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Studies have shown negative impacts of increased human pressures on biodiversity at local (alpha-diversity) and regional (gamma-diversity) scales. However, the diversity between local sites (beta-diversity) has received less attention. This is an important shortcoming since beta- diversity acts as a linkage between the local and regional scales. Decreased beta- diversity means that local sites lose their distinctiveness, becoming more similar to each other. This process is known as biotic homogenization. However, the mechanisms causing biotic homogenization have not been fully studied nor its impacts on different facets of biodiversity. We examined if land- use change due to human actions causes biotic homogenization of taxonomic, functional, and phylogenetic diversity in bird communities of forested habitats in the state of Minnesota, USA. We address if forest loss and increased human domination in a region were associated with decreased beta- diversity. Our results showed that elevated human pressure was not related to increased biotic homogenization in this study region. Effects of landscape change were incongruent among taxonomic, functional, and phylogenetic diversity. At all spatial scales, taxonomic diversity was unrelated to forest loss or human domination. Interestingly, increased human domination appeared to increase the functional beta- diversity of bird communities. This association was driven by a decrease in local diversity. Forest habitat loss was associated with de -creasing functional and phylogenetic diversity in local communities (alpha- diversity) and in regional species pool (gamma-diversity), but not in beta- diversity. We highlight the importance of considering multiple facets of biodiversity as their responses to human land- use is varied. Conservation significance of beta- diversity hinges on local and regional diversity responses to human land- use intensification, and organization of biodiversity should therefore be analyzed at multiple spatial scales. peerReviewed

Sexually transmissible infectious agents such as human immunodeficiency virus (HIV) and hepatitis B virus (HBV) have renewed the attention paid to viruses capable of infecting the male genital tract. The presence of viruses at this level may not only lead to their transmission and spread via semen but may also impact on male fertility and/or represent a potential cause of male genital organ cancers. This review summarizes the currently available data on the various viruses identified in the human semen and male reproductive tract, their distribution in tissues and fluids, their possible target cells and the functional consequences of their infectivity on the reproductive and endocrine systems and on genital organs cancer aetiology.

Studies have shown negative impacts of increased human pressures on biodiversity at local (alpha-diversity) and regional (gamma-diversity) scales. However, the diversity between local sites (beta-diversity) has received less attention. This is an important shortcoming since beta-diversity acts as a linkage between trends at the local and regional scales. Decreased beta-diversity means that local sites lose their distinctiveness, becoming more similar to each other. This process, known as biotic homogenization, is predicted to arise through the replacement of native specialists with native and non-native generalists. However, the mechanisms causing biotic homogenization have not been fully studied nor its impacts on different facets of biodiversity. We examined if land-use change due to human actions causes biotic homogenization of taxonomic, functional and phylogenetic diversity in bird communities of forested habitats in the state of Minnesota, USA. Our aim was to study if increased human pressure, which included human population density, land transformation, transport infrastructure, and electrical power infrastructure, was associated with increased similarity among bird point count sites. Our results showed that elevated human pressure was not related with increased biotic homogenization in this study region. Interestingly, increased human pressure appeared to increase the between-site functional diversity of bird communities. This association was driven by a decrease in local diversity, which, due to the nature of beta-diversity, led to an increase in between-site diversity. We highlight the importance of considering multiple facets of biodiversity and the use of beta-diversity in a conservation setting.

International audience; The male genital tract (MGT) is the target of a number of viral infections that can have deleterious consequences at the individual, offspring and population levels. These consequences include infertility, cancers of male organs, transmission to the embryo/fetal development abnormalities and sexual dissemination of major viral pathogens such as human immunodeficiency virus (HIV) and hepatitis B virus (HBV). Lately, two emerging viruses, Zika and Ebola, have additionally revealed that the human MGT can constitute a reservoir for viruses cleared from peripheral circulation by the immune system, leading to their sexual transmission by cured men. This represents a concern for future epidemics and further underlines the need for a better understanding of the interplay between viruses and the MGT. We review here how viruses, from ancient viruses that integrated the germ line during evolution through old viruses (e.g. papillomaviruses originating from Neanderthals) and more modern sexually-transmitted infections (e.g. simian zoonotic HIV) to emerging viruses (e.g. Ebola and Zika) take advantage of genital tract colonization for horizontal dissemination, viral persistence, vertical transmission and endogenization. The MGT immune responses to viruses and the impact of these infections are discussed. We summarize the latest data regarding the sources of viruses in semen and the complex role of this body fluid in sexual transmission. Finally, we introduce key animal findings that are relevant for our understanding of viral infection and persistence in the human MGT and suggest future research directions.

International audience; Ubiquitin-specific peptidase 18 (USP18) acts as gatekeeper of type I interferon (IFN) responses by binding to the IFN receptor subunit IFNAR2 and preventing activation of the downstream JAK/STAT pathway. In any given cell type, the level of USP18 is a key determinant of the output of IFN-stimulated transcripts. How the baseline level of USP18 is finely tuned in different cell types remains ill defined. Here, we identified microRNAs (miRNAs) that efficiently target USP18 through binding to the 3’untranslated region (3’UTR). Among these, three miRNAs are particularly enriched in circulating monocytes which exhibit low baseline USP18. Intriguingly, the USP18 3’UTR sequence is duplicated in human and chimpanzee genomes. In humans, four USP18 3’UTR copies were previously found to be embedded in long intergenic non-coding (linc) RNA genes residing in chr22q11.21 and known as FAM247A-D. Here, we further characterized their sequence and measured their expression profile in human tissues. Importantly, we describe an additional lincRNA bearing USP18 3’UTR (here linc-UR-B1) that is expressed only in testis. RNA-seq data analyses from testicular cell subsets revealed a positive correlation between linc-UR-B1 and USP18 expression in spermatocytes and spermatids. Overall, our findings uncover a set of miRNAs and lincRNAs, which may be part of a network evolved to fine-tune baseline USP18, particularly in cell types where IFN responsiveness needs to be tightly controlled.

Ubiquitin-specific peptidase 18 (USP18) acts as gatekeeper of type I interferon (IFN) responses by binding to the IFN receptor subunit IFNAR2 and preventing activation of the downstream JAK/STAT pathway. In any given cell type, the level of USP18 is a key determinant of the output of interferon-stimulated transcripts. How the baseline level of USP18 is finely tuned in different cell types remains ill defined. Here we explored post-transcriptional regulation of USP18 by microRNAs (miRNAs) and identified four miRNAs (miR-24-3p, miR-191-5p, miR-423-5pandmiR-532-3p) that efficiently targetUSP18through binding to the 3’UTR. Among these, three miRNAs are particularly enriched in circulating monocytes which exhibit low baselineUSP18. Intriguingly, theUSP183’UTR sequence is duplicated in human and chimpanzee genomes. In human, we found several copies of the 3’UTR that are embedded in long intergenic non-coding (linc) RNA genes residing in chr22q11.21 and exhibiting a tissue-specific expression pattern. Interestingly, one of these lincRNAs (here namedlinc-UR-B1) is uniquely and highly expressed in testis. RNA-seq data analyses from testicular cell subsets revealed a positive correlation betweenlinc-UR-B1andUSP18expression in spermatocytes and spermatids. Overall, our findings uncover a set of miRNAs and lincRNAs, which may be part of a network evolved to fine-tune baseline USP18, particularly in cell types where IFN responsiveness needs to be tightly controlled.SIGNIFICANT STATEMENTUSP18 is a non-redundant negative feedback regulator of type I IFN signaling and a key determinant of cell responsiveness to IFN. How baseline USP18 is set in different human cell types is ill defined. We identified three microRNAs that restrain USP18 level notably in primary monocytes through binding the 3’UTR. We found several copies of the USP18 3’UTR embedded in long intergenic non-coding (linc) RNAs which reside in a complex region of human chromosome 22. These lincRNAs are expressed in a tissue-specific manner. We describe one lincRNA expressed only in testis, and most notably in germ cells. Correlative analyses suggest that microRNAs and lincRNAs may form a network controlling baseline USP18 and IFN responsiveness.

International audience

Conflicts among different ecosystem services have been shown to be common and potentially exacerbated by management interventions. In order to improve the sustainability of natural resource use, the occurrence of these conflicts and the effects that management actions have on them need to be understood. We studied the conflicts between ecosystem services and the potential to solve them by management choices in boreal production forests. Our study area consisted of nearly 30,000 forest stands which were simulated for 50 years into the future under alternative management scenarios. The study included four ecosystem services – timber production, bilberry production, carbon storage, and pest regulation – and one biodiversity conservation objective defined as availability of deadwood resources. We 1) measured the conflicts among each pair of objectives, and 2) identified a compromise solution for each pairwise conflict defined as one which simultaneously minimizes the losses for both objectives. Our results show that conflicts between timber production and other objectives are typical, severe, and difficult to solve, while non-extractive benefits including biodiversity conservation can be more easily reconciled with each other. To mitigate the most severe conflicts in boreal forests, increased diversity in management regimes is required. peerReviewed

We developed a temperature sum model to predict the daily pollen release of alder, based on pollen data collected with pollen traps at seven locations in Finland over the years 2000–2014. We estimated the model parameters by minimizing the sum of squared errors (SSE) of the model, with weights that put more weight on binary recognition of daily presence or absence of pollen. The model results suggest that alder pollen ripens after a couple of warm days in February, while the whole pollen release period typically takes up to 4 weeks. We tested the model residuals against air humidity, precipitation and wind speed, but adding these meteorological features did not improve the model prediction capacity. Our model was able to predict the onset of pollen season with similar accuracy as models describing only the start of the pollen release period (average prediction error 8.3, median 5.0 days), while for the end of the pollen release period the accuracy of our predictions was not as good. We split the pollen data into odd and even years, and fitted our model separately to each half. Difference in the parameter values suggests a biennial behavior in the onset of pollen ripening, with almost two weeks of difference in the modeled starting date of the pollen development. Monte Carlo resampling of the observation data confirmed that the difference is not just a random anomaly in the data.

International audience

Summary The boreal biome, representing approximately one-third of remaining global forests, provides a number of crucial ecosystem services. A particular challenge in forest ecosystems is to reconcile demand for an increased timber production with provisioning of other ecosystem services and biodiversity. However, there is still little knowledge about how forest management could help solve this challenge. Hence, studies that investigate how to manage forests to reduce trade-offs between ecosystem services and biodiversity are urgently needed to help forest owners and policy makers take informed decisions. We applied seven alternative forest management regimes using a forest growth simulator in a large boreal forest production landscape. First, we estimated the potential of the landscape to provide harvest revenues, store carbon and maintain biodiversity across a 50-year time period. Then, we applied multiobjective optimization to identify the trade-offs between these three objectives and to identify the optimal combination of forest management regimes to achieve these objectives. It was not possible to achieve high levels of either carbon storage or biodiversity if the objective of forest management was to maximize timber harvest revenues. Moreover, conflicts between biodiversity and carbon storage became stronger when simultaneously targeting high levels of timber revenues. However, with small reductions in timber revenues, it was possible to greatly increase the multifunctionality of the landscape, especially the biodiversity indicators. Forest management actions, alternative to business-as-usual management, such as reducing thinnings, extending the rotation period and increasing the amount of area set aside from forestry may be necessary to safeguard biodiversity and non-timber ecosystem services in Fennoscandia. Synthesis and applications. Our results show that no forest management regime alone is able to maximize timber revenues, carbon storage and biodiversity individually or simultaneously and that a combination of different regimes is needed to resolve the conflicts among these objectives. We conclude that it is possible to reduce the trade-offs between different objectives by applying diversified forest management planning at the boreal landscape level and that we need to give up the all-encompassing objective of very intensive timber production, which is prevailing particularly in Fennoscandian countries.

The toxic dinoflagellate Alexandrium ostenfeldii is the only bioluminescent bloom-forming phytoplankton in coastal waters of the Baltic Sea. We analysed partial luciferase gene (lcf) sequences and bioluminescence production in Baltic A. ostenfeldii bloom populations to assess the distribution and consistency of the trait in the Baltic Sea, and to evaluate applications for early detection of toxic blooms. Lcf was consistently present in 61 Baltic Sea A. ostenfeldii strains isolated from six separate bloom sites. All Baltic Sea strains except one produced bioluminescence. In contrast, the presence of lcf and the ability to produce bioluminescence did vary among strains from other parts of Europe. In phylogenetic analyses, lcf sequences of Baltic Sea strains clustered separately from North Sea strains, but variation between Baltic Sea strains was not sufficient to distinguish between bloom populations. Clustering of the lcf marker was similar to internal transcribed spacer (ITS) sequences with differences being minor and limited to the lowest hierarchical clusters, indicating a similar rate of evolution of the two genes. In relation to monitoring, the consistent presence of lcf and close coupling of lcf with bioluminescence suggests that bioluminescence can be used to reliably monitor toxic bloom-forming A. ostenfeldii in the Baltic Sea.

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International audience; Sexually transmitted viruses infect the genital and colorectal mucosa of the partner exposed to contaminated genital secretions through a wide range of mechanisms, dictated in part by the organization of the mucosa. Because understanding the modes of entry into the organism of viruses transmitted through sexual intercourse is a necessary prerequisite to the design of treatments to block those infections, in vitro modeling of the transmission is essential. The aim of this review is to present the models and methodologies available for the in vitro study of the interactions between viruses and mucosal tissue and for the preclinical evaluation of antiviral compounds, and to point out their advantages and limitations according to the question being studied.

This chapter discusses challenges and possibilities involved in preserving biological diversity and the diversity of ecosystem services in the boreal zone and yet at the same time maintaining intensive timber extraction in boreal forests. Our focus is on Fennoscandian forests at the landscapes level, and we consider economic, social and ecological in the sustainability of forest management. We provide an outlook to boreal forest ecosystems and their history, and an overview of the forestry practices and policies that aim to ensure multi-functionality of Fennoscandian forests, i.e. diversity of efforts on sustaining biodiversity, timber production and other ecosystem services from forest landscapes. We review the current scientific understanding management effects on the structure and dynamics of the forest at different spatial, and the consequent repercussions on forest biodiversity and ecosystem services. Evidence suggests that many ecosystem services and biodiversity are in conflict with intensive timber production in boreal forests. We therefore present methods for assessing conflicts among alternative forest uses and for finding solutions for conflicts. We conclude the chapter by providing insights for future management aiming at sustainability from economic, ecological and social perspectives. peerReviewed

Sexually transmitted viruses infect the genital and colorectal mucosa of the partner exposed to contaminated genital secretions through a wide range of mechanisms, dictated in part by the organization of the mucosa. Because understanding the modes of entry into the organism of viruses transmitted through sexual intercourse is a necessary prerequisite to the design of treatments to block those infections, in vitro modeling of the transmission is essential. The aim of this review is to present the models and methodologies available for in vitro study of interactions between viruses and mucosal tissue and for preclinical evaluation of antiviral compounds, and to point out their advantages and limitations according to the question being studied.

Competition, habitat structure and predation risk may alter mobility and activity of animals. In particular, small predators need to weigh the positive and negative impacts of the presence of competing larger predator species. Other predators present a risk but may also enhance the predation efficiency of smaller predators if avoiding one predator species increases prey exposure to the other. We studied how habitat structure and the presence of avian predators affected the activity patterns of radio-collared least weasels Mustela nivalis nivalis, small-bodied predators highly specialized on hunting small rodents and subject to intraguild predation. Least weasels appeared to schedule their mobility according to the peak activity of the avian predator present in large outdoor enclosures. In the presence of diurnal European kestrels Falco tinnunculus, least weasels moved less during night compared with evening and day, whereas in the presence of nocturnal Tengmalm's owls Aegolius funereus, least weasels moved more during night than during other time periods. Least weasels almost exclusively used the tall grass habitat in all treatments, whereas owls used the short grass habitat most and kestrels used both habitats equally. Our results suggest that beneficial interactions play an important role in the interaction between least weasels, kestrels and owls, and that the avoidance of risky habitats by least weasels minimizes the risk of intraguild predation.