Modeling Species Distributions from Heterogeneous Data for the Biogeographic Regionalization of the European Bryophyte Flora

The definition of biogeographic regions provides a fundamental framework for a range of basic and applied questions in biogeography, evolutionary biology, systematics and conservation. Previous research suggested that environmental forcing results in highly congruent regionalization patterns across taxa, but that the size and number of regions depends on the dispersal ability of the taxa considered. We produced a biogeographic regionalization of European bryophytes and hypothesized that (1) regions defined for bryophytes would differ from those defined for other taxa due to the highly specific eco-physiology of the group and (2) their high dispersal ability would result in the resolution of few, large regions. Species distributions were recorded using 10,000 km² MGRS pixels. Because of the lack of data across large portions of the area, species distribution models employing macroclimatic variables as predictors were used to determine the potential composition of empty pixels. K-means clustering analyses of the pixels based on their potential species composition were employed to define biogeographic regions. The optimal number of regions was determined by v-fold cross-validation and Moran’s I statistic. The spatial congruence of the regions identified from their potential bryophyte assemblages with large-scale vegetation patterns is at odds with our primary hypothesis. This reinforces the notion that post-glacial migration patterns might have been much more similar in bryophytes and vascular plants than previously thought. The substantially lower optimal number of clusters and the absence of nested patterns within the main biogeographic regions, as compared to identical analyses in vascular plants, support our second hypothesis. The modelling approach implemented here is, however, based on many assumptions that are discussed but can only be tested when additional data on species distributions become available, highlighting the substantial importance of developing integrated mapping projects for all taxa in key biogeographically areas of Europe, and the Mediterranean peninsulas in particular.     

Determination and Modulation of Total and Surface Calcium-Sensing Receptor Expression in Monocytes In Vivo and In Vitro

Expression of the calcium-sensing receptor (CaSR) has previously been demonstrated in human circulating monocytes (HCM). The present study was designed to measure CaSR expression in HCM and to examine its potential modulation by pro-inflammatory cytokines, Ca2+, vitamin D sterols in U937 cell line. Twenty healthy volunteers underwent blood sampling with subsequent isolation of peripheral blood mononuclear cells (PBMC) at 3 visits. Flow cytometry analysis (FACS) was performed initially (V1) and 19 days later (V2) to examine intra- and intersubject fluctuations of total and surface CaSR expression in HCM and 15 weeks later (V3) to study the effect of vitamin D supplementation. In vitro experiments were conducted to assess the effects of pro-inflammatory cytokines, calcidiol, calcitriol and Ca2+ on CaSR expression in U937 cell line. By FACS analysis, more than 95% of HCM exhibited cell surface CaSR staining. In contrast, CaSR staining failed to detect surface CaSR expression in other PBMC. After cell permeabilization, total CaSR expression was observed in more than 95% of all types of PBMC. Both total and surface CaSR expression in HCM showed a high degree of intra-assay reproducibility (<3%) and a moderate intersubject fluctuation. In response to vitamin D supplementation, there was no significant change for both total and surface CaSR expression. In the in vitro study, U937 cells showed strong total and surface CaSR expression, and both were moderately increased in response to calcitriol exposure. Neither total nor surface CaSR expression was modified by increasing Ca2+ concentrations. Total CaSR expression was concentration dependently decreased by TNFα exposure. In conclusion, CaSR expression can be easily measured by flow cytometry in human circulating monocytes. In the in vitro study, total and surface CaSR expression in the U937 cell line were increased by calcitriol but total CaSR expression was decreased by TNFα stimulation.     

How metabolomics can contribute to bio-processes: a proof of concept study for biomarkers discovery in the context of nitrogen-starved microalgae grown in photobioreactors

Microalgae appear to be one of the most promising sustainable resources as alternative crops for the production of renewable transport fuel. The exploitation of this bioresource requires, however, a fine monitoring of the culture conditions, for example by using more relevant control variables than usual macroscopic indicators (biomass or pigment estimation). In this proof of concept study, we propose to search potential biomarkers of progressive nitrogen regime culture conditions using an untargeted metabolomic approach based on LC-HRMS combined to a non-invasive analysis based on FTIR spectroscopy. One microalgae model was investigated i.e. Chlamydomonas reinhardtii to characterize the effect of progressive nitrogen regime in batch culture conditions on its metabolome. FTIR allowed assessing the intracellular macrometabolic perturbations, highlighting the over-accumulation of carbohydrates. LC-HRMS complemented the macromolecular information by revealing the dependence of microalgae metabotypes on nitrogen regime conditions tested for cells culture. Patterns of significantly modulated metabolites were also detected during those slight contrasted nitrogen regimes and interesting features were structurally elucidated. This included metabolites belonging to the pantothenate, branched chain and aromatic amino acids pathways. In the last step of this proof of concept study, amino acid targets proposed by metabolomic investigations were assessed on nitrogen-limited continuous culture on photobioreactors. This was performed to test the validity of proposed targets in real small-scale industrial production conditions. Results were very encouraging and suggested the possibility of using potentially relevant metabolites as intracellular biomarkers only (tryptophan) or as both intra and extracellular biomarkers (e.g. 2-methylbutyric acid and ketoleucine).     

Oleic,Linoleic and Linolenic Acids Increase ROS Production by Fibroblasts via NADPH Oxidase Activation

The effect of oleic, linoleic and γ-linolenic acids on ROS production by 3T3 Swiss and Rat 1 fibroblasts was investigated. Using lucigenin-amplified chemiluminescence, a dose-dependent increase in extracellular superoxide levels was observed during the treatment of fibroblasts with oleic, linoleic and γ-linolenic acids. ROS production was dependent on the addition of β-NADH or NADPH to the medium. Diphenyleneiodonium inhibited the effect of oleic, linoleic and γ-linolenic acids on fibroblast superoxide release by 79%, 92% and 82%, respectively. Increased levels of p47^phox phosphorylation due to fatty acid treatment were detected by Western blotting analyses of fibroblast proteins. Increased p47^phox mRNA expression was observed using real-time PCR. The rank order for the fatty acid stimulation of the fibroblast oxidative burst was as follows: γ-linolenic > linoleic > oleic. In conclusion, oleic, linoleic and γ-linolenic acids stimulated ROS production via activation of the NADPH oxidase enzyme complex in fibroblasts.     

Bee Venom Phospholipase A2, a Good “Chauffeur” for Delivering Tumor Antigen to the MHC I and MHC II Peptide-Loading Compartments of the Dendritic Cells: The Case of NY-ESO-1

Bee venom phospholipase A2 (bvPLA2) is a small, 15kDa enzyme which hydrolyses many phospholipids through interfacial binding. The mutated bvPLA2H34Q (bvPLA2m), in which histidine-34 is replaced by glutamine, is not catalytically active. This protein has been shown to be a suitable membrane anchor and has been suggested as a suitable tumor-antigen vector for the development of novel dendritic cell-based vaccines. To confirm this feature, in this study the fusion protein PNY, composed of NY-ESO-1(NY(s)) fused to the C-terminus of bvPLA2m, was engineered. bvPLA2m enhanced the binding of NY(s) to the membrane of human monocyte-derived dendritic cells (DCs) and, once taken up by the cells, the antigen fused to the vector was directed to both MHC I and MHC II peptide-loading compartments. bvPLA2m was shown to increase the cross-presentation of the NY(s)-derived, restricted HLA-A*02 peptide, NY-ESO-1_157-165(NY_157-165), at the T1 cell surface. DCs loaded with the fusion protein induced cross-priming of NY(s)-specific CD8 + T-cells with greater efficiency than DCs loaded with NY(s). Sixty-five percent of these NY(s)-specific CD8+ T-cell lines could also be activated with the DCs pulsed with the peptide, NY_157-165. Of these CD8+ T-cell lines, two were able to recognize the human melanoma cell line, SK-MEL-37, in a context of HLA-A*02. Only a small number of bvPLA2m CD8+ T-cell lines were induced, indicating the low immunogenicity of the protein. It was concluded that bvPLA2m can be used as a membrane-binding vector to promote MHC class II peptide presentation and MHC class I peptide cross-presentation. Such a system can, therefore, be tested for the preparation of cell-based vaccines.     

Contrasted TCRβ Diversity of CD8+ and CD8? T Cells in Rainbow Trout

Teleost fish express highly diverse naive TCRβ (TRB) repertoires and mount strong public and private clonal responses upon infection with pathogens. Fish T cells express typical markers such as CD8, CD4-1 and CD4-2, CD3, CD28 and CTLA4. Fish CD8⁺ T cells have been shown to be responsible for antigen-specific cell-mediated cytotoxicity in in vitro systems using histo-compatible effector and target cells. We compare here the complexity of TRB repertoires between FACS sorted CD8⁺ and CD8⁻ T cells from spleen and pronephros of rainbow trout. In contrast to human, while the TRB repertoire is highly diverse and polyclonal in CD8⁺ T cells of naïve fish, it appeared very different in CD8⁻ lymphocytes with irregular CDR3 length distributions suggesting a dominance of activated clones already in naïve fish or the presence of non conventional T cells. After infection with a systemic virus, CD8⁺ T cells mount a typical response with significant skewing of CDR3 length profiles. The infection also induces significant modifications of the TRB repertoire expressed by the CD8⁻ fraction, but for a different set of V/J combinations. In this fraction, the antiviral response results in an increase of the peak diversity of spectratypes. This unusual observation reflects the presence of a number of T cell expansions that rise the relative importance of minor peaks of the highly skewed distributions observed in unchallenged animals. These results suggest that the diversity of TRB expressed by CD8⁺ and CD8⁻ αβ T cells may be subjected to different regulatory patterns in fish and in mammals.