates found in the literature. Altogether, these results indicate that AFM could supplement traditional methods for high-resolution measurements of radiation damage to DNA, while providing new and relevant information.
Plasmid DNA; Fragment-size distributions; AFM; Gamma radiation; Electron beams
In this paper, we present a biologically detailed mathematical model of tripartite synapses, where astrocytes modulate short-term synaptic plasticity. The model consists of a pre-synaptic bouton, a post-synaptic dendritic spine-head, a synaptic cleft and a peri-synaptic astrocyte controlling Ca2 + dynamics inside the synaptic bouton. This in turn controls glutamate release dynamics in the cleft. As a consequence of this, glutamate concentration in the cleft has been modeled, in which glutamate reuptake by astrocytes has also been incorporated. Finally, dendritic spine-head dynamics has been modeled. As an application, this model clearly shows synaptic potentiation in the hippocampal region, i.e., astrocyte Ca2 + mediates synaptic plasticity, which is in conformity with the majority of the recent findings (Perea and Araque (Science 317, 1083–1086, 2007); Henneberger et al. (Nature 463, 232–236, 2010); Navarrete et al. (PLoS Biol. 10, e1001259, 2012)).
Electronic supplementary material
The online version of this article (doi:10.1007/s10867-012-9267-7) contains supplementary material, which is available to authorized users.
Astrocyte; Calcium dynamics; Short-term potentiation; Tripartite synapse
By implementing a simple reduced dimensionality model to describe the interactions in finite systems composed of two seven-amino-acid peptides, the thermodynamic properties of ordered and disordered aggregates were computed. Within this model, the hydrophobicity of each amino acid was varied, and the stability of the systems computed. Accurate averages in the canonical ensemble were obtained using various replica exchange Monte Carlo algorithms. Low and high temperature regions were encountered where the ordered and disordered aggregates were stabilized. It was observed that as the degree of hydrophobicity increased, the stability of the aggregates increased, with a significant energetic stabilization obtained for the ordered aggregates. Upon decreasing the concentration of the solution, the stability of the amorphous aggregates increased when compared to the ordered systems.
Finite systems; Peptides; Monte Carlo; Replica exchange
It is known that the presence of calcium ions (Ca2 + ) is necessary for the enterobacterial virus ΦX174 to inject its DNA into the host cell, and that some mutations in the major capsid proteins lead to better survivability at higher temperatures. Our goal in the current study is to determine the physical changes in both the wild-type and mutant virus due to the binding of Ca2 + . Thus, we performed molecular dynamics simulations of the ΦX174 major capsid protein complex with and without Ca2 + bound. Our results show that binding of Ca2 + leads to energetic and dynamical changes in the virus proteins. In particular, the results suggest that binding of Ca2 + is energetically favorable and that the mutation leads to increased fluctuations of the protein complex (especially with the calcium ions bound to the complex), which may increase the rate of genome packaging and ejection for ΦX174.
ΦX174 virus; ΦX174 major capsid protein; F242 mutation; Calcium ion binding; Viral dynamics; Viral structure & stability; Molecular dynamics simulation
The formation of a protective protein container is an essential step in the life-cycle of most viruses. In the case of single-stranded (ss)RNA viruses, this step occurs in parallel with genome packaging in a co-assembly process. Previously, it had been thought that this process can be explained entirely by electrostatics. Inspired by recent single-molecule fluorescence experiments that recapitulate the RNA packaging specificity seen in vivo for two model viruses, we present an alternative theory, which recognizes the important cooperative roles played by RNA–coat protein interactions, at sites we have termed packaging signals. The hypothesis is that multiple copies of packaging signals, repeated according to capsid symmetry, aid formation of the required capsid protein conformers at defined positions, resulting in significantly enhanced assembly efficiency. The precise mechanistic roles of packaging signal interactions may vary between viruses, as we have demonstrated for MS2 and STNV. We quantify the impact of packaging signals on capsid assembly efficiency using a dodecahedral model system, showing that heterogeneous affinity distributions of packaging signals for capsid protein out-compete those of homogeneous affinities. These insights pave the way to a new anti-viral therapy, reducing capsid assembly efficiency by targeting of the vital roles of the packaging signals, and opens up new avenues for the efficient construction of protein nanocontainers in bionanotechnology.
Virus assembly mechanism; RNA–protein interactions; Packaging signals; Fluorescence spectroscopy; Assembly models
Yeast cells approach a mating partner by polarizing along a gradient of mating pheromones that are secreted by cells of the opposite mating type. The Bar1 protease is secreted by a-cells and, paradoxically, degrades the α-factor pheromones which are produced by cells of the opposite mating type and trigger mating in a-cells. This degradation may assist in the recovery from pheromone signaling but has also been shown to play a positive role in mating. Previous studies suggested that widely diffusing protease can bias the pheromone gradient towards the closest secreting cell. Here, we show that restricting the Bar1 protease to the secreting cell itself, preventing its wide diffusion, facilitates discrimination between equivalent mating partners. This may be mostly relevant during spore germination, where most mating events occur in nature.
Gradient; Yeast; Mating
To find out the evolutionary relationships among different tRNA sequences of 21 amino acids, 22 networks are constructed. One is constructed from whole tRNAs, and the other 21 networks are constructed from the tRNAs which carry the same amino acids. A new method is proposed such that the alignment scores of any two amino acids groups are determined by the average degree and the average clustering coefficient of their networks. The anticodon feature of isolated tRNA and the phylogenetic trees of 21 group networks are discussed. We find that some isolated tRNA sequences in 21 networks still connect with other tRNAs outside their group, which reflects the fact that those tRNAs might evolve by intercrossing among these 21 groups. We also find that most anticodons among the same cluster are only one base different in the same sites when S ≥ 70, and they stay in the same rank in the ladder of evolutionary relationships. Those observations seem to agree on that some tRNAs might mutate from the same ancestor sequences based on point mutation mechanisms.
tRNA sequences; Anticodon; Network; Phylogenetic tree