Heat-mediated micro- and nano-pore evolution in sea urchin biominerals

Biomineralized structures with intricate shapes and morphologies, such as sea urchin skeletal elements, grow via the deposition of hydrated amorphous calcium carbonate (ACC) particles that subsequently crystallizes into single-crystalline calcite. This process is accompanied by volume changes due to density differences between the initial and final mineral state as well as variations in hydration levels. For this reason, the presence of macroporosity in synthetic systems was shown to be pivotal in the formation of large single crystals through ACC precursors. However, the role of macroporosity down to nanoporosity in the formation of biogenic minerals remains unknown. Here, we investigate the micro- and nano-porosity as well as the evolution of internal interfaces in the spines and test plates of Paracentrotus lividus sea urchins during the heat-mediated crystallization of remnant ACC and the destruction of intracrystalline organic molecules, using SEM, FIB-SEM, and in situ heating synchrotron SAXS measurements. We show the presence of nanopores likely filled with hydrated organics and visualize the evolution of nano- to micro-pores induced by heating, which may serve to accommodate the volume changes between amorphous and crystalline phases. The obtained results analyzed using thermodynamical considerations suggest that the growth in size of the nanopores is controlled by Ostwald ripening and is well described in the framework of classical pore coarsening theories. The extracted activation energies manifest that nanopore coarsening in the test plates is governed by surface diffusion, whereas in the spines by bulk diffusion. We suggest that such striking differences in diffusion mechanisms are caused by dissimilar levels of macroporosity and distributions of nano- and micro-internal interfaces in pristine biominerals

A portable infrared laser spectrometer for flux measurements of trace gases at the geosphere-atmosphere interface

International audienceA portable infrared laser absorption spectrometer named SPIRIT (SPectrom'etre Infra-Rouge In situ Troposph'erique) has been set up for the simultaneous flux measurements of trace gases at the geosphere-atmosphere interface. It uses a continuous wave distributed feedback room temperature quantum cascade laser and a patented new optical multi-pass cell. The aim of SPIRIT field studies is to get a better understanding of land and water bodies to atmosphere exchange mechanisms of greenhouse gases (GHG). The analytical procedures to derive concentrations and fluxes are described, as well as the performances of the instrument under field conditions. The ability of SPIRIT to assess space and time dependence emissions of two GHG--nitrous oxide (N2O) and methane (CH4)--for different types of ecosystems is demonstrated through in situ measurements on peatland, on fertilized soil, and on water body systems. The objectives of these investigations and preliminary significant results are reported

Marked isotopic variability within and between the Amazon River and marine dissolved black carbon pools

Riverine dissolved organic carbon (DOC) contains charcoal byproducts, termed black carbon (BC). To determine the significance of BC as a sink of atmospheric CO2 and reconcile budgets, the sources and fate of this large, slow-cycling and elusive carbon pool must be constrained. The Amazon River is a significant part of global BC cycling because it exports an order of magnitude more DOC, and thus dissolved BC (DBC), than any other river. We report spatially resolved DBC quantity and radiocarbon (Δ14C) measurements, paired with molecular-level characterization of dissolved organic matter from the Amazon River and tributaries during low discharge. The proportion of BC-like polycyclic aromatic structures decreases downstream, but marked spatial variability in abundance and Δ14C values of DBC molecular markers imply dynamic sources and cycling in a manner that is incongruent with bulk DOC. We estimate a flux from the Amazon River of 1.9–2.7 Tg DBC yr−1 that is composed of predominately young DBC, suggesting that loss processes of modern DBC are important

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Development of an LC-MS-MS method for the quantification of taurine derivatives in marine invertebrates.

Sulfur amino acids, such as taurine, hypotaurine, and thiotaurine, were found in high quantities in tissues of marine symbiotic organisms (e.g., bivalves, tubeworms) living close to hydrothermal vent sites. Therefore, they are assumed to play a key role in the S-oxidizing base metabolism or sulfide detoxification. We propose here a specific, rapid, and original analytical procedure for the direct determination of sulfur amino acids at the level of a few parts per billion in biological samples, avoiding the classical low specific post-column ortho-phthaldialdehyde derivatization step required by non-ultraviolet-absorbing molecules. Indeed, by coupling liquid chromatography on a porous graphitic stationary phase under isocratic conditions (10 mM ammonium acetate buffer adjusted to pH 9.3) to tandem mass spectrometry (ionization process by pneumatically assisted electrospray in negative ion mode), it is possible to perform specific quantification of these metabolites in less than 10 min directly in biological matrices without any derivatization step or other tedious sample treatments. Thus, taurine, hypotaurine, and thiotaurine have been identified and assayed in several deep sea organisms, showing that the developed method is well suited for this kind of application

Etude régionale par éléments finis d'une nappe libre située dans les craies du Crétacé en Belgique

La nappe aquifère de Hesbaye située au Nord-Ouest de Liège (Belgique) est logée dans les craies du Crétacé, surmontées d'une épaisse couche de limon. L'alimentation en eau de la région est assurée par les 60 000 m3 extraits Joumel!ement des galeries captantes et des puits.Un modèle mathématique par éléments finis a été construit pour simuler numériquement le comportement de l'aquifère en régime transitoire. La complexité de la géologie locale a nécessité l'emploi d'une méthode par éléments finis permettant une discrétisatlon 30 souple et détaillée de la zone étudiée, modélisation réalisée avec un maillage fixe en condition de nappe libre.Des développements numériques comprenant la simulation de la surface libre en mode transitoire, ont été introduits dans le modèle LAGATHER du programme LAGAMINE (Université de Liège). Le programme a été testé sur des exemples bidimensionnels avant d'étre appliqué en 30 à l'aquifère de Hesbaye.La discrétisation et les principaux résultats sont présentés.The Hesbaye aquifer located in Cretaceous chalks near Liège (Belgium), is recharged by infiltration through the overlying loess and conglomerate.Wells and collecting adits produce a daily flow of 60 000 m3 out of this aquifer, to provide the alimentation of the area of Liège and its suburbs.More Man 500 boreholes, plezometers and wells give many informations for the idealization and the calibration procedures. Variation ranges of permeability and effective porosity are determined from 150 pumping tests. The main drainance axis of the aquifer (called « dry valleys ») are located and characterized by higher permeabilities.Finite element modelling has been developed to foresee the evolution of the water table and to get some additional informations especially about these main drainance axis.The modelling method is based on the LAGAMINE code (from Liège University). The LAGATHER code is one of the module of the LAGAMINE which is initially adapted to treat non-linear thermic problems. Here, it has been developed to compute flows in porous media in transient conditions. The water table is calculated with a fixed mesh structure using a new method developed by (CHARLIER et al., 1988). Constitutive laws of the flow are changed to take into account the state of saturation or no-saturation of the media. Then the flow equation (the Darcy's law) becomes non-linear. The transition from unsaturated to saturated field is treated at a constant zero pressure, according to the analogy with thermodynamical phase changes at constant temperature. The method has been checked on uniaxial and two dimensionnal sections.3D discretisation and modelling of the whole aquifer has been realized. The problem requires about 2 670 8-nodes isoparametric brick finite elements. The complexity of the geological conditions justifies fully the use of finite element method by the diversity and the wide range of the hydrogeological parameters to introduce in the model.The discretisation is described and some of the must significant results are presented