Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets

Background

Evidence is accumulating that perturbation of early life microbial colonization of the gut induces long-lasting adverse health effects in individuals. Understanding the mechanisms behind these effects will facilitate modulation of intestinal health. The objective of this study was to identify biological processes involved in these long lasting effects and the (molecular) factors that regulate them. We used an antibiotic and the same antibiotic in combination with stress on piglets as an early life perturbation. Then we used host gene expression data from the gut (jejunum) tissue and community-scale analysis of gut microbiota from the same location of the gut, at three different time-points to gauge the reaction to the perturbation. We analysed the data by a new combination of existing tools. First, we analysed the data in two dimensions, treatment and time, with quadratic regression analysis. Then we applied network-based data integration approaches to find correlations between host gene expression and the resident microbial species.

Results

The use of a new combination of data analysis tools allowed us to identify significant long-lasting differences in jejunal gene expression patterns resulting from the early life perturbations. In addition, we were able to identify potential key gene regulators (hubs) for these long-lasting effects. Furthermore, data integration also showed that there are a handful of bacterial groups that were associated with temporal changes in gene expression.

Conclusion

The applied systems-biology approach allowed us to take the first steps in unravelling biological processes involved in long lasting effects in the gut due to early life perturbations. The observed data are consistent with the hypothesis that these long lasting effects are due to differences in the programming of the gut immune system as induced by the temporary early life changes in the composition and/or diversity of microbiota in the gut.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1733-8) contains supplementary material, which is available to authorized users.     

Importance of molehill disturbances for invasion by Bunias orientalis in meadows and pastures

Small-scale soil disturbances by fossorial animals can change physical and biotic conditions in disturbed patches and influence spatial and temporal dynamics, and the composition of plant communities. They create regeneration niches and colonization openings for native plants and, according to the intermediate disturbance hypothesis, they are expected to increase plant community diversity. However, it also has been reported that increased disturbance resource availability and decreased competition with native species may result in the invasion of communities by alien plant species, as predicted by the fluctuating resources theory of invasibility. In this study, we investigated the importance of European mole disturbances for the invasion of semi-natural fresh meadows and pastures by the alien plant, Bunias orientalis, which has mainly spread throughout Central Europe on anthropogenically disturbed sites. We hypothesized that the invader, being particularly well adapted to anthropogenic disturbances, enters into dense vegetation of meadows and pastures mainly on mole mounds. To assess the seedling recruitment of B. orientalis in relation to disturbance, we counted the number of seedlings that emerged on molehills and control plots in meadows and pastures. The establishment of juvenile (0–1 year) rosette plants on and off molehills was surveyed on 5 × 5 m plots. In accordance with our hypothesis, mole disturbances were found to serve as a gateway for B. orientalis by which the invader may colonize semi-natural grasslands. The seedlings of the species emerged almost solely on molehills and the young rosettes were established predominantly on mole mounds. Although the seedling density did not differ significantly between the meadows and pastures, the number of established plants in the pastures was considerably higher. We suggest that the invasion by B. orientalis in pastures may be facilitated by vegetative regeneration following root fragmentation by sheep pasturing.     

How pulse disturbances shape size‐abundance pyramids

Ecological pyramids represent the distribution of abundance and biomass of living organisms across body‐sizes. Our understanding of their expected shape relies on the assumption of invariant steady‐state conditions. However, most of the world’s ecosystems experience disturbances that keep them far from such a steady state. Here, using the allometric scaling between population growth rate and body‐size, we predict the response of size‐abundance pyramids within a trophic guild to any combination of disturbance frequency and intensity affecting all species in a similar way. We show that disturbances narrow the base of size‐abundance pyramids, lower their height and decrease total community biomass in a nonlinear way. An experimental test using microbial communities demonstrates that the model captures well the effect of disturbances on empirical pyramids. Overall, we demonstrate both theoretically and experimentally how disturbances that are not size‐selective can nonetheless have disproportionate impacts on large species.     

一个关于害虫管理的时滞脉冲生态传染病模型

本文建立了一个通过脉冲投放含有感染病毒的染病者的阶段结构SI传染病模型。并且作出了相应的数学和生物的研究．获得了当脉冲释放率大于一个关键值μ^＊时全局吸引的害虫根除的周期解．当易感害虫存在时,可以通过染病者的脉冲释放量把易感害虫控制在经济危害水平（EIL）以下．     

Asymptotic Methods for Reaction-Diffusion Systems: Past and Present

A brief historical survey of the development of asymptotic and analytical methodologies for the analysis of spatio-temporal patterns in reaction-diffusion (RD) and related systems is given. Although far from complete, the bibliography is hopefully representative of some of the advances in this area over the past 40 years. Within the scope of this survey, some of the key research contributions of Lee Segel are highlighted.     

On second order sensitivity for stage-based population projection matrix models

In this paper we present a simple method for identifying life-history perturbations in population projection matrices that yield an accelerating population growth rate. Accelerating growth means that the dependence of the growth rate on the perturbation is convex. Convexity, when the second sensitivity of the growth rate is positive, is calculated using a new formula derived from the transfer function of the perturbed system. This formula is used to explore the relationship between stasis and growth probabilities from stage-structured population projection matrices.     

Osgstu3 and osgtu4, encoding tau class glutathione S-transferases, are heavy metal- and hypoxic stress-induced and differentially salt stress-responsive in rice roots

Glutathione S-transferases (GSTs) have poorly understood roles in plant responses to environmental stresses. A polyethylene glycol (PEG)-induced tau class GST was identified in rice roots by protein microsequencing. PEG and the heavy metals Cd (20 microM), Zn (30 microM), Co and Ni rapidly and markedly induced osgstu4 and osgstu3 in rice seedling roots. Osgstu4 and osgstu3 were also induced in roots by hypoxic stress but not by cold nor heat shock. Salt stress and abscisic acid (ABA) rapidly induced osgstu3 in rice roots, whereas osgstu4 exhibited a late salt stress and no ABA response. Salicylic acid, jasmonic acid and the auxin alpha-naphthalene acetic acid triggered osgstu4 and osgstu3 expression. Osgstu4 and osgstu3 were rapidly and markedly induced by the antioxidant dithiothreitol and the strong oxidant hydrogen peroxide, which suggested that redox perturbations and reactive oxygen species are involved in their stress response regulations.     

In vivo force-velocity relation of human muscle: a modelling from sinusoidal oscillation behaviour

Isokinetic tests performed on human muscle in vivo during plantar flexion contractions lead to torque–angular velocity relationships usually fitted by Hill's equation expressed in angular terms. However, such tests can lead to discrepant results since they require maximal voluntary contractions performed in dynamic conditions. In the present study, another way to approach mechanical behaviour of a musculo-articular structure was used, i.e. sinusoidal oscillations during sub-maximal contractions. This led to the expression of (i) Bode diagrams allowing the determination of a damping coefficient (B_bode); and (ii) a viscous parameter (B_sin) using an adaptation of Hill's equation to sinusoidal oscillations. Then torque–angular velocity relationships were predicted from a model based on the interrelation between B_bode and B_sin and on the determination of optimal conditions of contraction. This offers the possibility of characterizing muscle dynamic properties by avoiding the use of isokinetic maximal contractions.     

Transport effects on surface–volume biological reactions

Many cellular reactions involve a reactant in solution binding to or dissociating from a reactant confined to a surface. This is true as well for a BIAcore, an optical biosensor that is widely used to study the interaction of biomolecules. In the flow cell of this instrument, one of the reactants is immobilized on a flat sensor surface while the other reactant flows past the surface. Both diffusion and convection play important roles in bringing the reactants into contact. Usually BIAcore binding data are analyzed using well known expressions that are valid only in the reaction-limited case when the Damk?hler number Da is small. Asymptotic and singular perturbation techniques are used to analyze dissociation of the bound state when Da is small and O(1). Linear and nonlinear integral equations result from the analysis; explicit and asymptotic solutions are constructed for physically realizable cases. In addition, effective rate constants are derived that illustrate the effects of transport on the measured rate constants. All these expressions provide a direct way to estimate the rate constants from BIAcore binding data.     

Helical Perturbations of the Flagellar Filament:Rhizobium lupiniH13–3 at 13 Å Resolution

Flagellar filaments are highly conserved structures in terms of the underlying symmetry of the polymer, subunit domain organization of the flagellin monomer, amino acid composition and primary sequence at the N and C termini. Traditionally, filaments are classified as “plain” or “complex.” In complex filaments, the helical lattice is perturbed in a pairwise manner such that the symmetry is reduced along the 6-start helical lines. Both plain (unperturbed) and complex (helically perturbed) components are helically symmetric and share a common lattice. The perturbation inRhizobium lupiniH13–3 results in a subunit composed of a dimer of flagellin. We have generated a ≈13 Å resolution three-dimensional density map of the complex filament ofR. lupiniH13–3 from low-dose images of negatively stained filaments. Compared to a previous map, which extended to only ≈25 Å resolution and which was generated from only five filaments containing six layer-lines each, the current map is a product of merging 139 data sets containing 66 layer-lines each. The higher resolution and improved signal-to-noise yield a detailed and interpretable density map. The density map is divided into four concentric rings. These amount to two dense cylinders interconnected by low density radial spokes and wrapped by a three-start external winding. The unperturbed component of the map is strikingly similar to the known plain filament maps and, in particular, to that ofCaulobacter crescentus. The helically perturbed component contributes mainly to the filaments's exterior (domain D3) where it comprises the tips of the outer domains interconnecting, pairwise, along the 11-start protofilaments and, again, laterally along the 6-start lines forming vertical and horizontal loops. Strong intersubunit connectivity occurs in the D2 shell and in the inner shell which is dominated by 3-start densities. The contribution of the complex component to the radial spokes seems negligible.