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Many viruses block host gene expression to take over the infected cell. This process, termed host shutoff, is thought to promote viral replication by preventing antiviral responses and redirecting cellular resources to viral processes. Several viruses from divergent families accomplish host shutoff through RNA degradation by endoribonucleases. However, viruses also need to ensure expression of their own genes. The influenza A virus endoribonuclease PA-X solves this problem by sparing viral mRNAs and some host RNAs necessary for viral replication. To understand how PA-X distinguishes between RNAs, we characterized PA-X cut sites transcriptome-wide using 5' rapid amplification of complementary DNA ends coupled to high-throughput sequencing. This analysis, along with RNA structure predictions and validation experiments using reporters, shows that PA-Xs from multiple influenza strains preferentially cleave RNAs at GCUG tetramers in hairpin loops. Importantly, GCUG tetramers are enriched in the human but not the influenza transcriptome. Moreover, optimal PA-X cut sites inserted in the influenza A virus genome are quickly selected against during viral replication in cells. This finding suggests that PA-X evolved these cleavage characteristics to preferentially target host over viral mRNAs in a manner reminiscent of cellular self versus non-self discrimination.

Wetlands perform important functions and provide essential ecological services, including flood attenuation, groundwater recharge and discharge, and water purification. Human activities such as urban and rural development, drainage, and land alteration can cause major disturbances, often resulting in the drying up of wetlands. Therefore, many restoration projects aim to restore wetland hydrology. Hydrology significantly affects wetland functions by modifying and determining the wetlands physicochemical environment that allows for the development of a specific biota. Despite the importance of hydrology, monitoring efforts are mainly focused on surveying and characterizing wetland habitats or plant composition. There are few datasets available from the monitoring of the depth to water table (DTW) in wetlands and when available they are rarely shared. Collecting hydrological data can contribute to a better understanding of the relationship between hydrology, soil and habitat and can help understand the effect of climate change. From 2021 to 2023, depth to water table, soil and habitat data were collected across a variety of wetland types in France with a focus on hydrological data. Using data loggers placed in 37 monitoring wells across 17 wetlands, 469001 hourly depth to water table and water temperature data were collected. The dataset includes two files containing a total of 22 variables that describe the location of sites, habitat (EUNIS: European Nature Information System), soil hydromorphy, depth to water table, and water temperature. The dataset can be used to better understand wetland hydrology and its relationship to soil and habitat. The data collection process may be used to help restoration project achieve their goal.

HERV-K(HML-2), the youngest clade of human endogenous retroviruses (HERVs), includes many intact or nearly intact proviruses, but no replication competent HML-2 proviruses have been identified in humans. HML-2-related proviruses are present in other primates, including rhesus macaques, but the extent and timing of HML-2 activity in macaques remains unclear. We have identified 145 HML-2-like proviruses in rhesus macaques, including a clade of young, rhesus-specific insertions. Age estimates, intact open reading frames, and insertional polymorphism of these insertions are consistent with recent or ongoing infectious activity in macaques. 106 of the proviruses form a clade characterized by an ~750 bp sequence between env and the 3′ long terminal repeat (LTR), derived from an ancient recombination with a HERV-K(HML-8)-related virus. This clade is found in Old World monkeys (OWM), but not great apes, suggesting it originated after the ape/OWM split. We identified similar proviruses in white-cheeked gibbons; the gibbon insertions cluster within the OWM recombinant clade, suggesting interspecies transmission from OWM to gibbons. The LTRs of the youngest proviruses have deletions in U3, which disrupt the Rec Response Element (RcRE), required for nuclear export of unspliced viral RNA. We show that the HML-8-derived region functions as a Rec-independent constitutive transport element (CTE), indicating the ancestral Rec–RcRE export system was replaced by a CTE mechanism.

In France, sickle cell disease newborn screening (SCD NBS) has been targeted to at-risk regions since 1984, but generalization to the whole population will be implemented from November 2024. Although tandem mass spectrometry (MS/MS) is already used for the NBS of several inherited metabolic diseases, its application for SCD NBS has not been widely adopted worldwide. The aim of this study was to evaluate a dedicated MS/MS kit (Targeted MS/MS Hemo, ZenTech, LaCAR Company, Liege, Belgium) for SCD NBS and to compare the results obtained with those from an NBS reference center using matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) and cation-exchange high-performance liquid chromatography (CE-HPLC, Variant NBS, Biorad Laboratories, Inc., Hercules, CA, USA) as confirmatory method. The MS/MS Hemo kit was used according to the manufacturer’s instructions and performed on a Waters Xevo TQ-D (Waters Corporation, USA). The software provided by the manufacturer was used for the calculation and analysis of peptide signal ratios. Among the 1333 samples, the results of 1324 samples were consistent with the HPLC and/or MALDI-TOF results (1263 FA, 50 FAS, 7 FAC, 1 FAO-Arab, and 3 FS). All the discordant results (one FAS on MS/MS vs. FA in CE-HPLC, one FA on MS/MS vs. FAS in CE-HPLC, seven FS on MS/MS vs. FAS in CE-HPLC) were corrected after modifying the peptide signal ratios thresholds, allowing the MS/MS Hemo kit to achieve near-100% sensitivity and specificity for SCD NBS. In conclusion, the MS/MS Hemo kit appears to be an effective method for SCD NBS, particularly for laboratories already equipped with MS/MS technology. However, these results should be confirmed in a larger cohort including a greater number of positive samples for SCD.

Many viruses shut off host gene expression to inhibit antiviral responses. Viral proteins and host proteins required for viral replication are typically spared in this process, but the mechanisms of target selectivity during host shutoff remain poorly understood. Using transcriptome-wide and targeted reporter experiments, we demonstrate that the influenza A virus endoribonuclease PA-X usurps RNA splicing to selectively target host RNAs for destruction. Proximity-labeling proteomics reveals that PA-X interacts with cellular RNA processing proteins, some of which are partially required for host shutoff. Thus, PA-X taps into host nuclear pre-mRNA processing mechanisms to destroy nascent mRNAs shortly after their synthesis. This mechanism sets PA-X apart from other viral host shutoff proteins that target actively translating mRNAs in the cytoplasm. Our study reveals a unique mechanism of host shutoff that helps us understand how influenza viruses suppress host gene expression.

La loi pour la biodiversité de 2016 a introduit dans la réglementation française la compensation dite «par l’offre» avec la création de sites naturels de compensation (SNC). La procédure d’agrément associée et les premiers retours d’expérience mettent en avant le besoin d’un cadre méthodologique transparent pour élaborer et évaluer les projets. C’est dans ce contexte que les auteurs de cet article ont élaboré une feuille de route organisée autour de critères partagés permettant d’appuyer l’élaboration de projets de SNC pertinents sur le plan écologique. La méthodologie fait actuellement l’objet de tests auprès d’opérateurs de compensation sur un échantillon de projets plus important.

Alors qu’elle occupe une part croissante du débat public ces dernières années, la séquence « Éviter-Réduire-Compenser » est un instrument de l’action publique ayant pour objectif une non-perte nette de biodiversité lors d’opérations d’aménagement du territoire. Avec l’adoption de la loi pour la reconquête de la biodiversité, de la nature et des paysages de 2016, les mesures compensatoires peuvent désormais être mises en œuvre au sein de sites naturels de compensation gérés par un opérateur en anticipation de futures demandes de compensation. Comment ces sites peuvent-ils contribuer à atteindre l’objectif de non-perte nette de biodiversité et quels sont les risques associés à leur émergence ? Dans cette introduction les auteurs proposent quelques pistes de réflexion qui seront approfondies dans ce numéro.

Un grand nombre d’opérations de restauration/création de zones humides voient le jour en France. L’efficacité de ces dernières doit être évaluée à court, moyen et long terme. C’est d’ailleurs le cas des opérations de compensation qui sont désormais soumises à obligation de résultat et doivent, pour démontrer l’efficacité de leurs opérations de restauration/création, disposer d’indicateurs robustes et facilement mobilisables. L’indicateur HYDRINDIC a ainsi été construit pour permettre le suivi et l’évaluation de l’efficacité des opérations de restauration/création de zones humides d’un point de vue hydrologique.

This review explores the fascinating world of molecules featuring multiple stereogenic elements, unraveling the different strategies designed over the years for their enantioselective synthesis. Specifically, (dynamic) kinetic resolutions, desymmetrisations and simultaneous installation of stereogenic elements exploiting either metal- or organo-catalysis are the principal approaches to efficiently create and control the three-dimensional shapes of these attractive molecules. Although most molecules presented in this review possess a stereogenic carbon atom in combination with a stereogenic axis, other combinations with helices or planes of chirality have started to emerge, as well as molecules displaying more than two different stereogenic elements. [ABSTRACT FROM AUTHOR]

While Dicer plays an important antiviral role through the RNAi pathway in plants and invertebrates, its contribution to antiviral immunity in vertebrates and more specifically mammals is more controversial. The apparent limited RNAi activity in mammalian cells has been attributed to the reduced long dsRNA processive activity of mammalian Dicer, as well as a functional incompatibility between the RNAi and IFN pathways. Why Dicer has lost this antiviral activity in the profit of the IFN pathway is still unclear. We propose that the primary direct antiviral activity of Dicer has been functionally replaced by other sensors in the IFN pathway, leading to its specialization toward microRNA maturation. As a result, Dicer can regulate the innate immune response and prevent basal activation of the IFN pathway in mammals. Here, we discuss this hypothesis, highlighting how the adaptation of the helicase domain of mammalian Dicer may be key to this process. [ABSTRACT FROM AUTHOR]

Worldwide wetland loss over the past 50 years has made wetland conservation a public policy priority, leading to an increase in wetland restoration programs. However, predicting long‐term restoration outcomes remains difficult. The monitoring of these programs rarely exceeds 5–10 years, forcing wetland managers to rely on short‐term success criteria that may be criticized by the scientific community. Our objective was to assess the significance of four short‐term success criteria (Carex ssp. shoot density, Salix ssp. survival, invasive species cover, and hydrologic dissimilarity to reference sites) used in a restoration program of 12 wetlands monitored for 5 years post‐restoration in predicting restoration outcomes 15 years post‐restoration. We defined the success of restoration efforts after 15 years using a cluster analysis‐based approach, and the clusters were described using principal coordinate analysis and Tukey's post hoc honest significant difference test. Finally, we assessed the pertinence of each short‐term success criteria in predicting long‐term restoration outcomes using Pearson correlation tests and spatial regressive models. Our results demonstrate that stress‐based short‐term success criteria can be reliable predictors of longer‐term success for communities with shallow water tables, whereas target‐species‐based short‐term success criteria are not. Hydrologic dissimilarity to the reference site was appropriate for willow‐sedge community outcome predictions, while invasive species cover was best for sedge community outcome predictions. For communities in drier habitats, such as the willow‐herb community, none of the tested short‐term success criteria were significant predictors of long‐term restoration outcomes, and further research is required to identify suitable short‐term success criteria. [ABSTRACT FROM AUTHOR]

Alors qu’elle occupe une part croissante du débat public ces dernières années, la séquence « Éviter-Réduire-Compenser » est un instrument de l’action publique ayant pour objectif une non-perte nette de biodiversité lors d’opérations d’aménagement du territoire. Avec l’adoption de la loi pour la reconquête de la biodiversité, de la nature et des paysages de 2016, les mesures compensatoires peuvent désormais être mises en œuvre au sein de sites naturels de compensation gérés par un opérateur en anticipation de futures demandes de compensation. Comment ces sites peuvent-ils contribuer à atteindre l’objectif de non-perte nette de biodiversité et quels sont les risques associés à leur émergence ? Dans cette introduction les auteurs proposent quelques pistes de réflexion qui seront approfondies dans ce numéro.

Organisé le 15 décembre 2020, le colloque « Sites naturels de compensation : quels freins et perspectives ? » a fait le point des opportunités et des écueils rencontrés lors de la mise en œuvre, en France et à l'étranger, de dispositifs de compensation par l'offre. Vous trouverez dans ce numéro de la revue Sciences Eaux & Territoires la valorisation des présentations de scientifiques et d'acteurs impliqués dans des projets de sites naturels de compensation.

Ultime étape de la séquence Eviter-Réduire-Compenser (ERC), la compensation écologique fait face à des critiques liées à la nature et à la localisation des projets de compensation. Confrontés à l’obligation de générer des gains écologiques réels et durables, la « pertinence écologique » d’un certain nombre de sites et de projets est remise en question. La loi pour la Biodiversité de 2016, qui introduit dans la réglementation française la compensation dite « par l’offre » avec les Sites Naturels de Compensation (SNC), ouvre de nouvelles opportunités pour anticiper ces problématiques. La procédure d’agrément associée et les retours des premières expérimentations SNC mettent en avant le besoin d’un cadre méthodologique transparent, aussi bien pour l’élaboration que pour l’évaluation des projets. Nous présentons ici une définition de la pertinence écologique de projets de SNC, détaillons les critères permettant de la caractériser et proposons une méthodologie encadrant son évaluation. Traduits en une grille de lecture thématique organisée autour de critères partagés, ces travaux pourraient venir appuyer dans le futur les porteurs de SNC ainsi que les services instructeurs dans l’élaboration et l’évaluation de projets de compensation écologiquement pertinents.

Dans ce regard croisé, scientifiques, acteurs économique et public des territoires et représentant d’un bureau d’étude abordent quelques questions clés posées par l’application de la séquence Éviter-Réduire-Compenser (ERC) à l’échelle de territoires. Quelle ambition lui donner en matière de conservation de la biodiversité ? Comment s’organiser dans les territoires pour la mettre en œuvre et assurer son suivi ? Et comment les chercheurs peuvent-ils accompagner les acteurs pour qu’à l’échelle choisie, les décisions prises en faveur de la biodiversité soient le plus efficaces possibles.