Search

The geological record of marine animal biodiversity reflects the interplay between changing rates of speciation versus extinction. Compared to mass extinctions, background extinctions have received little attention. To disentangle the different contributions of global climate state, continental configuration, and atmospheric oxygen concentration (pO2) to variations in background extinction rates, we drive an animal physiological model with the environmental outputs from an Earth system model across intervals spanning the past 541 million years. We find that climate and continental configuration combined to make extinction susceptibility an order of magnitude higher during the Early Paleozoic than during the rest of the Phanerozoic, consistent with extinction rates derived from paleontological databases. The high extinction susceptibility arises in the model from the limited geographical range of marine organisms. It stands even when assuming present-day pO2, suggesting that increasing oxygenation through the Paleozoic is not necessary to explain why extinction rates apparently declined with time.

Abstract Background Viperin, also known as radical S-adenosyl-methionine domain containing protein 2 (RSAD2), is an interferon-inducible protein that is involved in the innate immune response against a wide array of viruses. In mammals, Viperin exerts its antiviral function through enzymatic conversion of cytidine triphosphate (CTP) into its antiviral analog ddhCTP as well as through interactions with host proteins involved in innate immune signaling and in metabolic pathways exploited by viruses during their life cycle. However, how Viperin modulates the antiviral response in fish remains largely unknown. Results For this purpose, we developed a fathead minnow (Pimephales promelas) clonal cell line in which the unique viperin gene has been knocked out by CRISPR/Cas9 genome-editing. In order to decipher the contribution of fish Viperin to the antiviral response and its regulatory role beyond the scope of the innate immune response, we performed a comparative RNA-seq analysis of viperin −/− and wildtype cell lines upon stimulation with recombinant fathead minnow type I interferon. Conclusions Our results revealed that Viperin does not exert positive feedback on the canonical type I IFN but acts as a negative regulator of the inflammatory response by downregulating specific pro-inflammatory genes and upregulating repressors of the NF-κB pathway. It also appeared to play a role in regulating metabolic processes, including one carbon metabolism, bone formation, extracellular matrix organization and cell adhesion.

Abstract Exon junction complexes are deposited at exon-exon junctions during splicing. They are primarily known to activate non-sense mediated degradation of transcripts harbouring premature stop codons before the last intron. According to a popular model, exon-junction complexes accompany mRNAs to the cytoplasm where the first translating ribosome pushes them out. However, they are also removed by uncharacterized, translation-independent mechanisms. Little is known about kinetic and transcript specificity of these processes. Here we tag core subunits of exon-junction complexes with complementary split nanoluciferase fragments to obtain sensitive and quantitative assays for complex formation. Unexpectedly, exon-junction complexes form large stable mRNPs containing stalled ribosomes. Complex assembly and disassembly rates are determined after an arrest in transcription and/or translation. 85% of newly deposited exon-junction complexes are disassembled by a translation-dependent mechanism. However as this process is much faster than the translation-independent one, only 30% of the exon-junction complexes present in cells at steady state require translation for disassembly. Deep RNA sequencing shows a bias of exon-junction complex bound transcripts towards microtubule and centrosome coding ones and demonstrate that the lifetimes of exon-junction complexes are transcript-specific. This study provides a dynamic vision of exon-junction complexes and uncovers their unexpected stable association with ribosomes.

Abstract Background The exon junction complex (EJC) is involved in most steps of the mRNA life cycle, ranging from splicing to nonsense-mediated mRNA decay (NMD). It is assembled by the splicing machinery onto mRNA in a sequence-independent manner. A fundamental open question is whether the EJC is deposited onto all exon‒exon junctions or only on a subset of them. Several previous studies have made observations supportive of the latter, yet these have been limited by methodological constraints. Results In this study, we sought to overcome these limitations via the integration of two different approaches for transcriptome-wide mapping of EJCs. Our results revealed that nearly all, if not all, internal exons consistently harbor an EJC in Drosophila, demonstrating that EJC presence is an inherent consequence of the splicing reaction. Furthermore, our study underscores the limitations of eCLIP methods in fully elucidating the landscape of RBP binding sites. Our findings highlight how highly specific (low false positive) methodologies can lead to erroneous interpretations due to partial sensitivity (high false negatives). Conclusions This study contributes to our understanding of EJC deposition and its association with pre-mRNA splicing. The universal presence of EJC on internal exons underscores its significance in ensuring proper mRNA processing. Additionally, our observations highlight the need to consider both specificity and sensitivity in RBP mapping methodologies.

Catalyst recovery is a major challenge for reaching the objectives of green chemistry for industry. Indeed, catalysts enable quick and selective syntheses with high reaction yields. This is especially the case for homogeneous platinoid catalysts which are almost indispensable for cross-coupling reactions often used by the pharmaceutical industry. However, they are based on scarce, expensive, and toxic resources. In addition, they are quite sensitive and degrade over time at the end of the reaction. Once degraded, their regeneration is complex and hazardous to implement. Working on their recovery could lead to highly effective catalytic chemistries while limiting the environmental and economic impacts of their one-time uses. This review aims to describe and compare conventional processes for metal removal while discussing their advantages and drawbacks considering the objective of homogeneous catalyst recovery. Most of them lead to difficulty recycling active catalysts due to their ability to only treat metal ions or to chelate catalysts without the possibility to reverse the mechanism. However, membrane processes seem to offer some perspectives with limiting degradations. While membranes are not systematically the best option for recycling homogeneous catalysts, current development might help improve the separation between pharmaceutical active ingredients and catalysts and enable their recycling.

Geological evidence indicates that grounded ice sheets reached sea level at all latitudes during two long-lived Cryogenian (58 and ≥5 My) glaciations. Combined uranium-lead and rhenium-osmium dating suggests that the older (Sturtian) glacial onset and both terminations were globally synchronous. Geochemical data imply that CO2 was 102 PAL (present atmospheric level) at the younger termination, consistent with a global ice cover. Sturtian glaciation followed breakup of a tropical supercontinent, and its onset coincided with the equatorial emplacement of a large igneous province. Modeling shows that the small thermal inertia of a globally frozen surface reverses the annual mean tropical atmospheric circulation, producing an equatorial desert and net snow and frost accumulation elsewhere. Oceanic ice thickens, forming a sea glacier that flows gravitationally toward the equator, sustained by the hydrologic cycle and by basal freezing and melting. Tropical ice sheets flow faster as CO2 rises but lose mass and become sensitive to orbital changes. Equatorial dust accumulation engenders supraglacial oligotrophic meltwater ecosystems, favorable for cyanobacteria and certain eukaryotes. Meltwater flushing through cracks enables organic burial and submarine deposition of airborne volcanic ash. The subglacial ocean is turbulent and well mixed, in response to geothermal heating and heat loss through the ice cover, increasing with latitude. Terminal carbonate deposits, unique to Cryogenian glaciations, are products of intense weathering and ocean stratification. Whole-ocean warming and collapsing peripheral bulges allow marine coastal flooding to continue long after ice-sheet disappearance. The evolutionary legacy of Snowball Earth is perceptible in fossils and living organisms.

Exon junction complexes (EJCs) that mark untranslated mRNA are involved in transport, translation and nonsense-mediated mRNA decay. Here the authors show centrosomal localization of EJCs which appears to be required for both the localization of NIN mRNA around centrosomes and ciliogenesis.

Centrosomes function as microtubule organizing centers where several mRNAs accumulate. By employing high-throughput single molecule FISH screening, the authors discover that 8 human mRNAs localize to centrosomes with unique cell cycle dependent patterns using an active polysome targeting mechanism.

The Cenozoic inception and development of the Asian monsoons remain unclear and have generated much debate, as several hypotheses regarding circulation patterns at work in Asia during the Eocene have been proposed in the few last decades. These include (a) the existence of modern-like monsoons since the early Eocene; (b) that of a weak South Asian monsoon (SAM) and little to no East Asian monsoon (EAM); or (c) a prevalence of the Intertropical Convergence Zone (ITCZ) migrations, also referred to as Indonesian–Australian monsoon (I-AM). As SAM and EAM are supposed to have been triggered or enhanced primarily by Asian palaeogeographic changes, their possible inception in the very dynamic Eocene palaeogeographic context remains an open question, both in the modelling and field-based communities. We investigate here Eocene Asian climate conditions using the IPSL-CM5A2 (Sepulchre et al., 2019) earth system model and revised palaeogeographies. Our Eocene climate simulation yields atmospheric circulation patterns in Asia substantially different from modern conditions. A large high-pressure area is simulated over the Tethys ocean, which generates intense low tropospheric winds blowing southward along the western flank of the proto-Himalayan–Tibetan plateau (HTP) system. This low-level wind system blocks, to latitudes lower than 10∘ N, the migration of humid and warm air masses coming from the Indian Ocean. This strongly contrasts with the modern SAM, during which equatorial air masses reach a latitude of 20–25∘ N over India and southeastern China. Another specific feature of our Eocene simulation is the widespread subsidence taking place over northern India in the midtroposphere (around 5000 m), preventing deep convective updraught that would transport water vapour up to the condensation level. Both processes lead to the onset of a broad arid region located over northern India and over the HTP. More humid regions of high seasonality in precipitation encircle this arid area, due to the prevalence of the Intertropical Convergence Zone (ITCZ) migrations (or Indonesian–Australian monsoon, I-AM) rather than monsoons. Although the existence of this central arid region may partly result from the specifics of our simulation (model dependence and palaeogeographic uncertainties) and has yet to be confirmed by proxy records, most of the observational evidence for Eocene monsoons are located in the highly seasonal transition zone between the arid area and the more humid surroundings. We thus suggest that a zonal arid climate prevailed over Asia before the initiation of monsoons that most likely occurred following Eocene palaeogeographic changes. Our results also show that precipitation seasonality should be used with caution to infer the presence of a monsoonal circulation and that the collection of new data in this arid area is of paramount importance to allow the debate to move forward.

Abstract Background The last 10 years have seen the rise of countless functional genomics studies based on Next-Generation Sequencing (NGS). In the vast majority of cases, whatever the species, whatever the experiment, the two first steps of data analysis consist of a quality control of the raw reads followed by a mapping of those reads to a reference genome/transcriptome. Subsequent steps then depend on the type of study that is being made. While some tools have been proposed for investigating data quality after the mapping step, there is no commonly adopted framework that would be easy to use and broadly applicable to any NGS data type. Results We present ALFA, a simple but universal tool that can be used after the mapping step on any kind of NGS experiment data for any organism with available genomic annotations. In a single command line, ALFA can compute and display distribution of reads by categories (exon, intron, UTR, etc.) and biotypes (protein coding, miRNA, etc.) for a given aligned dataset with nucleotide precision. We present applications of ALFA to Ribo-Seq and RNA-Seq on Homo sapiens, CLIP-Seq on Mus musculus, RNA-Seq on Saccharomyces cerevisiae, Bisulfite sequencing on Arabidopsis thaliana and ChIP-Seq on Caenorhabditis elegans. Conclusions We show that ALFA provides a powerful and broadly applicable approach for post mapping quality control and to produce a global overview using common or dedicated annotations. It is made available to the community as an easy to install command line tool and from the Galaxy Tool Shed.

DspA/E is a type three effector injected by the pathogenic bacterium Erwinia amylovora inside plant cells. In non-host Arabidopsis thaliana, DspA/E inhibits seed germination, root growth, de novo protein synthesis and triggers localized cell death. To better understand the mechanisms involved, we performed EMS mutagenesis on a transgenic line, 13-1-2, containing an inducible dspA/E gene. We identified three suppressor mutants, two of which belonged to the same complementation group. Both were resistant to the toxic effects of DspA/E. Metabolome analysis showed that the 13-1-2 line was depleted in metabolites of the TCA cycle and accumulated metabolites associated with cell death and defense. TCA cycle and cell-death associated metabolite levels were respectively increased and reduced in both suppressor mutants compared to the 13-1-2 line. Whole genome sequencing indicated that both suppressor mutants displayed missense mutations in conserved residues of Glycolate oxidase 2 (GOX2), a photorespiratory enzyme that we confirmed to be localized in the peroxisome. Leaf GOX activity increased in leaves infected with E. amylovora in a DspA/E-dependent manner. Moreover, the gox2-2 KO mutant was more sensitive to E. amylovora infection and displayed reduced JA-signaling. Our results point to a role for glycolate oxidase in type II non-host resistance and to the importance of central metabolic functions in controlling growth/defense balance.

UPF1 is a highly processive helicase that plays an essential role in nonsense-mediated mRNA decay. Here the authors use single molecule binding assays to establish a functionally important relationship between helicase grip to nucleic acids, binding lifetime and the duration of translocation.

UPF1 is a central protein in nonsense-mediated mRNA decay (NMD), but contribution of its RNA processivity to NMD is unclear. Here, the authors show how the retroviral Tax protein interacts with and inhibits UPF1, and demonstrate that UPF1’s translocase activity contributes to NMD.

The optimal duration of anticoagulation after a first episode of unprovoked deep-vein thrombosis is uncertain. We aimed to assess the benefits and risks of an additional 18 months of treatment with warfarin versus placebo, after an initial 6 months of anticoagulation for a first unprovoked proximal deep-vein thrombosis. We conducted a multicenter, randomized, double-blind, controlled trial comparing an additional 18 months of warfarin with placebo in patients with a unprovoked proximal deep-vein thrombosis initially treated for 6 months (treatment period: 18 months; follow up after treatment period: 24 months). The primary outcome was the composite of recurrent venous thromboembolism or major bleeding at 18 months. Secondary outcomes were the composite at 42 months, as well as each component of the composite, and death unrelated to pulmonary embolism or major bleeding, at 18 and 42 months. All outcomes were centrally adjudicated. A total of 104 patients, enrolled between July 2007 and October 2013 were analyzed on an intention-to-treat basis; no patient was lost to follow-up. During the 18-month treatment period, the primary outcome occurred in none of the 50 patients in the warfarin group and in 16 out of 54 patients (cumulative risk, 29.6%) in the placebo group (hazard ratio, 0.03; 95% confidence interval: 0.01 to 0.09; P

Phytoplasmas inhabit phloem sieve elements and cause abnormal growth and altered sugar partitioning. However, how they interact with phloem functions is not clearly known. The phloem responses were investigated in tomatoes infected by “Candidatus Phytoplasma solani” at the beginning of the symptomatic stage, the first symptoms appearing in the newly emerged leaf at the stem apex. Antisense lines impaired in the phloem sucrose transporters SUT1 and SUT2 were included. In symptomatic sink leaves, leaf curling was associated with higher starch accumulation and the expression of defense genes. The analysis of leaf midribs of symptomatic leaves indicated that transcript levels for genes acting in the glycolysis and peroxisome metabolism differed from these in noninfected plants. The phytoplasma also multiplied in the three lower source leaves, even if it was not associated with the symptoms. In these leaves, the rate of phloem sucrose exudation was lower for infected plants. Metabolite profiling of phloem sap-enriched exudates revealed that glycolate and aspartate levels were affected by the infection. Their levels were also affected in the noninfected SUT1- and SUT2-antisense lines. The findings suggest the role of sugar transporters in the responses to infection and describe the consequences of impaired sugar transport on the primary metabolism.

The 58–51 Ma interval was characterized by a long-term increase of global temperatures (+4 to +6 °C) up to the Early Eocene Climate Optimum (EECO, 52.9–50.7 Ma), the warmest interval of the Cenozoic. It was recently suggested that sustained high atmospheric pCO2, controlling warm early Cenozoic climate, may have been released during Neo-Tethys closure through the subduction of large amounts of pelagic carbonates and their recycling as CO2 at arc volcanoes. To analyze the impact of Neo-Tethys closure on early Cenozoic warming, we have modeled the volume of subducted sediments and the amount of CO2 emitted along the northern Tethys margin. The impact of calculated CO2 fluxes on global temperature during the early Cenozoic have then been tested using a climate carbon cycle model (GEOCLIM). We show that CO2 production may have reached up to 1.55 × 1018 mol Ma−1 specifically during the EECO, ~ 4 to 37 % higher that the modern global volcanic CO2 output, owing to a dramatic India-Asia plate convergence increase. The subduction of thick Greater Indian continental margin carbonate sediments at ~ 55–50 Ma may also have led to additional CO2 production of 3.35 × 1018 mol Ma−1 during the EECO, making a total of 85 % of the global volcanic CO2 outgassed. However, climate modeling demonstrates that timing of maximum CO2 release only partially fits with the EECO, and that corresponding maximum pCO2 values (750 ppm) and surface warming (+2 °C) do not reach values inferred from geochemical proxies, a result consistent with conclusions arising from modeling based on other published CO2 fluxes. These results demonstrate that CO2 derived from decarbonation of Neo-Tethyan lithosphere may have possibly contributed to, but certainly cannot account alone for early Cenozoic warming. Other commonly cited sources of excess CO2 such as enhanced igneous province volcanism also appear to be up to 1 order of magnitude below fluxes required by the model to fit with proxy data of pCO2 and temperature at that time. An alternate explanation may be that CO2 consumption, a key parameter of the long-term atmospheric pCO2 balance, may have been lower than suggested by modeling. These results call for a better calibration of early Cenozoic weathering rates.

Perceiving the surrounding environment in terms of objects is useful for any general purpose intelligent agent. In this paper, we investigate a fundamental mechanism making object perception possible, namely the identification of spatio-temporally invariant structures in the sensorimotor experience of an agent. We take inspiration from the Sensorimotor Contingencies Theory to define a computational model of this mechanism through a sensorimotor, unsupervised and predictive approach. Our model is based on processing the unsupervised interaction of an artificial agent with its environment. We show how spatio-temporally invariant structures in the environment induce regularities in the sensorimotor experience of an agent, and how this agent, while building a predictive model of its sensorimotor experience, can capture them as densely connected subgraphs in a graph of sensory states connected by motor commands. Our approach is focused on elementary mechanisms, and is illustrated with a set of simple experiments in which an agent interacts with an environment. We show how the agent can build an internal model of moving but spatio-temporally invariant structures by performing a Spectral Clustering of the graph modeling its overall sensorimotor experiences. We systematically examine properties of the model, shedding light more globally on the specificities of the paradigm with respect to methods based on the supervised processing of collections of static images.

The capacity of an advection/diffusion model to predict sand transport under varying wave and current conditions is evaluated. The horizontal sand transport rate is computed by vertical integration of the suspended sediment flux. A correction procedure for the near-bed concentration is proposed so that model results are independent of the vertical resolution. The method can thus be implemented in regional models with operational applications. Simulating equilibrium sand transport rates, when erosion and deposition are balanced, requires a new empirical erosion law that involves the non-dimensional excess shear stress and a parameter that depends on the size of the sand grain. Comparison with several datasets and sediment transport formulae demonstrated the model’s capacity to simulate sand transport rates for a large range of current and wave conditions and sand diameters in the range 100–500 μm. Measured transport rates were predicted within a factor two in 67% of cases with current only and in 35% of cases with both waves and current. In comparison with the results obtained by Camenen and Larroudé (2003), who provided the same indicators for several practical transport rate formulations (whose means are respectively 72% and 37%), the proposed approach gives reasonable results. Before fitting a new erosion law to our model, classical erosion rate formulations were tested but led to poor comparisons with expected sediment transport rates. We suggest that classical erosion laws should be used with care in advection/diffusion models similar to ours, and that at least a full validation procedure for transport rates involving a range of sand diameters and hydrodynamic conditions should be carried out.

The Ordovician Period (485–443 Ma) is characterized by abundant evidence for continental-sized ice sheets. Modeling studies published so far require a sharp CO2 drawdown to initiate this glaciation. They mostly used non-dynamic slab mixed-layer ocean models. Here, we use a general circulation model with coupled components for ocean, atmosphere, and sea ice to examine the response of Ordovician climate to changes in CO2 and paleogeography. We conduct experiments for a wide range of CO2 (from 16 to 2 times the preindustrial atmospheric CO2 level (PAL)) and for two continental configurations (at 470 and at 450 Ma) mimicking the Middle and the Late Ordovician conditions. We find that the temperature-CO2 relationship is highly non-linear when ocean dynamics are taken into account. Two climatic modes are simulated as radiative forcing decreases. For high CO2 concentrations (≥ 12 PAL at 470 Ma and ≥ 8 PAL at 450 Ma), a relative hot climate with no sea ice characterizes the warm mode. When CO2 is decreased to 8 PAL and 6 PAL at 470 and 450 Ma, a tipping point is crossed and climate abruptly enters a runaway icehouse leading to a cold mode marked by the extension of the sea ice cover down to the mid-latitudes. At 450 Ma, the transition from the warm to the cold mode is reached for a decrease in atmospheric CO2 from 8 to 6 PAL and induces a ~9 °C global cooling. We show that the tipping point is due to the existence of a 95% oceanic Northern Hemisphere, which in turn induces a minimum in oceanic heat transport located around 40° N. The latter allows sea ice to stabilize at these latitudes, explaining the potential existence of the warm and of the cold climatic modes. This major climatic instability potentially brings a new explanation to the sudden Late Ordovician Hirnantian glacial pulse that does not require any large CO2 drawdown.

During the Archaean, the Sun's luminosity was 18 to 25% lower than the present day. One-dimensional radiative convective models (RCM) generally infer that high concentrations of greenhouse gases (CO2, CH4) are required to prevent the early Earth's surface temperature from dropping below the freezing point of liquid water and satisfying the faint young Sun paradox (FYSP, an Earth temperature at least as warm as today). Using a one-dimensional (1-D) model, it was proposed in 2010 that the association of a reduced albedo and less reflective clouds may have been responsible for the maintenance of a warm climate during the Archaean without requiring high concentrations of atmospheric CO2 (pCO2). More recently, 3-D climate simulations have been performed using atmospheric general circulation models (AGCM) and Earth system models of intermediate complexity (EMIC). These studies were able to solve the FYSP through a large range of carbon dioxide concentrations, from 0.6 bar with an EMIC to several millibars with AGCMs. To better understand this wide range in pCO2, we investigated the early Earth climate using an atmospheric GCM coupled to a slab ocean. Our simulations include the ice-albedo feedback and specific Archaean climatic factors such as a faster Earth rotation rate, high atmospheric concentrations of CO2 and/or CH4, a reduced continental surface, a saltier ocean, and different cloudiness. We estimated full glaciation thresholds for the early Archaean and quantified positive radiative forcing required to solve the FYSP. We also demonstrated why RCM and EMIC tend to overestimate greenhouse gas concentrations required to avoid full glaciations or solve the FYSP. Carbon cycle–climate interplays and conditions for sustaining pCO2 will be discussed in a companion paper.

The regulation of sugar metabolism and partitioning plays an essential role for a plant’s acclimation to its environment, with specific responses in autotrophic and heterotrophic organs. In this work, we analyzed the effects of high salinity on sugar partitioning and vascular anatomy within the floral stem. Stem sucrose and fructose content increased, while starch reduced, in contrast to the response observed in rosette leaves of the same plants. In the stem, the effects were associated with changes in the expression of SWEET and TMT2 genes encoding sugar transporters, SUSY1 encoding a sucrose synthase and several FRK encoding fructokinases. By contrast, the expression of SUC2, SWEET11 and SWEET12, encoding sugar transporters for phloem loading, remained unchanged in the stem. Both the anatomy of vascular tissues and the composition of xylem secondary cell walls were altered, suggesting that high salinity triggered major readjustments of sugar partitioning in this heterotrophic organ. There were changes in the composition of xylem cell walls, associated with the collapse and deformation of xylem vessels. The data are discussed regarding sugar partitioning and homeostasis of sugars in the vascular tissues of the stem.

Plant responses to abiotic stresses entail adaptive processes that integrate both physiological and developmental cues. However, the adaptive traits that are involved in the responses to a high soil salinity during reproductive growth are still poorly studied. To identify new clues, we studied the halophyte, Thellungiella salsuginea, and three Arabidopsis accessions, known as tolerant or salt-sensitive. We focused on the quantitative traits associated with the stem growth, sugar content, and anatomy of the plants subjected to the salt treatment, with and without a three-day acclimation, applied during the reproductive stage. The stem growth of Thellungiella salsuginea was not affected by the salt stress. By contrast, salt affected all of the Arabidopsis accessions, with a natural variation in the effect of the salt on growth, sugar content, and stem anatomy. In response to the high salinity, irregular xylem vessels were observed, independently of the accession’s tolerance to salt treatment, while the diameter of the largest xylem vessels was reduced in the tolerant accessions. The stem height, growth rate, hexoses-to-sucrose ratio, and phloem-to-xylem ratio also varied, in association with both the genotype and its tolerance to salt stress. Our findings indicate that several quantitative traits for salt tolerance are associated with the control of inflorescence growth and the adjustment of the phloem-to-xylem ratio.

Organic (e.g., sugars and amino acids) and inorganic (e.g., K+, Na+, PO42−, and SO42−) solutes are transported long-distance throughout plants. Lateral movement of these compounds between the xylem and the phloem, and vice versa, has also been reported in several plant species since the 1930s, and is believed to be important in the overall resource allocation. Studies of Arabidopsis thaliana have provided us with a better knowledge of the anatomical framework in which the lateral transport takes place, and have highlighted the role of specialized vascular and perivascular cells as an interface for solute exchanges. Important breakthroughs have also been made, mainly in Arabidopsis, in identifying some of the proteins involved in the cell-to-cell translocation of solutes, most notably a range of plasma membrane transporters that act in different cell types. Finally, in the future, state-of-art imaging techniques should help to better characterize the lateral transport of these compounds on a cellular level. This review brings the lateral transport of sugars and inorganic solutes back into focus and highlights its importance in terms of our overall understanding of plant resource allocation.

Normania triphylla is an endemic species from Madeira island (Portugal) extinct in the wild since 1991. The aim of this work was to culture the meristems of this species in vitro and to multiply its shoots in order to preserve this endangered species. The best results in terms of multiplication were obtained in Murashige and Skoog medium supplemented with 10 µM 6‑benzylaminopurine (BAP). The number of shoots, the number of nodes and the number of leaves were the most important in this medium. However, the best results concerning the total shoot length were obtained when BAP was not supplemented into the medium and in the presence of 5 or 7.5 µM 1-naphtalene acetic acid (NAA). This is the first report on the in vitro culture of N. triphylla which could brings new avenues for the development of this species.

The Snowball Earth theory initially proposed by Kirschvink (1992) to explain the Neoproterozoic glacial episodes, suggested that the Earth was fully ice-covered at 720 Ma (Sturtian episode) and 640 Ma (Marinoan episode). This succession of extreme climatic crises induced environmental perturbations which are considered as a strong selective pressure on the evolution of life (Hoffman et al., 1998). Using a numerical model of carbon-alkalinity global cycles, we quantify environmental stresses caused by a global glaciation. According to our results, we suggest that during global glaciations, the ocean becomes acidic (pH~6), and undersaturated with respect to carbonate minerals. Moreover the quick transition from ice-house to greenhouse conditions implies an abrupt and large shift of the oceanic surface temperature which causes an extended hypoxia. The intense continental weathering, in the aftermath of the glaciation, deeply affects the seawater composition inducing rapid changes in terms of pH and alkalinity. We also propose a new timing for post glacial perturbations and for the cap carbonates deposition, ~2 Myr instead of 200 kyr as suggested in a previous modelling study. In terms of Precambrian life sustainability, seawater pH modifications appear drastic all along the glaciation, but we suggest that the buffering action of the oceanic crust dissolution avoids a total collapse of biological productivity. But short-lived and large post-glacial perturbations are more critical and may have played the role of an environmental filter proposed in the classic snowball Earth theory. Although the link between environmental changes and life sustainability cannot be modelled accurately, we suggest that only a permissive life (Knoll, 2003) may explain the relative continuity in microfossils diversity observed before, during and after Neoproterozoic glaciation events.

The phloem is a complex tissue composed of highly specialized cells with unique subcellular structures and a compact organization that is challenging to study in vivo at cellular resolution. We used confocal scanning laser microscopy and subcellular fluorescent markers in companion cells and sieve elements, for live imaging of the phloem in Arabidopsis leaves. This approach provided a simple framework for identifying phloem cell types unambiguously. It highlighted the compactness of the meshed network of organelles within companion cells. By contrast, within the sieve elements, unknown bodies were observed in association with the PP2-A1:GFP, GFP:RTM1 and RTM2:GFP markers at the cell periphery. The phloem lectin PP2-A1:GFP marker was found in the parietal ground matrix. Its location differed from that of the P-protein filaments, which were visualized with SEOR1:GFP and SEOR2:GFP. PP2-A1:GFP surrounded two types of bodies, one of which was identified as mitochondria. This location suggested that it was embedded within the sieve element clamps, specific structures that may fix the organelles to each another or to the plasma membrane in the sieve tubes. GFP:RTM1 was associated with a class of larger bodies, potentially corresponding to plastids. PP2-A1:GFP was soluble in the cytosol of immature sieve elements. The changes in its subcellular localization during differentiation provide an in vivo blueprint for monitoring this process. The subcellular features obtained with these companion cell and sieve element markers can be used as landmarks for exploring the organization and dynamics of phloem cells in vivo.