Exon skipping as a therapeutic strategy applied to an RYR1 mutation with pseudo-exon inclusion causing a severe core myopathy.

International audienceCentral core disease is a myopathy often arising from mutations in the type 1 ryanodine receptor (RYR1) gene, encoding the sarcoplasmic reticulum calcium release channel RyR1. No treatment is currently available for this disease. We studied the pathological situation of a severely affected child with two recessive mutations, which resulted in a massive reduction in the amount of RyR1. The paternal mutation induced the inclusion of a new in-frame pseudo-exon in RyR1 mRNA that resulted in the insertion of additional amino acids leading to the instability of the protein. We hypothesized that skipping this additional exon would be sufficient to restore RyR1 expression and to normalize calcium releases. We therefore developed U7-AON lentiviral vectors to force exon skipping on affected primary muscle cells. The efficiency of the exon skipping was evaluated at the mRNA level, at the protein level, and at the functional level using calcium imaging. In these affected cells, we observed a decreased inclusion of the pseudo-exon, an increased RyR1 protein expression, and a restoration of calcium releases of normal amplitude either upon direct RyR1 stimulation or in response to membrane depolarization. This study is the first demonstration of the potential of exon-skipping strategy for the therapy of central core disease, from the molecular to the functional level

Toward spatial fit in the governance of global commodity flows

Unidad de excelencia María de Maeztu CEX2019-000940-MGlobal commodity flows between distally connected social-ecological systems pose important challenges to sustainability governance. These challenges are partly due to difficulties in designing and implementing governance institutions that fit or match the scale of the environmental and social problems generated in such telecoupled systems. We focus on the spatial dimension of governance fit in relation to global commodity flows and telecoupled systems. Specifically, we draw on examples from land use and global agricultural commodity governance to examine two overarching types of governance mismatches: boundary mismatches and resolution mismatches. We argue that one way to address mismatches is through governance rescaling and illustrate this approach with reference to examples of three broad types of governance approaches: trade agreements, due diligence laws, and landscape approaches to supply chain governance. No single governance approach is likely to address all mismatches, highlighting the need to align multiple governance approaches to govern telecoupled systems effectively

Workshop on accounting for fishers and other stakeholders’ perceptions of the dynamics of fish stocks in ICES advice (WKAFPA)

The objective of the Workshop on accounting for fishers and other stakeholders’ perceptions of the dynamics of fish stocks in ICES advice (WKAFPA) was to identify where and how stake- holder information could be incorporated in the ICES fisheries advice process. It adopted an operational definition of the concept of perception, where perceptions result from observations, interpreted in light of experience, that can be supported by data, information and knowledge to generate evidence about them. Stakeholder information can be either structured (e.g. routinely collected information in a standardized format) or unstructured (e.g. experiential information) and either of those can inform decisions made during the production of ICES advice. Most notably, the group identified there was a need to engage with stakeholders earlier in the process, i.e. before benchmarks meetings take place and before preliminary assessment results are used as the basis to predict total allowable catches for upcoming advice (Figure 4.2). It was therefore recommended to include in the ICES process the organisation of pre-bench- mark/roadmap workshops where science and data needs of upcoming benchmarks can be iden- tified, followed by making arrangements how scientists and stakeholders can collaborate to ac- cess, prepare for use (where relevant) and document the structured and unstructured infor- mation well ahead of the benchmark meetings. It was also recommended to organise ‘sense-checking’ sessions with stakeholders when prelim- inary assessments are available but not yet used as the basis for advisory production. This would allow stakeholders and assessment scientists to verify available knowledge and data against stock perceptions and provide additional considerations relevant for the production of TAC ad- vice. Next to these two additional activities, it is recommended that communication on differ- ences in stakeholder perception or data derived perceptions are communicated within the ICES assessment reports as well as in the ICES advice in a transparent manner. Not only should dif- ferences or similarities be documented and communicated, in those cases where there are differ- ences in perception between ICES stock assessments and stakeholders, a working group, external to the assessment working groups, should evaluate these differences and describe whether these differences can be logically explained or require further investigation. This outcome of this pro- cess may potentially lead to new data collection or additional analyses suitable for input to benchmarks. Essential in this entire process is making sure the same language is spoken between scientists and stakeholders, that there are clear and transparent processes in place on how to deal with stakeholder information and communicate clearly how this information is used in the prepara- tion of ICES advice.info:eu-repo/semantics/publishedVersio

3 years of liraglutide versus placebo for type 2 diabetes risk reduction and weight management in individuals with prediabetes: a randomised, double-blind trial

Background: Liraglutide 3·0 mg was shown to reduce bodyweight and improve glucose metabolism after the 56-week period of this trial, one of four trials in the SCALE programme. In the 3-year assessment of the SCALE Obesity and Prediabetes trial we aimed to evaluate the proportion of individuals with prediabetes who were diagnosed with type 2 diabetes. Methods: In this randomised, double-blind, placebo-controlled trial, adults with prediabetes and a body-mass index of at least 30 kg/m2, or at least 27 kg/m2 with comorbidities, were randomised 2:1, using a telephone or web-based system, to once-daily subcutaneous liraglutide 3·0 mg or matched placebo, as an adjunct to a reduced-calorie diet and increased physical activity. Time to diabetes onset by 160 weeks was the primary outcome, evaluated in all randomised treated individuals with at least one post-baseline assessment. The trial was conducted at 191 clinical research sites in 27 countries and is registered with ClinicalTrials.gov, number NCT01272219. Findings: The study ran between June 1, 2011, and March 2, 2015. We randomly assigned 2254 patients to receive liraglutide (n=1505) or placebo (n=749). 1128 (50%) participants completed the study up to week 160, after withdrawal of 714 (47%) participants in the liraglutide group and 412 (55%) participants in the placebo group. By week 160, 26 (2%) of 1472 individuals in the liraglutide group versus 46 (6%) of 738 in the placebo group were diagnosed with diabetes while on treatment. The mean time from randomisation to diagnosis was 99 (SD 47) weeks for the 26 individuals in the liraglutide group versus 87 (47) weeks for the 46 individuals in the placebo group. Taking the different diagnosis frequencies between the treatment groups into account, the time to onset of diabetes over 160 weeks among all randomised individuals was 2·7 times longer with liraglutide than with placebo (95% CI 1·9 to 3·9, p<0·0001), corresponding with a hazard ratio of 0·21 (95% CI 0·13–0·34). Liraglutide induced greater weight loss than placebo at week 160 (–6·1 [SD 7·3] vs −1·9% [6·3]; estimated treatment difference −4·3%, 95% CI −4·9 to −3·7, p<0·0001). Serious adverse events were reported by 227 (15%) of 1501 randomised treated individuals in the liraglutide group versus 96 (13%) of 747 individuals in the placebo group. Interpretation: In this trial, we provide results for 3 years of treatment, with the limitation that withdrawn individuals were not followed up after discontinuation. Liraglutide 3·0 mg might provide health benefits in terms of reduced risk of diabetes in individuals with obesity and prediabetes. Funding: Novo Nordisk, Denmark

DMTs and Covid-19 severity in MS: a pooled analysis from Italy and France

We evaluated the effect of DMTs on Covid-19 severity in patients with MS, with a pooled-analysis of two large cohorts from Italy and France. The association of baseline characteristics and DMTs with Covid-19 severity was assessed by multivariate ordinal-logistic models and pooled by a fixed-effect meta-analysis. 1066 patients with MS from Italy and 721 from France were included. In the multivariate model, anti-CD20 therapies were significantly associated (OR = 2.05, 95%CI = 1.39–3.02, p < 0.001) with Covid-19 severity, whereas interferon indicated a decreased risk (OR = 0.42, 95%CI = 0.18–0.99, p = 0.047). This pooled-analysis confirms an increased risk of severe Covid-19 in patients on anti-CD20 therapies and supports the protective role of interferon

TRY plant trait database – enhanced coverage and open access

Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Extracorporeal Membrane Oxygenation for Severe Acute Respiratory Distress Syndrome associated with COVID-19: An Emulated Target Trial Analysis.

RATIONALE: Whether COVID patients may benefit from extracorporeal membrane oxygenation (ECMO) compared with conventional invasive mechanical ventilation (IMV) remains unknown. OBJECTIVES: To estimate the effect of ECMO on 90-Day mortality vs IMV only Methods: Among 4,244 critically ill adult patients with COVID-19 included in a multicenter cohort study, we emulated a target trial comparing the treatment strategies of initiating ECMO vs. no ECMO within 7 days of IMV in patients with severe acute respiratory distress syndrome (PaO2/FiO2 <80 or PaCO2 ≥60 mmHg). We controlled for confounding using a multivariable Cox model based on predefined variables. MAIN RESULTS: 1,235 patients met the full eligibility criteria for the emulated trial, among whom 164 patients initiated ECMO. The ECMO strategy had a higher survival probability at Day-7 from the onset of eligibility criteria (87% vs 83%, risk difference: 4%, 95% CI 0;9%) which decreased during follow-up (survival at Day-90: 63% vs 65%, risk difference: -2%, 95% CI -10;5%). However, ECMO was associated with higher survival when performed in high-volume ECMO centers or in regions where a specific ECMO network organization was set up to handle high demand, and when initiated within the first 4 days of MV and in profoundly hypoxemic patients. CONCLUSIONS: In an emulated trial based on a nationwide COVID-19 cohort, we found differential survival over time of an ECMO compared with a no-ECMO strategy. However, ECMO was consistently associated with better outcomes when performed in high-volume centers and in regions with ECMO capacities specifically organized to handle high demand. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/)

A multimodal cell census and atlas of the mammalian primary motor cortex

ABSTRACT We report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex (MOp or M1) as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties, and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Together, our results advance the collective knowledge and understanding of brain cell type organization: First, our study reveals a unified molecular genetic landscape of cortical cell types that congruently integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a unified taxonomy of transcriptomic types and their hierarchical organization that are conserved from mouse to marmoset and human. Third, cross-modal analysis provides compelling evidence for the epigenomic, transcriptomic, and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types and subtypes. Fourth, in situ single-cell transcriptomics provides a spatially-resolved cell type atlas of the motor cortex. Fifth, integrated transcriptomic, epigenomic and anatomical analyses reveal the correspondence between neural circuits and transcriptomic cell types. We further present an extensive genetic toolset for targeting and fate mapping glutamatergic projection neuron types toward linking their developmental trajectory to their circuit function. Together, our results establish a unified and mechanistic framework of neuronal cell type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties

Bi-dimensional feeding ecologies and food web structure: a conceptual framework linking trophic and spatial processes in aquatic ecosystems, with application to mercury bioaccumulation in fish

This thesis presents the results of a study of the ecology of fish communities of lakes and reservoirs in Labrador, Canada. The first objective of the thesis was to evaluate the relevance and implications of a bi-dimensional framework to integrate spatially-explicit energy flows in consumer feeding ecology and food web structure. Second objective was to assess whether spatially-explicit bi-dimensional feeding ecologies and food web structures can improve the assessment of mercury (Hg) bioaccumulation in fish. A bi-dimensional framework consists in the integration of horizontal (spatially-explicit) and vertical (trophic) energy flows. This approach is demonstrated in comparative studies of fish populations and communities from four pristine lakes. Horizontal energy flows here distinguished between littoral and pelagic carbon contributions to fish consumers in lakes, quantified by variations in stable isotope ratios of carbon in fish tissue. Vertical energy flows described variations in fish trophic position quantified by variations in stable isotope ratios of nitrogen. Comparing life-stage and among-lake patterns of trophic position and littoral-pelagic resource use in four fish species demonstrated that bi-dimensional feeding strategies are determined by species ontogeny and ecosystem characteristics. Comparisons of lake-specific bi-dimensional food web structures estimated from community averages of fish trophic position and littoral-pelagic foraging demonstrated that spatially-explicit community organization is related to consumer species composition, to primary productivity constraints and to physical ecosystem structure. Applied to the understanding of Hg bioaccumulation, a bi-dimensional framework integrated spatial influences on Hg exposure and trophic transfers in aquatic ecosystems and improved predictions of fish Hg concentrations. Horizontal energy flows in this case further distinguished between allochthonous-autochthonous carbon contributions to primary producer-consumer. A bi-dimensional approach revealed that aquatic ecosystems with longer food chains, greater assimilation of autochthonous carbon at lower trophic levels and greater reliance on littoral carbon by fish, reach greater Hg contamination. The influence of littoral-pelagic resource use on fish Hg levels varied with the type and size of prey consumed across habitat boundaries. Autecological types distinguish consumers bi-dimensional feeding ecologies as shaped mainly by ontogeny (Quis type), by ecosystem features (Ubi type) or both (Aequivocus type). This classification provided species-specific distinctions for the importance of biological and environmental determinants of Hg bioaccumulation in fish. A bi-dimensional framework provides a solid conceptual basis for spatially-explicit cological understanding that can improve the assessment of environmental issues

Fish harvesting advice under climate change: A risk-equivalent empirical approach.

The rate of climate change (CC) has accelerated to the point where it now affects the mid- to long-term sustainability of fishing strategies. Therefore, it is important to consider practical and effective ways to incorporate CC into fisheries advice so that the advice can be considered conditioned to CC. We developed a model to characterise the empirical relationship between a variable affected by climate and fish production. We then used model projections as a foundation for a risk analysis of CC effects on harvesting of Greenland halibut Reinhardtius hippoglossoides in the Gulf of St Lawrence, Canada. The risk-based approach quantified a) the relative change in risk of a status quo fishing strategy under various CC scenarios, and b) the change in fishery exploitation rates required to achieve a management objective over a specified time period at a level of risk considered acceptable (risk equivalent fishery exploitation advice). This empirical approach can be used to develop risk-based advice for any other external variable that affects stock production in addition to climate-related variables and it can be applied in most situations where there is an index of stock biomass and fisheries catch. Shifting the focus from process-based understanding of the responses of fish stocks to CC to quantification of how CC-contributed uncertainty can alter the risks associated with different fishing strategies and/or management options, can ensure timely delivery of robust scientific advice for fisheries under non-stationary environmental conditions