Comprehensive data management for an ocean observatory: ONC\u27s Oceans 2.0

Ocean Networks Canada operates several comprehensive cabled ocean networks and a suite of single-point marine observing systems across Canada. Data flow in real-time from hundreds of sensors, installed beneath the ocean bottom, though the water column, and at the ocean surface. ONC has built a complimentary data management system, Oceans 2.0 that allows for real-time acquisition, secure storage, data exploration, and data product delivery. Key elements of the Oceans 2.0 data management system will be high-lighted, with a focus on best practices and lessons learned

Biallelic mutations in nucleoporin NUP88 cause lethal fetal akinesia deformation sequence

Nucleoporins build the nuclear pore complex (NPC), which, as sole gate for nuclear-cytoplasmic exchange, is of outmost importance for normal cell function. Defects in the process of nucleocytoplasmic transport or in its machinery have been frequently described in human diseases, such as cancer and neurodegenerative disorders, but only in a few cases of developmental disorders. Here we report biallelic mutations in the nucleoporin NUP88 as a novel cause of lethal fetal akinesia deformation sequence (FADS) in two families. FADS comprises a spectrum of clinically and genetically heterogeneous disorders with congenital malformations related to impaired fetal movement. We show that genetic disruption of nup88 in zebrafish results in pleiotropic developmental defects reminiscent of those seen in affected human fetuses, including locomotor defects as well as defects at neuromuscular junctions. Phenotypic alterations become visible at distinct developmental stages, both in affected human fetuses and in zebrafish, whereas early stages of development are apparently normal. The zebrafish phenotypes caused by nup88 deficiency are rescued by expressing wild-type Nup88 but not the disease-linked mutant forms of Nup88. Furthermore, using human and mouse cell lines as well as immunohistochemistry on fetal muscle tissue, we demonstrate that NUP88 depletion affects rapsyn, a key regulator of the muscle nicotinic acetylcholine receptor at the neuromuscular junction. Together, our studies provide the first characterization of NUP88 in vertebrate development, expand our understanding of the molecular events causing FADS, and suggest that variants in NUP88 should be investigated in cases of FADS

STRAW-b (STRings for Absorption length in Water-b): the second pathfinder mission for the Pacific Ocean Neutrino Experiment

Since 2018, the potential for a high-energy neutrino telescope, named the Pacific Ocean Neutrino Experiment (P-ONE), has been thoroughly examined by two pathfinder missions, STRAW and STRAW-b, short for short for Strings for Absorption Length in Water. The P-ONE project seeks to install a neutrino detector with a one cubic kilometer volume in the Cascadia Basin's deep marine surroundings, situated near the western shores of Vancouver Island, Canada. To assess the environmental conditions and feasibility of constructing a neutrino detector of that scale, the pathfinder missions, STRAW and STRAW-b, have been deployed at a depth of 2.7 km within the designated site for P-ONE and were connected to the NEPTUNE observatory, operated by Ocean Networks Canada (ONC). While STRAW focused on analyzing the optical properties of water in the Cascadia Basin, \ac{strawb} employed cameras and spectrometers to investigate the characteristics of bioluminescence in the deep-sea environment. This report introduces the STRAW-b concept, covering its scientific objectives and the instrumentation used. Furthermore, it discusses the design considerations implemented to guarantee a secure and dependable deployment process of STRAW-b. Additionally, it showcases the data collected by battery-powered loggers, which monitored the mechanical stress on the equipment throughout the deployment. The report also offers an overview of STRAW-b's operation, with a specific emphasis on the notable advancements achieved in the data acquisition (DAQ) system and its successful integration with the server infrastructure of ONC.Comment: 20 pages, 11 figures, 2 table

Integrating Diel Vertical Migrations of Bioluminescent Deep Scattering Layers Into Monitoring Programs

International audienceThe deep sea (i.e., >200 m depth) is a highly dynamic environment where benthic ecosystems are functionally and ecologically connected with the overlying water column and the surface. In the aphotic deep sea, organisms rely on external signals to synchronize their biological clocks. Apart from responding to cyclic hydrodynamic patterns and periodic fluctuations of variables such as temperature, salinity, phytopigments, and oxygen concentration, the arrival of migrators at depth on a 24-h basis (described as Diel Vertical Migrations; DVMs), and from well-lit surface and shallower waters, could represent a major response to a solar-based synchronization between the photic and aphotic realms. In addition to triggering the rhythmic behavioral responses of benthic species, DVMs supply food to deep seafloor communities through the active downward transport of carbon and nutrients. Bioluminescent species of the migrating deep scattering layers play a not yet quantified (but likely important) role in the benthopelagic coupling, raising the need to integrate the efficient detection and quantification of bioluminescence into large-scale monitoring programs. Here, we provide evidence in support of the benefits for quantifying and continuously monitoring bioluminescence in the deep sea. In particular, we recommend the integration of bioluminescence studies into long-term monitoring programs facilitated by deep-sea neutrino telescopes, which offer photon counting capability. Their Photo-Multiplier Tubes and other advanced optical sensors installed in neutrino telescope infrastructures can boost the study of bioluminescent DVMs in concert with acoustic backscatter and video imagery from ultra-low-light cameras. Such integration will enhance our ability to monitor proxies for the mass and energy transfer from the upper ocean into the deep-sea Benthic Boundary Layer (BBL), a key feature of the ocean biological pump and crucial for monitoring the effects of climate-change. In addition, it will allow for investigating the role of deep scattering DVMs in the behavioral responses, abundance and structure of deep-sea benthic communities. The proposed approach may represent a new frontier for the study and discovery of new, taxon-specific bioluminescence capabilities. It will thus help to expand our knowledge of poorly described deep-sea biodiversity inventories and further elucidate the connectivity between pelagic and benthic compartments in the deep-sea

Absence of the Adaptor Protein PEA-15 Is Associated with Altered Pattern of Th Cytokines Production by Activated CD4+ T Lymphocytes In Vitro, and Defective Red Blood Cell Alloimmune Response In Vivo

International audienceTCR-dependent and costimulation signaling, cell division, and cytokine environment are major factors driving cytokines expression induced by CD4+ T cell activation. PEA-15 15 (Protein Enriched in Astrocyte / 15kDa) is an adaptor protein that regulates death receptor-induced apoptosis and proliferation signaling by binding to FADD and relocating ERK1/2 to the cytosol, respectively. By using PEA-15-deficient mice, we examined the role of PEA-15 in TCR-dependent cytokine production in CD4+ T cells. TCR-stimulated PEA-15-deficient CD4+ T cells exhibited defective progression through the cell cycle associated with impaired expression of cyclin E and phosphoRb, two ERK1/2-dependent proteins of the cell cycle. Accordingly, expression of the division cycle-dependent cytokines IL-2 and IFNγ, a Th1 cytokine, was reduced in stimulated PEA-15-deficient CD4+ T cells. This was associated with abnormal subcellular compartmentalization of activated ERK1/2 in PEA-15-deficient T cells. Furthermore, in vitro TCR-dependent differentiation of naive CD4+ CD62L+ PEA-15-deficient T cells was associated with a lower production of the Th2 cytokine, IL-4, whereas expression of the Th17-associated molecule IL4I1 was enhanced. Finally, a defective humoral response was shown in PEA-15-deficient mice in a model of red blood cell alloimmunization performed with Poly IC, a classical adjuvant of Th1 response in vivo. Collectively, our data suggest that PEA-15 contributes to the specification of the cytokine pattern of activated Th cells, thus highlighting a potential new target to interfere with T cell functional polarization and subsequent immune response

Thank You to Our 2021 Reviewers

International audienceOn behalf of the Editorial Board and Staff of Earth and Space Science, I thank the reviewers whose selfless dedication to science has ensured, once again, that the papers published in our journal in 2021 highlight the best Earth and space science in a manner that does justice to the authors and their work. All of us at Earth Peer reviewing is a demanding and often thankless job. It is however an essential component of the scientific process, ensuring the highest standards of integrity and rigor. Without the work of reviewers, who check data and procedures for possible bias and to ensure reproducibility, and who share their expertise to verify that the interpretations and conclusions of a paper are consistent with assumptions and existing knowledge, it would not be possible to trust in the scientific process. Our journal is particularly indebted to our reviewers: Earth and Space Science is a multidisciplinary journal that highlights methods, instruments, data and algorithms, and therefore we rely heavily on the direct expertise of our reviewers to verify and vouch for the quality of the papers we publish. We are indebted to all our reviewers, and we are delighted to acknowledge them publicly in this Editorial

Individual red blood cell fetal hemoglobin quantification allows to determine protective thresholds in sickle cell disease

International audiencePolymerization of the sickle hemoglobin (HbS) is a key determinant of sickle cell disease (SCD), an inherited blood disorder. Fetal hemoglobin (HbF) is a major modulator of the disease severity by both decreasing HbS intracellular concentration and inhibiting its polymerization. However, heterocellular distribution of HbF is common in SCD. For HbS polymerization inhibition, the hypothesis of an "HbF per red blood cell (HbF/RBC) threshold" requires accurate measurement of HbF in individual RBC. To date, HbF detection methods are limited to a qualitative measurement of RBC populations containing HbF - the F cells, which are variable. We developed an accurate method for HbF quantification in individual RBC. A linear association between mean HbF content and mean RBC fluorescence by flow cytometry, using an anti-Human-HbF antibody, was obtained from non-SCD subjects presenting homogeneous HbF distribution. This correlation was then used to measure HbF/RBC. Hydroxyurea (HU) improves SCD clinical manifestations, mainly through its ability to induce HbF synthesis. The HbF distribution was analyzed in 14 SCD patients before and during HU treatment. A significant decrease in RBC population containing less than 2 pg of HbF/RBC was observed. Therefore, we tested associations for %RBC above different HbF/RBC thresholds and showed a decrease in the pathognomonic vaso-occlusive crisis incidence from the threshold of 4 pg. This quantity was also correlated with the level of sickle RBC after in vitro deoxygenation. This new method allows the comparison of HbF/RBC distributions and could be a useful tool to characterize baseline patients HbF distribution and therapeutic response to HbF inducers

Geoscientists, Who Have Documented the Rapid and Accelerating Climate Crisis for Decades, Are Now Pleading for Immediate Collective Action

International audienceOur planet is in crisis! The latest report of the United Nations Intergovernmental Panel on Climate Change (IPCC AR6) confirms that human influence is causing widespread, rapid, and intensifying changes in our weather and climate that are affecting every region on Earth in multiple ways. With every additional ton of carbon we emit, the frequency and intensity of storms, floods, droughts, and fires become greater and the effects on the environment and on human health and civilization become more severe.As geoscientists and journal editors, most of us have been accustomed to being on the leading edge of human knowledge and understanding of climate change, where we deal in objectivity, uncertainty, and debate, but now we find ourselves at the core of this climate crisis. It is no longer scientific discoveries at stake, but also humanity itself. This is an uncomfortable place for many of us. We are trained to be dispassionate observers and cautious thinkers, yet the alarming rate of recent climate change impels us to turn our attention directly toward mitigating this impending crisis.We are making a plea for collective action: we must make the switch to a green economy, put a just and effective price on carbon now, and consider a portfolio of other equitable public investments in climate solutions. These actions will ensure that the true costs and risks of burning fossil fuels are accounted for and global carbon emissions are rapidly reduced. Rich countries must lead the way in making drastic cuts to carbon emissions and in helping low- and middle-income countries to develop sustainably. We are running out of time.For decades, American Geophysical Union (AGU) journals have been at the forefront of documenting human-caused climate change and warning of a worsening climate crisis. Over 2,000 publications from AGU journals are cited in the new IPCC AR6 report. But we too can do more than just document and scientifically explain the ongoing crisis—our profession must help lead the way to solutions.Finding solutions and adapting to change have become not only necessary, but essential in ensuring safe, sustainable, and healthy human communities in the future. The geosciences have an essential role to play in these efforts by pivoting toward more cross-sector, solution-based science. To help lead this vision, the AGU is adding a new publication forum for community science in partnership with associations outside the geosciences. This forum will enhance interactions among AGU's existing, more disciplinary journals and give local communities a voice in leading solutions to global challenges.We are scientists, but we also have families and loved ones alongside our fellow citizens on this planet. The time to bridge the divide between scientist and citizen, head and heart, is now. The lead-up to the 2021 UN Climate Change Conference, COP26, being held in Glasgow in November, is our “last best chance” to urge world leaders to come together and commit to keeping climate change and its devastating impacts in check