Neutral and non-neutral factors shape an emergent plant–antagonist interaction

Discerning the mechanisms responsible for emergent evolutionary radiations, community assembly, and the maintenance of diversity is necessary for understanding the evolutionary ecology of species interactions in changing landscapes. These processes can be driven by stochastic (neutral) factors, such as genetic drift, or deterministic (non-neutral) factors, such as the external environment and heritable phenotypic variation. Neutral and non-neutral factors can shape species interactions, but the relative influence of these different processes on antagonistic relationships is not well understood. We leveraged the recent discovery of a novel herbivore (Caloptilia triadicae) on invasive Chinese tallow (Triadica sebifera) to investigate the nature and relative importance of different factors influencing plant–antagonist interactions. We assessed measures of host attributes, herbivore demography and herbivory across the North American range of Triadica according to geography, environmental variation, and host genetic variation. We found that leaf toughness corresponded to genetic variation in Triadica, longitude, and mean temperature. Genetic variation in Triadica was the strongest predictor of herbivore abundance, especially for the early leaf mining stages, though herbivore abundance also corresponded to longitude. Model variables did not explain leaf damage, which was driven by interactions with late-stage larvae. Trends in herbivore demography were not consistent with previously reported geographic patterns of Triadica genetic variation related to tannin defense, but were consistent with patterns revealed by other studies of Triadica phenolic compounds and C:N, as well as low sensitivity of endophagous herbivores to tannins in the absence of parasitoids. Our findings suggest that even simple geographic mosaics of genetic and environmental variation, as well as distance-dependent dispersal, can influence the establishment and trajectory of novel species interactions.     

Host genetic variation and microenvironment shape an emergent plant–antagonist interaction

Geographic mosaics of interspecific interactions can arise as a consequence of intrinsic and extrinsic deterministic factors. In this study, we took advantage of the recent discovery of a specialist leaf-miner (Caloptilia triadicae) on invasive Chinese tallow (Triadica sebifera) in the southeastern United States to examine deterministic drivers of variation in plant–animal antagonistic interactions. We conducted a common garden study to assess the influence of intrinsic host genetic variation and extrinsic microenvironment on Triadica traits as well as Caloptilia infestation and mortality. We found that tree size, branch leaf density, and leaf toughness differed according to multilocus estimates of genetic variation. Host genetic variation also influenced mortality of early instar Caloptilia, but had little effect on peak or late season infestation. Triadica from hyperinvasive populations were larger, exhibited reduced leaf density and tougher leaves, and had the lowest levels of peak season Caloptilia infestation, but also had the lowest levels of early instar mortality. Microhabitat variation associated with edge effects influenced tree size as well as late season infestation. These findings indicate that Caloptilia–Triadica interactions reflect seasonal shifts in the relative influence of intrinsic and extrinsic drivers, where peak season interactions largely reflect genetic variation in hosts, and late–season interactions reflect microenvironmental conditions. Further study of Caloptilia infestations could offer additional understanding of novel interactions that arise following species introductions.     

ProPose: a docking engine based on a fully configurable protein–ligand interaction model

Virtual high-throughput screening of molecular databases and in particular high-throughput protein–ligand docking are both common methodologies that identify and enrich hits in the early stages of the drug design process. Current protein–ligand docking algorithms often implement a program-specific model for protein–ligand interaction geometries. However, in order to create a platform for arbitrary queries in molecular databases, a new program is desirable that allows more manual control of the modeling of molecular interactions.For that reason, ProPose, an advanced incremental construction docking engine, is presented here that implements a fast and fully configurable molecular interaction and scoring model. This program uses user-defined, discrete, pharmacophore-like representations of molecular interactions that are transformed on-the-fly into a continuous potential energy surface, allowing for the incorporation of target specific interaction mechanisms into docking protocols in a straightforward manner. A torsion angle library, based on semi-empirical quantum chemistry calculations, is used to provide minimum energy torsion angles for the incremental construction algorithm. Docking results of a diverse set of protein–ligand complexes from the Protein Data Bank demonstrate the feasibility of this new approach.As a result, the seamless integration of pharmacophore-like interaction types into the docking and scoring scheme implemented in ProPose opens new opportunities for efficient, receptor-specific screening protocols. Figure ProPose — a fully configurable protein-ligand docking program — transforms pharmacophores into a smooth potential energy surface.This revised version was published online in October 2004 with corrections to the Graphical Abstract.     

Dating and localizing an invasion from post-introduction data and a coupled reaction–diffusion–absorption model

Journal of Mathematical Biology - Invasion of new territories by alien organisms is of primary concern for environmental and health agencies and has been a core topic in mathematical modeling, in...     

Predicting lncRNA–miRNA interactions based on interactome network and graphlet interaction

In the development and treatment of many human diseases, the regulatory roles between lncRNAs and miRNAs are important, but much remains unknown about them; moreover, experimental methods for analyzing them are expensive and time-consuming. In this work, we applied a semi-supervised interactome network-based approach to explore and forecast the latent interaction between lncRNAs and miRNAs. We constructed graphs according to the similarity of each of lncRNAs and miRNAs and determined the number of graphlet interaction isomers between nodes in these two graphs. According to the two graphs and the known interactive relationship, we calculated a score for lncRNA–miRNA pairs, as the prediction result. The results showed that the model (LMI-INGI) was reliable in fivefold cross-validation (AUC = 0.8957, PRE = 0.6815, REC = 0.8842, F1 score = 0.7452, AUPR = 0.9213). We also tested the model with data based on the similarity of expression profile and similarity of function for verifying the applicability of LMI-INGI, and the resulting AUC value was 0.9197 and 0.9006, respectively. Compared with the other four algorithms and variable similarity tests, our model successfully demonstrated superiority and good generalizability. LMI-INGI would be helpful in forecasting interactions between lncRNAs and miRNAs.     

An integrated fluid–structure interaction and thrombosis model for type B aortic dissection

False lumen thrombosis (FLT) in type B aortic dissection has been associated with the progression of dissection and treatment outcome. Existing computational models mostly assume rigid wall behavior which ignores the effect of flap motion on flow and thrombus formation within the FL. In this study, we have combined a fully coupled fluid–structure interaction (FSI) approach with a shear-driven thrombosis model described by a series of convection–diffusion reaction equations. The integrated FSI-thrombosis model has been applied to an idealized dissection geometry to investigate the interaction between vessel wall motion and growing thrombus. Our simulation results show that wall compliance and flap motion can influence the progression of FLT. The main difference between the rigid and FSI models is the continuous development of vortices near the tears caused by drastic flap motion up to 4.45 mm. Flap-induced high shear stress and shear rates around tears help to transport activated platelets further to the neighboring region, thus speeding up thrombus formation during the accelerated phase in the FSI models. Reducing flap mobility by increasing the Young’s modulus of the flap slows down the thrombus growth. Compared to the rigid model, the predicted thrombus volume is 25% larger using the FSI-thrombosis model with a relatively mobile flap. Furthermore, our FSI-thrombosis model can capture the gradual effect of thrombus growth on the flow field, leading to flow obstruction in the FL, increased blood viscosity and reduced flap motion. This model is a step closer toward simulating realistic thrombus growth in aortic dissection, by taking into account the effect of intimal flap and vessel wall motion.

     

Irreversibility of the interaction of human growth hormone with its receptor and analysis of irreversible reactions in radioreceptor assays—Theoretical considerations

Kinetic studies of the binding and dissociation of [¹²⁵I]-human growth hormone to rabbit liver and mammary gland membrane receptors have showed that the binding of [¹²⁵I]-human growth hormone was largely irreversible to liver membrane receptors and completely to the solubilised mammary gland receptor. As Scatchard analysis assumes complete reversibility of the hormone-receptor interaction the validity of estimates of affinity and capacity of receptors derived by this analysis may be questionable. Theoretical considerations show that in unimolecular irreversible interactions of hormone and receptor, a nonlinear (concave) or a linear Scatchard plot can be obtained. In linear Scatchard plots the capacity of the receptor obtained by extrapolation represents an overestimation of true capacity. This overestimation correlates with the value of the intercept in the Scatchard plot.     

Insulin–eukaryotic model membrane interaction: Mechanistic insight of insulin fibrillation and membrane disruption

Injection of exogenous insulin in the subcutaneous mass has been a proven therapy for type II diabetes. However, chronic administration of insulin often develops local amyloidosis at the injection site, pathologically known as “Insulin Ball”. This reduces the insulin bioavailability and exacerbates the disease pathology. Thus, the molecular interaction between insulin and the recipient's membrane surface plays a co-operative role in accelerating the amyloidosis. This interaction, however, is different from the molecular interaction of insulin with the native membranous environment of the pancreatic β-cells. The differential membrane mediated interaction that directly affects the aggregation kinetics of insulin remains elusive yet intriguing to understand the mechanism of pathological development. In this study we have characterized the interactions of insulin at different states with model eukaryotic membranes using high and low-resolution spectroscopic techniques in combination with microscopic investigation. Our results show that insulin amyloid intermediates are capable of interacting with model membranes with variable functional affinity towards the different compositions. Fluorescence correlation spectroscopy confirms the aggregation states of insulin in presence of the eukaryotic model membranes while solid-state NMR spectroscopy in conjugation with differential scanning calorimetry elucidates the molecular interaction of insulin intermediates with the lipid head groups along with the acyl chains. Additionally, dye leakage assays support the eukaryotic model membrane disruption by insulin intermediates, similar to hIAPP and Aβ40, as previously reported. Thus, the present study establishes the distinct mode of interactions of insulin amyloid with pancreatic β-cell and general mammalian cell mimicking membranes.     

Effects of curvature and cell–cell interaction on cell adhesion in microvessels

It has been found that both circulating blood cells and tumor cells are more easily adherent to curved microvessels than straight ones. This motivated us to investigate numerically the effect of the curvature of the curved vessel on cell adhesion. In this study, the fluid dynamics was carried out by the lattice Boltzmann method (LBM), and the cell dynamics was governed by the Newton’s law of translation and rotation. The adhesive dynamics model involved the effect of receptor-ligand bonds between circulating cells and endothelial cells (ECs). It is found that the curved vessel would increase the simultaneous bond number, and the probability of cell adhesion is increased consequently. The interaction between traveling cells would also affect the cell adhesion significantly. For two-cell case, the simultaneous bond number of the rear cell is increased significantly, and the curvature of microvessel further enhances the probability of cell adhesion.     

Computational modelling and analysis of mechanical conditions on cell locomotion and cell–cell interaction

Between other parameters, cell migration is partially guided by the mechanical properties of its substrate. Although many experimental works have been developed to understand the effect of substrate mechanical properties on cell migration, accurate 3D cell locomotion models have not been presented yet. In this paper, we present a novel 3D model for cells migration. In the presented model, we assume that a cell follows two main processes: in the first process, it senses its interface with the substrate to determine the migration direction and in the second process, it exerts subsequent forces to move. In the presented model, cell traction forces are considered to depend on cell internal deformation during the sensing step. A random protrusion force is also considered which may change cell migration direction and/or speed. The presented model was applied for many cases of migration of the cells. The obtained results show high agreement with the available experimental and numerical data.     

Host–virus interaction and viral evasion

With each infectious pandemic or outbreak, the medical community feels the need to revisit basic concepts of immunology to understand and overcome the difficult times brought about by these infections. Regarding viruses, they have historically been responsible for many deaths, and such a peculiarity occurs because they are known to be obligate intracellular parasites that depend upon the host's cell machinery for their replication. Successful infection with the production of essential viral components requires constant viral evolution as a strategy to manipulate the cellular environment, including host internal factors, the host's nonspecific and adaptive immune responses to viruses, the metabolic and energetic state of the infected cell, and changes in the intracellular redox environment during the viral infection cycle. Based on this knowledge, it is fundamental to develop new therapeutic strategies for controlling viral dissemination, by means of antiviral therapies, vaccines, or antioxidants, or by targeting the inhibition or activation of cell signaling pathways or metabolic pathways that are altered during infection. The rapid recovery of altered cellular homeostasis during viral infection is still a major challenge. Here, we review the strategies by which viruses evade the host's immune response and potential tools used to develop more specific antiviral therapies to cure, control, or prevent viral diseases.     

Fluid–structure interaction in a fully coupled three-dimensional mitral–atrium–pulmonary model

This paper aims to investigate detailed mechanical interactions between the pulmonary haemodynamics and left heart function in pathophysiological situations (e.g. atrial fibrillation and acute mitral regurgitation). This is achieved by developing a complex computational framework for a coupled pulmonary circulation, left atrium and mitral valve model. The left atrium and mitral valve are modelled with physiologically realistic three-dimensional geometries, fibre-reinforced hyperelastic materials and fluid–structure interaction, and the pulmonary vessels are modelled as one-dimensional network ended with structured trees, with specified vessel geometries and wall material properties. This new coupled model reveals some interesting results which could be of diagnostic values. For example, the wave propagation through the pulmonary vasculature can lead to different arrival times for the second systolic flow wave (S2 wave) among the pulmonary veins, forming vortex rings inside the left atrium. In the case of acute mitral regurgitation, the left atrium experiences an increased energy dissipation and pressure elevation. The pulmonary veins can experience increased wave intensities, reversal flow during systole and increased early-diastolic flow wave (D wave), which in turn causes an additional flow wave across the mitral valve (L wave), as well as a reversal flow at the left atrial appendage orifice. In the case of atrial fibrillation, we show that the loss of active contraction is associated with a slower flow inside the left atrial appendage and disappearances of the late-diastole atrial reversal wave (AR wave) and the first systolic wave (S1 wave) in pulmonary veins. The haemodynamic changes along the pulmonary vessel trees on different scales from microscopic vessels to the main pulmonary artery can all be captured in this model. The work promises a potential in quantifying disease progression and medical treatments of various pulmonary diseases such as the pulmonary hypertension due to a left heart dysfunction.

     

A multi-scale continuum model of skeletal muscle mechanics predicting force enhancement based on actin–titin interaction

Although recent research emphasises the possible role of titin in skeletal muscle force enhancement, this property is commonly ignored in current computational models. This work presents the first biophysically based continuum-mechanical model of skeletal muscle that considers, in addition to actin–myosin interactions, force enhancement based on actin–titin interactions. During activation, titin attaches to actin filaments, which results in a significant reduction in titin’s free molecular spring length and therefore results in increased titin forces during a subsequent stretch. The mechanical behaviour of titin is included on the microscopic half-sarcomere level of a multi-scale chemo-electro-mechanical muscle model, which is based on the classic sliding-filament and cross-bridge theories. In addition to titin stress contributions in the muscle fibre direction, the continuum-mechanical constitutive relation accounts for geometrically motivated, titin-induced stresses acting in the muscle’s cross-fibre directions. Representative simulations of active stretches under maximal and submaximal activation levels predict realistic magnitudes of force enhancement in fibre direction. For example, stretching the model by 20 % from optimal length increased the isometric force at the target length by about 30 %. Predicted titin-induced stresses in the muscle’s cross-fibre directions are rather insignificant. Including the presented development in future continuum-mechanical models of muscle function in dynamic situations will lead to more accurate model predictions during and after lengthening contractions.     

Direct and indirect effects of ocean acidification and warming on a marine plant–herbivore interaction

The impacts of climatic change on organisms depend on the interaction of multiple stressors and how these may affect the interactions among species. Consumer–prey relationships may be altered by changes to the abundance of either species, or by changes to the per capita interaction strength among species. To examine the effects of multiple stressors on a species interaction, we test the direct, interactive effects of ocean warming and lowered pH on an abundant marine herbivore (the amphipod Peramphithoe parmerong), and whether this herbivore is affected indirectly by these stressors altering the palatability of its algal food (Sargassum linearifolium). Both increased temperature and lowered pH independently reduced amphipod survival and growth, with the impacts of temperature outweighing those associated with reduced pH. Amphipods were further affected indirectly by changes to the palatability of their food source. The temperature and pH conditions in which algae were grown interacted to affect algal palatability, with acidified conditions only affecting feeding rates when algae were also grown at elevated temperatures. Feeding rates were largely unaffected by the conditions faced by the herbivore while feeding. These results indicate that, in addition to the direct effects on herbivore abundance, climatic stressors will affect the strength of plant–herbivore interactions by changes to the susceptibility of plant tissues to herbivory.     

Plant-mediated effects on an insect–pathogen interaction vary with intraspecific genetic variation in plant defences

Baculoviruses are food-borne microbial pathogens that are ingested by insects on contaminated foliage. Oxidation of plant-derived phenolics, activated by insect feeding, can directly interfere with infections in the gut. Since phenolic oxidation is an important component of plant resistance against insects, baculoviruses are suggested to be incompatible with plant defences. However, plants among and within species invest differently in a myriad of chemical and physical defences. Therefore, we hypothesized that among eight soybean genotypes, some genotypes would be able to maintain both high resistance against an insect pest and high efficacy of a baculovirus. Soybean constitutive (non-induced) and jasmonic acid (JA)-induced (anti-herbivore response) resistance was measured against the fall armyworm Spodoptera frugiperda (weight gain, leaf consumption and utilization). Indicators of phenolic oxidation were measured as foliar phenolic content and peroxidase activity. Levels of armyworm mortality inflicted by baculovirus (SfMNPV) did not vary among soybean genotypes when the virus was ingested with non-induced foliage. Ingestion of the virus on JA-induced foliage reduced armyworm mortality, relative to non-induced foliage, on some soybean genotypes. Baculovirus efficacy was lower when ingested with foliage that contained higher phenolic content and defensive properties that reduced armyworm weight gain and leaf utilization. However, soybean genotypes that defended the plant by reducing consumption rate and strongly deterred feeding upon JA-induction did not reduce baculovirus efficacy, indicating that these defences may be more compatible with baculoviruses to maximize plant protection. Differential compatibility of defence traits with the third trophic level highlights an important cost/trade-off associated with plant defence strategies.     

Rapid recovery of an insect–plant interaction following habitat loss and experimental wetland restoration

This study examined the impact of wetland habitat loss and isolation on an insect–plant interaction, and the subsequent rate of recovery of the interaction following experimental habitat restoration. We compared herbivore colonisation rates and herbivory damage by ‘Batrachedra’ sp. (Lepidoptera: Coleophoridae) on experimentally placed potted Sporadanthus ferrugineus (Restionaceae) plants at increasing distances (up to 800 m) from an intact habitat (the source population). These tests showed that even a moderate degree of isolation (i.e. greater than 400 m) from the intact wetland habitat caused an almost complete collapse of the insect–plant interaction, at least in the short term. The number of eggs and larvae of colonising ‘Batrachedra’ sp., as well as average larval size and the proportion of S. ferrugineus stems damaged, all decreased logarithmically with increasing distance from the intact habitat, presumably due to dispersal limitation of the herbivore. Subsequently, to test whether the interaction can recover following habitat restoration, we surveyed herbivore colonisation rates and herbivory damage on naturally regenerated S. ferrugineus plants on experimentally restored ‘islands’ at increasing distances (up to 800 m) from an intact habitat. The rate of recovery of the interaction was surprisingly rapid (i.e. between 196 and 308 weeks). The degree of difference in the density of eggs and larvae, and in the proportion of stems damaged with increasing isolation from the intact wetland, gradually diminished over 196 weeks. After 308 weeks there was no significant difference in the insect–plant interaction between the intact wetland sites and any of the experimentally restored sites up to 800 m away. These results suggest that some insect–plant interactions can recover rapidly from habitat loss with restoration management.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Community-driven dispersal in an individual-based predator–prey model

We present a spatial, individual-based predator–prey model in which dispersal is dependent on the local community. We determine species suitability to the biotic conditions of their local environment through a time and space varying fitness measure. Dispersal of individuals to nearby communities occurs whenever their fitness falls below a predefined tolerance threshold. The spatiotemporal dynamics of the model is described in terms of this threshold. We compare this dynamics with the one obtained through density-independent dispersal and find marked differences. In the community-driven scenario, the spatial correlations in the population density do not vary in a linear fashion as we increase the tolerance threshold. Instead we find the system to cross different dynamical regimes as the threshold is raised. Spatial patterns evolve from disordered, to scale-free complex patterns, to finally becoming well-organized domains. This model therefore predicts that natural populations, the dispersal strategies of which are likely to be influenced by their local environment, might be subject to complex spatiotemporal dynamics.     

Influences of plaque eccentricity and composition on the stent–plaque–artery interaction during stent implantation

Biomechanics and Modeling in Mechanobiology - This work aims to investigate the effects of plaque eccentricity and composition on the stent performance and stress distributions of plaque and artery...     

Study on the interaction and relation of society,economy and environment based on PCA–VAR model: As a case study of the Bohai Rim region,China

Ongoing success throughout regional development is contingent on maintaining the function, quality and harmony progress in society, economy and environment domains, so exploring the interaction and relation among them should be considerable significant. The model by coupling principal component analysis and vector autoregressive, which relate the aggregated values and dynamic analysis among factors, is proposed to achieve the qualitative and quantitative analysis of interaction and relation among society, economy and environment subsystem, providing a framework to conceptualize the influences among their changes and simulate the future scenarios in the Bohai Rim region. The impulse response analysis and variance decomposition of vector autoregressive method, in particular, permit dynamic interaction between every two systems and display clear decomposition of contribution for each change, respectively. This study results show that: there is a virtuous circle of promotion between economic growth and social progress no matter which is regarded as the endogenous variable during the study period, and yet the negative effect to environmental changes had been produced; what the improvement of social and environmental situation need most might be advancing its own progress; it is also reflected that the entire complicated system walk on the path of unsustainable development due to the evident disequilibrium of three subsystems; and the scenario analysis results obviously tell that in order to attain coordinated development, the annual growth rate of 12% to 16% of overall environmental level should be anticipated along with 8% of social and economic level improve. The study guide future possibilities for relatively more harmonious interconnections among social, economic and the environmental development.