BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution

Coffee is one of the world’s most important agricultural commodities. Coffee belongs to the Rubiaceae family in the euasterid I clade of dicotyledonous plants, to which the Solanaceae family also belongs. Two bacterial artificial chromosome (BAC) libraries of a homozygous doubled haploid plant of Coffea canephora were constructed using two enzymes, HindIII and BstYI. A total of 134,827 high quality BAC-end sequences (BESs) were generated from the 73,728 clones of the two libraries, and 131,412 BESs were conserved for further analysis after elimination of chloroplast and mitochondrial sequences. This corresponded to almost 13 % of the estimated size of the C. canephora genome. 6.7 % of BESs contained simple sequence repeats, the most abundant (47.8 %) being mononucleotide motifs. These sequences allow the development of numerous useful marker sites. Potential transposable elements (TEs) represented 11.9 % of the full length BESs. A difference was observed between the BstYI and HindIII libraries (14.9 vs. 8.8 %). Analysis of BESs against known coding sequences of TEs indicated that 11.9 % of the genome corresponded to known repeat sequences, like for other flowering plants. The number of genes in the coffee genome was estimated at 41,973 which is probably overestimated. Comparative genome mapping revealed that microsynteny was higher between coffee and grapevine than between coffee and tomato or Arabidopsis. BESs constitute valuable resources for the first genome wide survey of coffee and provide new insights into the composition and evolution of the coffee genome.     

Large-scale patterns of river inputs in southwestern Europe: seasonal and interannual variations and potential eutrophication effects at the coastal zone

We provide data on nutrient export for 28 rivers in southwestern Europe and analyze long-term changes in the context of anthropogenic pressures and regulation policies. Special attention is given to seasonal variations, because the integrated annual values that are usually provided do not allow us to establish comparisons with seasonal phytoplankton dynamics. The eutrophication risk associated with river inputs is addressed by means of an indicator (Index of Coastal Eutrophication Potential, ICEP, Billen and Garnier, Mar Chem 106:148–160, 2007). An overview of the temporal evolution and the intra-annual variability of the ICEP is discussed for specific rivers and integrated coastal regions. The annual dynamics of the eutrophication indicator is analyzed to delimit those periods when the risk of eutrophication is particularly high. The trends in nutrient fluxes and coastal phytoplankton are compared by means of a case study (Seine Bay). The decrease in phosphorus matches a general decrease in phytoplankton biomass in the summer. However, sustained high values of nitrogen still foster the emergence of harmful algal blooms, and we found an increase in the summer abundance of dinoflagellates. The abatement of phosphorus alone is not enough to shortcut harmful blooms and toxic outbreaks in the Seine Bay. A reduction in nitrogen inputs may be necessary to effectively minimize eutrophication problems.     

Modulations of EEG Beta Power during Planning and Execution of Grasping Movements

Although beta oscillations (≈ 13–35 Hz) are often considered as a sensorimotor rhythm, their functional role remains debated. In particular, the modulations of beta power during preparation and execution of complex movements in different contexts were barely investigated. Here, we analysed the beta oscillations recorded with electroencephalography (EEG) in a precued grasping task in which we manipulated two critical parameters: the grip type (precision vs. side grip) and the force (high vs. low force) required to pull an object along a horizontal axis. A cue was presented 3 s before a GO signal and provided full, partial or no information about the two movement parameters. We measured beta power over the centro-parietal areas during movement preparation and execution as well as during object hold. We explored the modulations of power in relation to the amount and type of prior information provided by the cue. We also investigated how beta power was affected by the grip and force parameters.We observed an increase in beta power around the cue onset followed by a decrease during movement preparation and execution. These modulations were followed by a transient power increase during object hold. This pattern of modulations did not differ between the 4 movement types (2 grips ×2 forces). However, the amount and type of prior information provided by the cue had a significant effect on the beta power during the preparatory delay. We discuss how these results fit with current hypotheses on the functional role of beta oscillations.     

An Optimized Immunohistochemistry Technique Improves NMO-IgG Detection: Study Comparison with Cell-Based Assays

Cell-based assays (CBA) have increased the sensitivity of the neuromyelitis optica (NMO)-IgG/aquaporin-4-antibody detection compared to classical tissue-based indirect assays. We describe the sensitivity of an optimized immunohistochemistry (IHC-o) to detect NMO-IgG/aquaporin-4-antibody in comparison with that of two CBA: an in-house (CBA-ih) and a commercial (CBA-c) assay (Euroimmun, Germany). Coded serum from 103 patients with definite NMO and 122 inflammatory controls were studied by IHC-o, CBA-ih, and CBA-c. IHC-o used the same protocol described to detect antibodies against cell surface antigens. CBA-ih used live cells transfected with the aquaporin-4-M23-isoform. The sensitivity of the IHC-o was 74.8% (95% confidence interval [CI] 65-83) and was similar to that of the CBA-ih 75.7% (95% CI 66-84) and the CBA-c 73.8% (95% CI 64-82). The specificity of the three assays was 100% (95% CI 97-100). Interassay concordance was high, 100 of 103 samples were coincident in all techniques. The optimized immunohistochemistry proves to be as sensitive and specific as the cell-based assays. This assay extends the available tools for NMO-IgG/aquaporin-4-antibody detection.     

Local adaptation to temperature in populations and clonal lineages of the Irish potato famine pathogen Phytophthora infestans

Environmental factors such as temperature strongly impact microbial communities. In the current context of global warming, it is therefore crucial to understand the effects of these factors on human, animal, or plant pathogens. Here, we used a common‐garden experiment to analyze the thermal responses of three life‐history traits (latent period, lesion growth, spore number) in isolates of the potato late blight pathogen Phytophthora infestans from different climatic zones. We also used a fitness index (FI) aggregating these traits into a single parameter. The experiments revealed patterns of local adaptation to temperature for several traits and for the FI, both between populations and within clonal lineages. Local adaptation to temperature could result from selection for increased survival between epidemics, when isolates are exposed to more extreme climatic conditions than during epidemics. We also showed different thermal responses among two clonal lineages sympatric in western Europe, with lower performances of lineage 13_A2 compared to 6_A1, especially at low temperatures. These data therefore stress the importance of thermal adaptation in a widespread, invasive pathogen, where adaptation is usually considered almost exclusively with respect to host plants. This must now be taken into account to explain, and possibly predict, the global distribution of specific lineages and their epidemic potential.     

Functional homogenization of flower visitor communities with urbanization

Land‐use intensification and resulting habitat loss are put forward as the main causes of flower visitor decline. However, the impact of urbanization, the prime driver of land‐use intensification in Europe, is poorly studied. In particular, our understanding of whether and how it affects the composition and functioning of flower visitor assemblages is scant, yet required to cope with increasing urbanization worldwide. Here, we use a nation‐wide dataset of plant‐flower visitor (Coleoptera, Diptera, Hymenoptera, Lepidoptera) interactions sampled by citizen scientists following a standardized protocol to assess macroecological changes in richness and composition of flower visitor communities with urbanization. We measured the community composition by quantifying the relative occurrence of generalist and specialist flower visitors based on their specialisation on flowering plant families. We show that urbanization is associated with reduced flower visitor richness and a shift in community composition toward generalist insects, indicating a modification of the functional composition of communities. These results suggest that urbanization affects not only the richness of flower visitor assemblages but may also cause their large‐scale functional homogenization. Future research should focus on designing measures to reconcile urban development with flower visitor conservation.     

Cecal Ligation and Puncture Results in Long-Term Central Nervous System Myeloid Inflammation

Survivors of sepsis often experience long-term cognitive and functional decline. Previous studies utilizing lipopolysaccharide injection and cecal ligation and puncture in rodent models of sepsis have demonstrated changes in depressive-like behavior and learning and memory after sepsis, as well as evidence of myeloid inflammation and cytokine expression in the brain, but the long-term course of neuroinflammation after sepsis remains unclear. Here, we utilize cecal ligation and puncture with greater than 80% survival as a model of sepsis. We found that sepsis survivor mice demonstrate deficits in extinction of conditioned fear, but no acquisition of fear conditioning, nearly two months after sepsis. These cognitive changes occur in the absence of neuronal loss or changes in synaptic density in the hippocampus. Sepsis also resulted in infiltration of monocytes and neutrophils into the CNS at least two weeks after sepsis in a CCR2 independent manner. Cellular inflammation is accompanied by long-term expression of pro-inflammatory cytokine and chemokine genes, including TNFα and CCR2 ligands, in whole brain homogenates. Gene expression analysis of microglia revealed that while microglia do express anti-microbial genes and damage-associated molecular pattern molecules of the S100A family of genes at least 2 weeks after sepsis, they do not express the cytokines observed in whole brain homogenates. Our results indicate that in a naturalistic model of infection, sepsis results in long-term neuroinflammation, and that this sustained inflammation is likely due to interactions among multiple cell types, including resident microglia and peripherally derived myeloid cells.