Ditch network sustains functional connectivity and influences patterns of gene flow in an intensive agricultural landscape

In intensive agricultural landscapes, plant species previously relying on semi-natural habitats may persist as metapopulations within landscape linear elements. Maintenance of populations'' connectivity through pollen and seed dispersal is a key factor in species persistence in the face of substantial habitat loss. The goals of this study were to investigate the potential corridor role of ditches and to identify the landscape components that significantly impact patterns of gene flow among remnant populations. Using microsatellite loci, we explored the spatial genetic structure of two hydrochorous wetland plants exhibiting contrasting local abundance and different habitat requirements: the rare and regionally protected Oenanthe aquatica and the more commonly distributed Lycopus europaeus, in an 83 km² agricultural lowland located in northern France. Both species exhibited a significant spatial genetic structure, along with substantial levels of genetic differentiation, especially for L. europaeus, which also expressed high levels of inbreeding. Isolation-by-distance analysis revealed enhanced gene flow along ditches, indicating their key role in effective seed and pollen dispersal. Our data also suggested that the configuration of the ditch network and the landscape elements significantly affected population genetic structure, with (i) species-specific scale effects on the genetic neighborhood and (ii) detrimental impact of human ditch management on genetic diversity, especially for O. aquatica. Altogether, these findings highlighted the key role of ditches in the maintenance of plant biodiversity in intensive agricultural landscapes with few remnant wetland habitats.     

Characterization of oxylipins and dioxygenase genes in the asexual fungus Aspergillus niger

Background  

Aspergillus niger is an ascomycetous fungus that is known to reproduce through asexual spores, only. Interestingly, recent genome analysis of A. niger has revealed the presence of a full complement of functional genes related to sexual reproduction [1]. An example of such genes are the dioxygenase genes which in Aspergillus nidulans, have been shown to be connected to oxylipin production and regulation of both sexual and asexual sporulation [2–4]. Nevertheless, the presence of sex related genes alone does not confirm sexual sporulation in A. niger.     

Reduced Plasmodium Parasite Burden Associates with CD38+ CD4+ T Cells Displaying Cytolytic Potential and Impaired IFN-γ Production

Using a unique resource of samples from a controlled human malaria infection (CHMI) study, we identified a novel population of CD4⁺ T cells whose frequency in the peripheral blood was inversely correlated with parasite burden following P. falciparum infection. These CD4⁺ T cells expressed the multifunctional ectoenzyme CD38 and had unique features that distinguished them from other CD4⁺ T cells. Specifically, their phenotype was associated with proliferation, activation and cytotoxic potential as well as significantly impaired production of IFN-γ and other cytokines and reduced basal levels of activated STAT1. A CD38⁺ CD4⁺ T cell population with similar features was identified in healthy uninfected individuals, at lower frequency. CD38⁺ CD4⁺ T cells could be generated in vitro from CD38^- CD4⁺ T cells after antigenic or mitogenic stimulation. This is the first report of a population of CD38⁺ CD4⁺ T cells with a cytotoxic phenotype and markedly impaired IFN-γ capacity in humans. The expansion of this CD38⁺ CD4⁺ T population following infection and its significant association with reduced blood-stage parasite burden is consistent with an important functional role for these cells in protective immunity to malaria in humans. Their ubiquitous presence in humans suggests that they may have a broad role in host-pathogen defense.

Trial Registration

ClinicalTrials.gov clinical trial numbers ACTRN12612000814875, ACTRN12613000565741 and ACTRN12613001040752     

MSDA,a proteomics software suite for in‐depth Mass Spectrometry Data Analysis using grid computing

One of the major bottlenecks in the proteomics field today resides in the computational interpretation of the massive data generated by the latest generation of high‐throughput MS instruments. MS/MS datasets are constantly increasing in size and complexity and it becomes challenging to comprehensively process such huge datasets and afterwards deduce most relevant biological information. The Mass Spectrometry Data Analysis (MSDA, https://msda.unistra.fr ) online software suite provides a series of modules for in‐depth MS/MS data analysis. It includes a custom databases generation toolbox, modules for filtering and extracting high‐quality spectra, for running high‐performance database and de novo searches, and for extracting modified peptides spectra and functional annotations. Additionally, MSDA enables running the most computationally intensive steps, namely database and de novo searches, on a computer grid thus providing a net time gain of up to 99% for data processing.     

Evolution of androgen-regulated mRNA expression in mouse kidney

To gain information on the evolution of mammalian gene expression patterns, we studied the androgen-inducible expression of three kidney mRNAs in several mouse species (genus Mus). The RP2, ornithine decarboxylase, and beta-glucuronidase mRNAs have each evolved independently, in that the pattern of variation among species is unique for each. This suggests a role for gene-specific, cis-acting genetic elements. Relationships between the regulatory phenotypes and the species phylogeny suggest that the variations in hormone-inducible mRNA expression were generated by a series of independent mutations that occurred in specific lineages, resulting in modifications of the progenitor phenotype. Alternatively, the variations may have preexisted within the progenitor population as polymorphisms that were fixed during establishment of individual lineages. Thus, significant alterations in the androgen-regulated mRNA phenotype have occurred either prior to or during speciation within the Mus genus. These alterations are presumed to be in regulatory sequences that control the expression of the corresponding genes and their response to testosterone; as such, they should be useful in further studying the genetic determinants of gene expression and its evolution.      

Hedgerows and Their Role in Agricultural Landscapes

Hedgerows, rows of trees or shrubs enclosing or separating fields, are man made. They are part of rural landscapes and should not be studied without considering the farming systems and the rural society as a whole. Their species composition depends on the history of the countryside, as well as current farming practices. Land use and boundary management play a major role in determining the floristic composition of hedgerows, and are strongly related to the grain size of the field's mosaic. Hedgerow networks, due to their rectilinear shape, and with their high degree of connection, enhance or interrupt many fluxes in the landscape. Hedgerows act as a corridor of movement and dispersal for many forest species, such as carabids, small mammals, and plants. On the other hand, hedgerows interrupt or slow down air fluxes and the propagules they carry. In the heterogeneous mosaic of fields and wooded patches, hedgerows often increase the functional connectivity of rural landscapes. The future of hedgerows depends on the changes of the rural society, which includes more and more nonfarmers. Hedgerows will be considered not only as a part of a productive area, but also as an element of a multifunctional landscape.