Bifurcation analysis of a two-compartment hippocampal pyramidal cell model

The Pinsky-Rinzel model is a non-smooth 2-compartmental CA3 pyramidal cell model that has been used widely within the field of neuroscience. Here we propose a modified (smooth) system that captures the qualitative behaviour of the original model, while allowing the use of available, numerical continuation methods to perform full-system bifurcation and fast-slow analysis. We study the bifurcation structure of the full system as a function of the applied current and the maximal calcium conductance. We identify the bifurcations that shape the transitions between resting, bursting and spiking behaviours, and which lead to the disappearance of bursting when the calcium conductance is reduced. Insights gained from this analysis, are then used to firstly illustrate how the irregular spiking activity found between bursting and stable spiking states, can be influenced by phase differences in the calcium and dendritic voltage, which lead to corresponding changes in the calcium-sensitive potassium current. Furthermore, we use fast-slow analysis to investigate the mechanisms of bursting and show that bursting in the model is dependent on the intermediately slow variable, calcium, while the other slow variable, the activation gate of the afterhyperpolarisation current, does not contribute to setting the intraburst dynamics but participates in setting the interburst interval. Finally, we discuss how some of the described bifurcations affect spiking behaviour, during sharp-wave ripples, in a larger network of Pinsky-Rinzel cells.     

Anti-biofouling property studies on carboxyl-modified multi-walled carbon nanotubes filled PDMS nanocomposites

Polydimethylsiloxane (PDMS) with exceptional fouling-release properties is extremely susceptible to the microfouling resulted from the colonization of the pioneer microorganisms in the marine environment. In this study, six carboxyl-modified multi-walled carbon nanotubes (cMWNTs) nanoparticles were incorporated into the PDMS matrix, respectively, in order to produce the cMWNTs-filled PDMS nanocomposites (CPs) with improved antifouling (AF) properties. The AF properties of the six CPs were examined via the field assays conducted in Weihai, China. The effects of the anti-biofouling potential of the CPs (i.e. the P₃ surface) on the colonization of the pioneer prokaryotic and eukaryotic microbes were investigated using the single-stranded conformation polymorphism technique via the comparison of the diversity indices. Different CPs have displayed differential and better AF properties as compared to that of the unfilled PDMS (P₀). The P₃ surface has exhibited exceptional anti-biofouling capacity compared with the other CPs surfaces, which can effectively prevent biofouling for more than 14 weeks in the field. The SSCP analysis revealed that the P₃ surface may have significant modulating effect on the pioneer microbial communities. The pioneer eukaryotic microbes seemed more susceptible than the pioneer prokaryotic microbes to be subjected to the major perturbations exerted by the P₃ surface. The dramatically reduced eukaryotic-microbial diversity may contribute to the impeding and weakening of the development and growth of the biofilm. The P₃ surface has the potential to be used for future maritime applications.     

Integrative computational approach for genome-based study of microbial lipid-degrading enzymes

Lipid-degrading or lipolytic enzymes have gained enormous attention in academic and industrial sectors. Several efforts are underway to discover new lipase enzymes from a variety of microorganisms with particular catalytic properties to be used for extensive applications. In addition, various tools and strategies have been implemented to unravel the functional relevance of the versatile lipid-degrading enzymes for special purposes. This review highlights the study of microbial lipid-degrading enzymes through an integrative computational approach. The identification of putative lipase genes from microbial genomes and metagenomic libraries using homology-based mining is discussed, with an emphasis on sequence analysis of conserved motifs and enzyme topology. Molecular modelling of three-dimensional structure on the basis of sequence similarity is shown to be a potential approach for exploring the structural and functional relationships of candidate lipase enzymes. The perspectives on a discriminative framework of cutting-edge tools and technologies, including bioinformatics, computational biology, functional genomics and functional proteomics, intended to facilitate rapid progress in understanding lipolysis mechanism and to discover novel lipid-degrading enzymes of microorganisms are discussed.     

Recovering mountain Mediterranean grasslands for breeding birds: ecology and population status shape species responses to management

The Mediterranean basin is considered one of the most important biodiversity hotspots. This extraordinary richness originates mainly from thousands of years of human activities that deeply modified the landscape. Safeguarding the so-called cultural landscapes plays a key role in biodiversity conservation. In this paper we present the results of our monitoring of the effects of the life project “Preservation of mountain grasslands of the Tuscan Apennines”, mainly characterized by shrub-cutting actions, on bird populations in the Pratomagno pasture, one of the two areas where the project was implemented, a SPA in eastern Tuscany. The monitoring plan covers a period of 5 years. We tested the effects of shrub clearing on a series of bird community parameters, such as abundance and richness of common species and of some ecological guilds. We also tested the timing of the response to the interventions (immediate or drawn out over time). Our results show a dramatic decrease of birds associated with shrubland, while there were no important increases in grassland species, with the sole exception of Woodlark. Regardless of their positive or negative effects, our results show different response times for individual species or groups of species. Moreover, species with a bad regional conservation status increased less than those with a good one. Broadly speaking, these results suggest that the efficacy of such projects depends on a careful preliminary assessment of a number of aspects, encompassing the nature of the interventions themselves and the characteristics of the target sites, but also the type of response of target species and the conservation status of target populations.     

Long-term bird colonization and turnover in restored woodlands

The long-term effectiveness of restored areas for biodiversity is poorly known for the majority of restored ecosystems worldwide. We quantified temporal changes in bird occurrence in restoration plantings of different ages and geometries, and compared observed patterns with a reference dataset from woodland remnants on the same farms as our plantings. Over time, bird species richness remained unchanged in spring but exhibited modest increases in winter. We found that wider plantings supported significantly greater bird species richness in spring and winter than narrow plantings. There was no evidence of a significant interaction between planting width and time. We recorded major temporal changes in the occurrence of a range of individual species that indicated a clear turnover of species as plantings matured. Our results further revealed marked differences in individual species occurrence between plantings and woodland remnants. Life-history attributes associated with temporal changes in the bird assemblage were most apparent in winter survey data, and included diet, foraging and nesting patterns, movement behaviour (e.g. migratory vs. dispersive), and body size. Differences in bird assemblages between plantings of different ages suggest that it is important that farms support a range of age classes of planted woodland, if the aim is to maximize the number of native bird species in restored areas. Our data also suggest that changes in the bird species occupying plantings of different ages can be anticipated in a broadly predictable way based on planting geometry (especially width) and key life-history attributes, particularly movement patterns and habitat and diet specialisation.     

What works in conservation? Using expert assessment of summarised evidence to identify practices that enhance natural pest control in agriculture

This paper documents an exercise to synthesize and assess the best available scientific knowledge on the effectiveness of different farm practices at enhancing natural pest regulation in agriculture. It demonstrates a novel combination of three approaches to evidence synthesis—systematic literature search, collated synopsis and evidence assessment using an expert panel. These approaches follow a logical sequence moving from a large volume of disparate evidence to a simple, easily understandable answer for use in policy or practice. The example of natural pest regulation in agriculture was selected as a case study within two independent science-policy interface projects, one European and one British. A third funder, a private business, supported the final stage to translate the synthesized findings into a useful, simplified output for agronomists. As a whole, the case study showcases how a network of scientific knowledge holders and knowledge users can work together to improve the use of science in policy and practice. The process identified five practices with good evidence of a benefit to natural pest regulation, with the most beneficial being ‘Combine trap and repellent crops in a push–pull system’. It highlights knowledge gaps, or potential research priorities, by showing practices considered important by stakeholders for which there is not enough evidence to make an assessment of effects on natural pest regulation, including ‘Alter the timing of pesticide application.’ Finally, the process identifies several important practices where the volume of evidence of effects on natural pest regulation was too large (>300 experimental studies) to be summarised with the resources available, and for which focused systematic reviews may be the best approach. These very well studied practices include ‘Reduce tillage’ and ‘Plant more than one crop per field’.