An efficient approach to collaborative simulation of variable structure systems on multi-core machines

Complex variable-structure systems (CVSSs) are a common type of complex systems that exhibit changes both at structural and behavior levels. Simulations of CVSSs challenge current collaborative execution methods with increasingly big and complex models. The emergence of multi-core paradigm presents an exciting opportunity to address such challenge, so an advanced parallel simulator under multi-core environments is proposed. The simulator: (1) provides thread simulation kernels and five kinds of management services to support dynamic model structure flexibly; (2) can explore both inherent and dynamic parallelism among models based on interaction relations, and employ the multi-thread paradigm to gain good speedup; (3) adopts an efficient dynamic load-balancing method, which can migrate models among cores with very low cost and support dynamic core allocation on demand, to address evident load-imbalance problems brought by variable-structure. The experiments show that structure changes can be supported while up to 23 % performance increase can be gained.     

Morphofunctional changes in the long tubular bones of animals which have developed while readapting after physical loads

The investigation has been performed on 120 white male rats of Wistar line. By means of the morphometry, electron microscopy and chemical methods dynamics of readaptive changes have been studied in long tubular bones during the period, when the effect of physical loadings both of dynamic and static character and of various intensity has been stopped, up to the old periods of the animals' life. Readaptation after moderate dynamic and static loadings is occurring for a long time and steadily. The changes caused by static loadings are nearly completely restored in a year. Morphofunctional rearrangements of the long tubular bones in the readaptation process after moderate dynamic loadings is characterized by residual manifestations. Prolonged readaptation after intensive physical loadings does not result in a complete restoration of all the parameters studied concerning growth and skeletal development. An intensive dynamic loading produces more stable changes, that are not subjected to a complete correction even after a passive readaptation for a year. Readaptation morphofunctional rearrangements of the long tubular skeletal bones depend on conditions of the previous regimen of the motor activity.     

The capsular dynamics of Cryptococcus neoformans

Cryptococcus neoformans is a soil-dwelling fungus that causes life-threatening illness in immunocompromised individuals and latently infects many healthy individuals. C. neoformans, unlike other human pathogenic fungi, is surrounded by a polysaccharide capsule that is essential for survival and enables C. neoformans to thwart the mammalian immune system. The capsule is a dynamic structure that undergoes changes in size and rearranges during budding. Here, the latest information and unresolved questions regarding capsule synthesis, structure, assembly, growth and rearrangements are discussed along with the concept that self-assembly is important in capsular dynamics.     

Structural and functional plasticity of dendritic spines – root or result of behavior?

Dendritic spines are multifunctional integrative units of the nervous system and are highly diverse and dynamic in nature. Both internal and external stimuli influence dendritic spine density and morphology on the order of minutes. It is clear that the structural plasticity of dendritic spines is related to changes in synaptic efficacy, learning and memory and other cognitive processes. However, it is currently unclear whether structural changes in dendritic spines are primary instigators of changes in specific behaviors, a consequence of behavioral changes, or both. In this review, we first examine the basic structure and function of dendritic spines in the brain, as well as laboratory methods to characterize and quantify morphological changes in dendritic spines. We then discuss the existing literature on the temporal and functional relationship between changes in dendritic spines in specific brain regions and changes in specific behaviors mediated by those regions. Although technological advancements have allowed us to better understand the functional relevance of structural changes in dendritic spines that are influenced by environmental stimuli, the role of spine dynamics as an underlying driver or consequence of behavior still remains elusive. We conclude that while it is likely that structural changes in dendritic spines are both instigators and results of behavioral changes, improved research tools and methods are needed to experimentally and directly manipulate spine dynamics in order to more empirically delineate the relationship between spine structure and behavior.     

Protein-water interactions in a dynamic world

Protein-water interactions are key to biological function. They have an underlying dynamic component that pervades the functional roles associated both with particular systems and with the properties of proteins in general. This article focuses on the specific ways in which the dynamics of water are important to protein structure, motion and adaptability to changes in the protein environment.     

Secondary structure formation during RNA synthesis.

We observed the secondary structures that formed in an RNA molecule during its synthesis. Some of the secondary structures seen in nascent chains were observed to form, then to dissociate in favor of an alternative structure, and then to reform, as chain growth continued. The results show that secondary structures in an RNA molecule are in a state of dynamic equilibrium, and that the extension of a sequence by chain growth, or the reduction of a sequence by processing, may result in significant changes in the secondary structures that are present.     

Analysis of the dynamic and steady-state responses of growth rate and turgor pressure to changes in cell parameters

The physical analysis of plant cell enlargment is extended to show the dependence of turgor pressure and growth rate under steady-state conditions on the parameters which govern cell wall extension and water transport in growing cells and tissues, and to show the dynamic responses of turgor and growth rate to instantaneous changes in one of these parameters. The analysis is based on the fact that growth requires simultaneous water uptake and irreversible wall expansion. It shows that when a growing cell is perturbed from its steady-state growth rate, it will approach the steady-state rate with exponential kinetics. The half-time of the transient adjustment depends on the biophysical parameters governing both water transport and irreversible wall expansion. When wall extensibility is small compared to hydraulic conductance, the growth rate is controlled by the yielding properties of the cell wall, while the half-time for changes in growth rate is controlled by the water transport parameters. The reverse situation occurs when hydraulic conductance is lower than wall extensibility. The analysis also shows explicitly that turgor pressure is tightly coupled with growth rate when growth is controlled by both water transport and wall yielding parameters.     

Analysis of oscillations in yeast continuous cultures by a new simplified model

The autonomous oscillations in yeast continuous cultures are investigated analytically and related to the behaviour of the single cell by means of a suitable modified version of Monod’s classical chemostat model. Two main cell phases or states are considered to account for the experimentally observed changes occurring in the cell growth course: the budded phase and the unbudded one. Thus, a sort of two compartment structure is given to the total biomass. The model so far obtained allows one to analyse the local properties of the predicted steady states under various assumptions, both on the yield coefficients and the specific growth rates. Necessary conditions for the local instability are derived and the existence of stable limit cycles is shown by computer simulation. With respect to the qualitative changes in the metabolic parameters, this analysis agrees with the results obtained by simulation of complex structured and segregated models. However, the oscillation period is too long compared with the experimental one and this fact may be mainly due to the strong simplifying assumptions on the dynamic evolution of the transfer rates between the two compartments. The model’s usefulness seems until now restricted to the identification of the relationships between the cell cycle regulation and the oscillation triggering.     

Focal loss of actin bundles causes microtubule redistribution and growth cone turning

It is commonly believed that growth cone turning during pathfinding is initiated by reorganization of actin filaments in response to guidance cues, which then affects microtubule structure to complete the turning process. However, a major unanswered question is how changes in actin cytoskeleton are induced by guidance cues and how these changes are then translated into microtubule rearrangement. Here, we report that local and specific disruption of actin bundles from the growth cone peripheral domain induced repulsive growth cone turning. Meanwhile, dynamic microtubules within the peripheral domain were oriented into areas where actin bundles remained and were lost from areas where actin bundles disappeared. This resulted in directional microtubule extension leading to axon bending and growth cone turning. In addition, this local actin bundle loss coincided with localized growth cone collapse, as well as asymmetrical lamellipodial protrusion. Our results provide direct evidence, for the first time, that regional actin bundle reorganization can steer the growth cone by coordinating actin reorganization with microtubule dynamics. This suggests that actin bundles can be potential targets of signaling pathways downstream of guidance cues, providing a mechanism for coupling changes in leading edge actin with microtubules at the central domain during turning.     

Structural dynamics of the mitochondrial compartment.

The metabolic activities of mitochondria have been extensively characterized. However, there is much less known about the morphogenic changes of the mitochondrial compartment during growth, development and aging of the cell and the consequences of those structural changes on cellular metabolism. There is a growing body of evidence for interactions of mitochondria with cytoskeletal components and changes of mitochondrial structure during development and in response to changing environmental conditions. Segregation and recombination of mitochondrial genomes are also processes dependent upon the dynamic nature of the mitochondrial compartment. These regulatory and structural aspects of mitochondrial compartment dynamics will play an important role in the analysis of mitochondrial function and pathology.     

Growing Out of Stress: The Role of Cell- and Organ-Scale Growth Control in Plant Water-Stress Responses

Water is the most limiting resource on land for plant growth, and its uptake by plants is affected by many abiotic stresses, such as salinity, cold, heat, and drought. While much research has focused on exploring the molecular mechanisms underlying the cellular signaling events governing water-stress responses, it is also important to consider the role organismal structure plays as a context for such responses. The regulation of growth in plants occurs at two spatial scales: the cell and the organ. In this review, we focus on how the regulation of growth at these different spatial scales enables plants to acclimate to water-deficit stress. The cell wall is discussed with respect to how the physical properties of this structure affect water loss and how regulatory mechanisms that affect wall extensibility maintain growth under water deficit. At a higher spatial scale, the architecture of the root system represents a highly dynamic physical network that facilitates access of the plant to a heterogeneous distribution of water in soil. We discuss the role differential growth plays in shaping the structure of this system and the physiological implications of such changes.     

Lessons of slicing membranes: interplay of packing, free area, and lateral diffusion in phospholipid/cholesterol bilayers

We employ 100-ns molecular dynamics simulations to study the influence of cholesterol on structural and dynamic properties of dipalmitoylphosphatidylcholine bilayers in the fluid phase. The effects of the cholesterol content on the bilayer structure are considered by varying the cholesterol concentration between 0 and 50%. We concentrate on the free area in the membrane and investigate quantities that are likely to be affected by changes in the free area and free volume properties. It is found that cholesterol has a strong impact on the free area properties of the bilayer. The changes in the amount of free area are shown to be intimately related to alterations in molecular packing, ordering of phospholipid tails, and behavior of compressibility moduli. Also the behavior of the lateral diffusion of both dipalmitoylphosphatidylcholine and cholesterol molecules with an increasing amount of cholesterol can in part be understood in terms of free area. Summarizing, our results highlight the central role of free area in comprehending the structural and dynamic properties of membranes containing cholesterol.     

Wall-modifying genes regulated by the Arabidopsis homolog of trithorax, ATX1: repression of the XTH33 gene as a test case

The plant cell wall is a dynamic structure playing important roles in the control of plant cell growth and differentiation. These processes involve global reprogramming of the genome driven by dynamic changes in chromatin structure. The chromatin modifier ARABIDOPSIS HOMOLOG OF TRITHORAX (ATX1) methylates lysine residue 4 on histone H3 (H3K4me), acting as an epigenetic mark on associated genes. The remarkable overrepresentation in the ATX1-regulated gene fraction of genes encoding plasma membrane and cell wall-remodeling activities suggested a link between two separate factors affecting growth, development and adaptation in Arabidopsis: the wall-modifying activities regulating cell extension, growth and fate, and the epigenetic mechanisms regulating chromatin structure and gene expression. A co-regulated fraction of specific wall-modifying proteins suggests that they may function together. Here, we study the ATX1-dependent expression of the gene encoding the wall-loosening factor XTH33 as a test case for development- and tissue-specific effects displayed by the chromatin modifier. In addition, we show that XTH33 is, most likely, an integral plasma membrane protein. A putative transmembrane domain is conserved in some, but not all, XTH family members, suggesting that they may be differently positioned when functioning as wall modifiers.     

Cell wall traits that influence plant development,immunity, and bioconversion

The architecture of the plant cell wall is highly dynamic, being substantially re‐modeled during growth and development. Cell walls determine the size and shape of cells and contribute to the functional specialization of tissues and organs. Beyond the physiological dynamics, the wall structure undergoes changes upon biotic or abiotic stresses. In this review several cell wall traits, mainly related to pectin, one of the major matrix components, will be discussed in relation to plant development, immunity and industrial bioconversion of biomass, especially for energy production. Plant cell walls are a source of oligosaccharide fragments with a signaling function for both development and immunity. Sensing cell wall damage, sometimes through the perception of released damage‐associated molecular patterns (DAMPs), is crucial for some developmental and immunity responses. Methodological advances that are expected to deepen our knowledge of cell wall (CW) biology will also be presented.     

Freshwater goby life history in a Mediterranean stream

The Italian goby Gobius nigricans is a running-water-dwelling species inhabiting the Tuscano-Latium district and threatened by several human activities. Many aspects of its biology are currently unknown, such as the dynamic potentialities. Since age determination and dynamic assessment are considered an important tool for a correct management strategy, we aimed to investigate some aspects of the Italian goby life history by applying the fish stock assessment principles, collecting data on fertility, population structure (age-class number), growth (i.e., curvature parameter and asymptotic length), mortality (natural and due to the fishing), and longevity of a central Italian goby population to know the status and dynamic properties of the Italian goby in Mediterranean river systems and to provide a baseline for comparison with other populations. Females are subject to a strong selective pressure to quickly reach a small size to optimize reproductive output, while acquisition of a large size favored males for a more easy access to breeder females (the asymptotic length was higher in males than in females). Moreover, appreciable between-sex differences were found in both growth pattern (the growth rate was lower in females than in males) and dynamic potentialities. In particular, the mortality rate was lower in females, whereas the longevity was slightly lower in males, although the two sexes showed similar values for the two latter properties. There is considerable scope for further work on the G. nigricans growth and other freshwater gobies because information on population and dynamic properties, and assessment of factors affecting growth are still very insufficient. Handling editor: P. Viaroli     

Predator–prey instability: individual-level mechanisms for population-level results

1. In previous work we established that increasing temperature led to a destabilization of the population dynamics of the invertebrate carnivore Mesostoma ehrenbergii and its prey Daphnia pulex , which ultimately resulted in the local extinction of Daphnia at higher temperatures. Two mechanisms are proposed to explain the population-level phenomena: (1) quantitative changes in carnivore vital rates with increasing temperature led to stronger functional and numerical response and (2) qualitative changes in the dynamic allocation of energy to reproduction by the predator with increasing temperature introduces inverse density dependence in the predator's response.
2. The growth of individual M. ehrenbergii was monitored under various food conditions to determine the effect of two temperatures (18 and 24 °C) and five food levels on rates of growth, prey consumption and reproduction and on reproductive allocation patterns.
3. The first mechanism was supported by both higher consumption rates (stronger functional response) and faster growth rates with earlier age at maturity and shorter generation time (stronger numerical response).
4. Evidence for mechanism two was also provided by an alteration of the reproductive allocation pattern with temperature. Viviparous (subitaneous) eggs were more likely to be produced by this carnivore at low food levels at 24 °C, while at 18 °C, high food levels were required before individuals made this switch. This shift actually introduces inverse density dependence in the predator's numerical response which is highly destabilizing.
5. Based on the results of this study, the differential effect of M. ehrenbergii on the dynamics and structure of its D. pulex prey populations can be attributed to changes in both physiological rates and reproductive allocation patterns with temperature.     

Proton NMR and photochemically induced dynamic nuclear polarization studies of peptide fragments obtained by controlled proteolysis of mouse epidermal growth factor

Controlled proteolysis of epidermal growth factor from the mouse leads to fragments of mouse epidermal growth factor containing residues 1-48 and 1-45. The COOH-terminal pentapeptide appears to play a crucial role in determining the hydrophobic interactions between the hormone and the stationary phase during gel chromatography on TSK-125 gel. Proton NMR studies indicate that the overall structure of mouse epidermal growth factor is retained in the protein devoid of the COOH-terminal pentapeptide, while subsequent cleavage of the peptide bond between Arg-45 and Asp-46 starts to perturb the proton resonances most characteristic of the tertiary structure of the hormone, especially those from the aromatic ring protons of Tyr-37. Consequently, photochemically induced dynamic nuclear polarization experiments show an increased exposure of Tyr-37 in the fragment of mouse epidermal growth factor containing residues 1-48. Nuclear Overhauser data suggest that structural changes do occur on fragmentation but seem to be localized in the tiered-beta-sheet domain which contains Tyr-37.