Pancreatic cancer intrinsic PI3Kα activity accelerates metastasis and rewires macrophage component

Pancreatic ductal adenocarcinoma (PDAC) patients frequently suffer from undetected micro-metastatic disease. This clinical situation would greatly benefit from additional investigation. Therefore, we set out to identify key signalling events that drive metastatic evolution from the pancreas. We searched for a gene signature that discriminate localised PDAC from confirmed metastatic PDAC and devised a preclinical protocol using circulating cell-free DNA (cfDNA) as an early biomarker of micro-metastatic disease to validate the identification of key signalling events. An unbiased approach identified, amongst actionable markers of disease progression, the PI3K pathway and a distinctive PI3Kα activation signature as predictive of PDAC aggressiveness and prognosis. Pharmacological or tumour-restricted genetic PI3Kα-selective inhibition prevented macro-metastatic evolution by hindering tumoural cell migratory behaviour independently of genetic alterations. We found that PI3Kα inhibition altered the quantity and the species composition of the produced lipid second messenger PIP3 , with a selective decrease of C36:2 PI-3,4,5-P3 . Tumoural PI3Kα inactivation prevented the accumulation of pro-tumoural CD206-positive macrophages in the tumour-adjacent tissue. Tumour cell-intrinsic PI3Kα promotes pro-metastatic features that could be pharmacologically targeted to delay macro-metastatic evolution.

Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis

In animals, distant H3K27me3-marked Polycomb targets can establish physical interactions forming repressive chromatin hubs. In plants, growing evidence suggests that H3K27me3 acts directly or indirectly to regulate chromatin interactions, although how this histone modification modulates 3D chromatin architecture remains elusive. To decipher the impact of the dynamic deposition of H3K27me3 on the Arabidopsis thaliana nuclear interactome, we combined genetics, transcriptomics, and several 3D epigenomic approaches. By analyzing mutants defective for histone H3K27 methylation or demethylation, we uncovered the crucial role of this chromatin mark in short- and previously unnoticed long-range chromatin loop formation. We found that a reduction in H3K27me3 levels led to a decrease in the interactions within Polycomb-associated repressive domains. Regions with lower H3K27me3 levels in the H3K27 methyltransferase clf mutant established new interactions with regions marked with H3K9ac, a histone modification associated with active transcription, indicating that a reduction in H3K27me3 levels induces a global reconfiguration of chromatin architecture. Altogether, our results reveal that the 3D genome organization is tightly linked to reversible histone modifications that govern chromatin interactions. Consequently, nuclear organization dynamics shapes the transcriptional reprogramming during plant development and places H3K27me3 as a key feature in the coregulation of distant genes.

Investigating Magma Ocean Solidification on Earth Through Laser-Heated Diamond Anvil Cell Experiments

We carried out a series of silicate fractional crystallization experiments at lower mantle pressures using the laser-heated diamond anvil cell. Phase relations and the compositional evolution of the cotectic melt and equilibrium solids along the liquid line of descent were determined and used to assemble the melting phase diagram. In a pyrolitic magma ocean, the first mineral to crystallize in the deep mantle is iron-depleted calcium-bearing bridgmanite. From the phase diagram, we estimate that the initial 33%-36% of the magma ocean will crystallize to form such a buoyant bridgmanite. Substantial calcium solubility in bridgmanite is observed up to 129 GPa, and significantly delays the crystallization of the calcium silicate perovskite phase during magma ocean solidification. Residual melts are strongly iron-enriched as crystallization proceeds, making them denser than any of the coexisting solids at deep mantle conditions, thus supporting the terrestrial basal magma ocean hypothesis (Labrosse et al., 2007).

Unraveling the features of somatic transposition in the Drosophila intestine

Transposable elements (TEs) play a significant role in evolution, contributing to genetic variation. However, TE mobilization in somatic cells is not well understood. Here, we address the prevalence of transposition in a somatic tissue, exploiting the Drosophila midgut as a model. Using whole-genome sequencing of in vivo clonally expanded gut tissue, we have mapped hundreds of high-confidence somatic TE integration sites genome-wide. We show that somatic retrotransposon insertions are associated with inactivation of the tumor suppressor Notch, likely contributing to neoplasia formation. Moreover, applying Oxford Nanopore long-read sequencing technology we provide evidence for tissue-specific differences in retrotransposition. Comparing somatic TE insertional activity with transcriptomic and small RNA sequencing data, we demonstrate that transposon mobility cannot be simply predicted by whole tissue TE expression levels or by small RNA pathway activity. Finally, we reveal that somatic TE insertions in the adult fly intestine are enriched in genic regions and in transcriptionally active chromatin. Together, our findings provide clear evidence of ongoing somatic transposition in Drosophila and delineate previously unknown features underlying somatic TE mobility in vivo.

Role of Atmospheric Indices in Describing Inshore Directional Wave Climate in the United Kingdom and Ireland

Improved understanding of how our coasts will evolve over a range of time scales (years-decades) is critical for effective and sustainable management of coastal infrastructure. A robust knowledge of the spatial, directional and temporal variability of the inshore wave climate is required to predict future coastal evolution and hence vulnerability. However, the variability of the inshore directional wave climate has received little attention, and an improved understanding could drive development of skillful seasonal or decadal forecasts of coastal response. We examine inshore wave climate at 63 locations throughout the United Kingdom and Ireland (1980-2017) and show that 73% are directionally bimodal. We find that winter-averaged expressions of six leading atmospheric indices are strongly correlated (r = 0.60-0.87) with both total and directional winter wave power (peak spectral wave direction) at all studied sites. Regional inshore wave climate classification through hierarchical cluster analysis and stepwise multi-linear regression of directional wave correlations with atmospheric indices defined four spatially coherent regions. We show that combinations of indices have significant skill in predicting directional wave climates (R 2  = 0.45-0.8; p < 0.05). We demonstrate for the first time the significant explanatory power of leading winter-averaged atmospheric indices for directional wave climates, and show that leading seasonal forecasts of the NAO skillfully predict wave climate in some regions.

Kinetochore individualization in meiosis I is required for centromeric cohesin removal in meiosis II

Partitioning of the genome in meiosis occurs through two highly specialized cell divisions, named meiosis I and meiosis II. Step-wise cohesin removal is required for chromosome segregation in meiosis I, and sister chromatid segregation in meiosis II. In meiosis I, mono-oriented sister kinetochores appear as fused together when examined by high-resolution confocal microscopy, whereas they are clearly separated in meiosis II, when attachments are bipolar. It has been proposed that bipolar tension applied by the spindle is responsible for the physical separation of sister kinetochores, removal of cohesin protection, and chromatid separation in meiosis II. We show here that this is not the case, and initial separation of sister kinetochores occurs already in anaphase I independently of bipolar spindle forces applied on sister kinetochores, in mouse oocytes. This kinetochore individualization depends on separase cleavage activity. Crucially, without kinetochore individualization in meiosis I, bivalents when present in meiosis II oocytes separate into chromosomes and not sister chromatids. This shows that whether centromeric cohesin is removed or not is determined by the kinetochore structure prior to meiosis II.

Seismic and Aseismic Fault Slip During the Initiation Phase of the 2017 M W = 6.9 Valparaíso Earthquake

Transient deformation associated with foreshocks activity has been observed before large earthquakes, suggesting the occurrence of a detectable preseismic slow slip during the initiation phase. A critical issue consists in discriminating the relative contributions from seismic and aseismic fault slip during the preparation phase of large earthquakes. We focus on the April-May 2017 Valparaíso earthquake sequence, which involved a M W  = 6.9 earthquake preceded by intense foreshock activity. To assess the relative contribution of seismic and aseismic slip, we compare surface displacement predicted from foreshocks source models with transient motion measured prior to the mainshock. The comparison between observed and predicted displacements shows that only half of the total displacement can be explained by the contribution of foreshocks. This result suggests the presence of aseismic pre-slip during an initiation phase preceding the mainshock.

Best practices for the visualization, mapping, and manipulation of R-loops

R-loops represent an abundant class of large non-B DNA structures in genomes. Even though they form transiently and at modest frequencies, interfering with R-loop formation or dissolution has significant impacts on genome stability. Addressing the mechanism(s) of R-loop-mediated genome destabilization requires a precise characterization of their distribution in genomes. A number of independent methods have been developed to visualize and map R-loops, but their results are at times discordant, leading to confusion. Here, we review the main existing methodologies for R-loop mapping and assess their limitations as well as the robustness of existing datasets. We offer a set of best practices to improve the reproducibility of maps, hoping that such guidelines could be useful for authors and referees alike. Finally, we propose a possible resolution for the apparent contradictions in R-loop mapping outcomes between antibody-based and RNase H1-based mapping approaches.

The Nature and Origins of Sub-Neptune Size Planets

Planets intermediate in size between the Earth and Neptune, and orbiting closer to their host stars than Mercury does the Sun, are the most common type of planet revealed by exoplanet surveys over the last quarter century. Results from NASA's Kepler mission have revealed a bimodality in the radius distribution of these objects, with a relative underabundance of planets between 1.5 and 2.0R ⊕ . This bimodality suggests that sub-Neptunes are mostly rocky planets that were born with primary atmospheres a few percent by mass accreted from the protoplanetary nebula. Planets above the radius gap were able to retain their atmospheres ("gas-rich super-Earths"), while planets below the radius gap lost their atmospheres and are stripped cores ("true super-Earths"). The mechanism that drives atmospheric loss for these planets remains an outstanding question, with photoevaporation and core-powered mass loss being the prime candidates. As with the mass-loss mechanism, there are two contenders for the origins of the solids in sub-Neptune planets: the migration model involves the growth and migration of embryos from beyond the ice line, while the drift model involves inward-drifting pebbles that coagulate to form planets close-in. Atmospheric studies have the potential to break degeneracies in interior structure models and place additional constraints on the origins of these planets. However, most atmospheric characterization efforts have been confounded by aerosols. Observations with upcoming facilities are expected to finally reveal the atmospheric compositions of these worlds, which are arguably the first fundamentally new type of planetary object identified from the study of exoplanets.

Syncytia formation by SARS-CoV-2-infected cells

Severe cases of COVID-19 are associated with extensive lung damage and the presence of infected multinucleated syncytial pneumocytes. The viral and cellular mechanisms regulating the formation of these syncytia are not well understood. Here, we show that SARS-CoV-2-infected cells express the Spike protein (S) at their surface and fuse with ACE2-positive neighboring cells. Expression of S without any other viral proteins triggers syncytia formation. Interferon-induced transmembrane proteins (IFITMs), a family of restriction factors that block the entry of many viruses, inhibit S-mediated fusion, with IFITM1 being more active than IFITM2 and IFITM3. On the contrary, the TMPRSS2 serine protease, which is known to enhance infectivity of cell-free virions, processes both S and ACE2 and increases syncytia formation by accelerating the fusion process. TMPRSS2 thwarts the antiviral effect of IFITMs. Our results show that SARS-CoV-2 pathological effects are modulated by cellular proteins that either inhibit or facilitate syncytia formation.

A combination of two human monoclonal antibodies cures symptomatic rabies

Rabies is a neglected disease caused by a neurotropic Lyssavirus, transmitted to humans predominantly by the bite of infected dogs. Rabies is preventable with vaccines or proper post-exposure prophylaxis (PEP), but it still causes about 60,000 deaths every year. No cure exists after the onset of clinical signs, and the case-fatality rate approaches 100% even with advanced supportive care. Here, we report that a combination of two potent neutralizing human monoclonal antibodies directed against the viral envelope glycoprotein cures symptomatic rabid mice. Treatment efficacy requires the concomitant administration of antibodies in the periphery and in the central nervous system through intracerebroventricular infusion. After such treatment, recovered mice presented good clinical condition, viral loads were undetectable, and the brain inflammatory profile was almost normal. Our findings provide the unprecedented proof of concept of an antibody-based therapeutic approach for symptomatic rabies.

Monocytopenia, monocyte morphological anomalies and hyperinflammation characterise severe COVID-19 in type 2 diabetes

Early in the COVID-19 pandemic, type 2 diabetes (T2D) was marked as a risk factor for severe disease and mortality. Inflammation is central to the aetiology of both conditions where variations in immune responses can mitigate or aggravate disease course. Identifying at-risk groups based on immunoinflammatory signatures is valuable in directing personalised care and developing potential targets for precision therapy. This observational study characterised immunophenotypic variation associated with COVID-19 severity in T2D. Broad-spectrum immunophenotyping quantified 15 leucocyte populations in peripheral circulation from a cohort of 45 hospitalised COVID-19 patients with and without T2D. Lymphocytopenia and specific loss of cytotoxic CD8+ lymphocytes were associated with severe COVID-19 and requirement for intensive care in both non-diabetic and T2D patients. A morphological anomaly of increased monocyte size and monocytopenia restricted to classical CD14Hi CD16- monocytes was specifically associated with severe COVID-19 in patients with T2D requiring intensive care. Increased expression of inflammatory markers reminiscent of the type 1 interferon pathway (IL6, IL8, CCL2, INFB1) underlaid the immunophenotype associated with T2D. These immunophenotypic and hyperinflammatory changes may contribute to increased voracity of COVID-19 in T2D. These findings allow precise identification of T2D patients with severe COVID-19 as well as provide evidence that the type 1 interferon pathway may be an actionable therapeutic target for future studies.

Seismic Stereometry Reveals Preparatory Behavior and Source Kinematics of Intermediate-Size Earthquakes

Although moderate-size earthquakes are poorly studied by lack of near-fault observations, they can provide key information about larger damaging earthquakes. Here we propose a new approach, inspired by double-difference relocation, that uses high-coherency waveforms recorded at neighboring sensors, to study the preparation phase and dynamics of moderate-size earthquakes. We validate this technique by analyzing the 2016, M w 5.2 Borrego Springs earthquake in Southern California and find consistent rupture velocities of 2 km/s highlighting two main rupture asperities. The analysis of the 2019, Ml5.2 Le Teil earthquake in France reveals slow nucleation at depth that migrates to the surface and propagates northward with a velocity of ∼2.8 km/s, highlighting two main rupture events also imaged by InSAR. By providing unprecedented resolution in our observation of the rupture dynamics, this approach will be useful in better understanding the preparation phase and rupture of both tectonic and induced earthquakes.

Extensive flavivirus E trimer breathing accompanies stem zippering of the post-fusion hairpin

Flaviviruses enter cells by fusion with endosomal membranes through a rearrangement of the envelope protein E, a class II membrane fusion protein, into fusogenic trimers. The rod-like E subunits bend into "hairpins" to bring the fusion loops next to the C-terminal transmembrane (TM) anchors, with the TM-proximal "stem" element zippering the E trimer to force apposition of the membranes. The structure of the complete class II trimeric hairpin is known for phleboviruses but not for flaviviruses, for which the stem is only partially resolved. Here, we performed comparative analyses of E-protein trimers from the tick-borne encephalitis flavivirus with sequential stem truncations. Our thermostability and antibody-binding data suggest that the stem "zipper" ends at a characteristic flavivirus conserved sequence (CS) that cloaks the fusion loops, with the downstream segment not contributing to trimer stability. We further identified a highly dynamic behavior of E trimers C-terminally truncated upstream the CS, which, unlike fully stem-zippered trimers, undergo rapid deuterium exchange at the trimer interface. These results thus identify important "breathing" intermediates in the E-protein-driven membrane fusion process.

Impacts of Degradation on Water, Energy, and Carbon Cycling of the Amazon Tropical Forests

Selective logging, fragmentation, and understory fires directly degrade forest structure and composition. However, studies addressing the effects of forest degradation on carbon, water, and energy cycles are scarce. Here, we integrate field observations and high-resolution remote sensing from airborne lidar to provide realistic initial conditions to the Ecosystem Demography Model (ED-2.2) and investigate how disturbances from forest degradation affect gross primary production (GPP), evapotranspiration (ET), and sensible heat flux (H). We used forest structural information retrieved from airborne lidar samples (13,500 ha) and calibrated with 817 inventory plots (0.25 ha) across precipitation and degradation gradients in the eastern Amazon as initial conditions to ED-2.2 model. Our results show that the magnitude and seasonality of fluxes were modulated by changes in forest structure caused by degradation. During the dry season and under typical conditions, severely degraded forests (biomass loss ≥66%) experienced water stress with declines in ET (up to 34%) and GPP (up to 35%) and increases of H (up to 43%) and daily mean ground temperatures (up to 6.5°C) relative to intact forests. In contrast, the relative impact of forest degradation on energy, water, and carbon cycles markedly diminishes under extreme, multiyear droughts, as a consequence of severe stress experienced by intact forests. Our results highlight that the water and energy cycles in the Amazon are driven by not only climate and deforestation but also the past disturbance and changes of forest structure from degradation, suggesting a much broader influence of human land use activities on the tropical ecosystems.

Homologous recombination and Mus81 promote replication completion in response to replication fork blockage

Impediments to DNA replication threaten genome stability. The homologous recombination (HR) pathway has been involved in the restart of blocked replication forks. Here, we used a method to increase yeast cell permeability in order to study at the molecular level the fate of replication forks blocked by DNA topoisomerase I poisoning by camptothecin (CPT). Our results indicate that Rad52 and Rad51 HR factors are required to complete DNA replication in response to CPT. Recombination events occurring during S phase do not generally lead to the restart of DNA synthesis but rather protect blocked forks until they merge with convergent forks. This fusion generates structures requiring their resolution by the Mus81 endonuclease in G2 /M. At the global genome level, the multiplicity of replication origins in eukaryotic genomes and the fork protection mechanism provided by HR appear therefore to be essential to complete DNA replication in response to fork blockage.

Dual lysine and N-terminal acetyltransferases reveal the complexity underpinning protein acetylation

Protein acetylation is a highly frequent protein modification. However, comparatively little is known about its enzymatic machinery. N-α-acetylation (NTA) and ε-lysine acetylation (KA) are known to be catalyzed by distinct families of enzymes (NATs and KATs, respectively), although the possibility that the same GCN5-related N-acetyltransferase (GNAT) can perform both functions has been debated. Here, we discovered a new family of plastid-localized GNATs, which possess a dual specificity. All characterized GNAT family members display a number of unique features. Quantitative mass spectrometry analyses revealed that these enzymes exhibit both distinct KA and relaxed NTA specificities. Furthermore, inactivation of GNAT2 leads to significant NTA or KA decreases of several plastid proteins, while proteins of other compartments were unaffected. The data indicate that these enzymes have specific protein targets and likely display partly redundant selectivity, increasing the robustness of the acetylation process in vivo. In summary, this study revealed a new layer of complexity in the machinery controlling this prevalent modification and suggests that other eukaryotic GNATs may also possess these previously underappreciated broader enzymatic activities.

Temporal specificity and heterogeneity of Drosophila immune cells

Immune cells provide defense against non-self and have recently been shown to also play key roles in diverse processes such as development, metabolism, and tumor progression. The heterogeneity of Drosophila immune cells (hemocytes) remains an open question. Using bulk RNA sequencing, we find that the hemocytes display distinct features in the embryo, a closed and rapidly developing system, compared to the larva, which is exposed to environmental and metabolic challenges. Through single-cell RNA sequencing, we identify fourteen hemocyte clusters present in unchallenged larvae and associated with distinct processes, e.g., proliferation, phagocytosis, metabolic homeostasis, and humoral response. Finally, we characterize the changes occurring in the hemocyte clusters upon wasp infestation, which triggers the differentiation of a novel hemocyte type, the lamellocyte. This first molecular atlas of hemocytes provides insights and paves the way to study the biology of the Drosophila immune cells in physiological and pathological conditions.

Evaluation of Data-Based Estimates of Anthropogenic Carbon in the Arctic Ocean

The Arctic Ocean is particularly vulnerable to ocean acidification, a process that is mainly driven by the uptake of anthropogenic carbon (Cant) from the atmosphere. Although Cant concentrations cannot be measured directly in the ocean, they have been estimated using data-based methods such as the transient time distribution (TTD) approach, which characterizes the ventilation of water masses with inert transient tracers, such as CFC-12. Here, we evaluate the TTD approach in the Arctic Ocean using an eddying ocean model as a test bed. When the TTD approach is applied to simulated CFC-12 in that model, it underestimates the same model's directly simulated Cant concentrations by up to 12%, a bias that stems from its idealized assumption of gas equilibrium between atmosphere and surface water, both for CFC-12 and anthropogenic CO2. Unlike the idealized assumption, the simulated partial pressure of CFC-12 (pCFC-12) in Arctic surface waters is undersaturated relative to that in the atmosphere in regions and times of deep-water formation, while the simulated equivalent for Cant is supersaturated. After accounting for the TTD approach's negative bias, the total amount of Cant in the Arctic Ocean in 2005 increases by 8% to 3.3 ± 0.3 Pg C. By combining the adjusted TTD approach with scenarios of future atmospheric CO2, it is estimated that all Arctic waters, from surface to depth, would become corrosive to aragonite by the middle of the next century even if atmospheric CO2 could be stabilized at 540 ppm.

Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver

Liver injury triggers adaptive remodeling of the hepatic transcriptome for repair/regeneration. We demonstrate that this involves particularly profound transcriptomic alterations where acute induction of genes involved in handling of endoplasmic reticulum stress (ERS) is accompanied by partial hepatic dedifferentiation. Importantly, widespread hepatic gene downregulation could not simply be ascribed to cofactor squelching secondary to ERS gene induction, but rather involves a combination of active repressive mechanisms. ERS acts through inhibition of the liver-identity (LIVER-ID) transcription factor (TF) network, initiated by rapid LIVER-ID TF protein loss. In addition, induction of the transcriptional repressor NFIL3 further contributes to LIVER-ID gene repression. Alteration to the liver TF repertoire translates into compromised activity of regulatory regions characterized by the densest co-recruitment of LIVER-ID TFs and decommissioning of BRD4 super-enhancers driving hepatic identity. While transient repression of the hepatic molecular identity is an intrinsic part of liver repair, sustained disequilibrium between the ERS and LIVER-ID transcriptional programs is linked to liver dysfunction as shown using mouse models of acute liver injury and livers from deceased human septic patients.

Improvement of the Irrigation Scheme in the ORCHIDEE Land Surface Model and Impacts of Irrigation on Regional Water Budgets Over China

In China, irrigation is widespread in 40.7% cropland to sustain crop yields. By its action on water cycle, irrigation affects water resources and local climate. In this study, a new irrigation module, including flood and paddy irrigation technologies, was developed in the ORCHIDEE-CROP land surface model which describes crop phenology and growth in order to estimate irrigation demands over China from 1982 to 2014. Three simulations were performed including NI (no irrigation), IR (with irrigation limited by local water resources), and FI (with irrigation demand fulfilled). Observations and census data were used to validate the simulations. Results showed that the estimated irrigation water withdrawal ( W ) based on IR and FI scenarios bracket statistical W with fair spatial agreements ( r = 0 . 68 ± 0 . 07 ; p < 0 . 01 ). Improving irrigation efficiency was found to be the dominant factor leading to the observed W decrease. By comparing simulated total water storage (TWS) with GRACE observations, we found that simulated TWS with irrigation well explained the TWS variation over China. However, our simulation overestimated the seasonality of TWS in the Yangtze River Basin due to ignoring regulation of artificial reservoirs. The observed TWS decrease in the Yellow River Basin caused by groundwater depletion was not totally captured in our simulation, but it can be inferred by combining simulated TWS with census data. Moreover, we demonstrated that land use change tended to drive W locally but had little effect on total W over China due to water resources limitation.

The many types of heterogeneity in replicative senescence

Replicative senescence, which is induced by telomere shortening, underlies the loss of regeneration capacity of organs and is ultimately detrimental to the organism. At the same time, it is required to protect organisms from unlimited cell proliferation that may arise from numerous stimuli or deregulations. One important feature of replicative senescence is its high level of heterogeneity and asynchrony, which promote genome instability and senescence escape. Characterizing this heterogeneity and investigating its sources are thus critical to understanding the robustness of replicative senescence. Here we review the different aspects of senescence driven by telomere attrition that are subject to variation in Saccharomyces cerevisiae, the current understanding of the molecular processes at play, and the consequences of heterogeneity in replicative senescence.

Including Stable Carbon Isotopes to Evaluate the Dynamics of Soil Carbon in the Land-Surface Model ORCHIDEE

Soil organic carbon (SOC) is a crucial component of the terrestrial carbon cycle and its turnover time in models is a key source of uncertainty. Studies have highlighted the utility of δ13C measurements for benchmarking SOC turnover in global models. We used 13C as a tracer within a vertically discretized soil module of a land-surface model, Organising Carbon and Hydrology In Dynamic Ecosystems- Soil Organic Matter (ORCHIDEE-SOM). Our new module represents some of the processes that have been hypothesized to lead to a 13C enrichment with soil depth as follows: 1) the Suess effect and CO2 fertilization, 2) the relative 13C enrichment of roots compared to leaves, and 3) 13C discrimination associated with microbial activity. We tested if the upgraded soil module was able to reproduce the vertical profile of δ13C within the soil column at two temperate sites and the short-term change in the isotopic signal of soil after a shift in C3/C4 vegetation. We ran the model over Europe to test its performance at larger scale. The model was able to simulate a shift in the isotopic signal due to short-term changes in vegetation cover from C3 to C4; however, it was not able to reproduce the overall vertical profile in soil δ13C, which arises as a combination of short and long-term processes. At the European scale, the model ably reproduced soil CO2 fluxes and total SOC stock. These findings stress the importance of the long-term history of land cover for simulating vertical profiles of δ13C. This new soil module is an emerging tool for the diagnosis and improvement of global SOC models.

Train Traffic as a Powerful Noise Source for Monitoring Active Faults With Seismic Interferometry

Laboratory experiments report that detectable seismic velocity changes should occur in the vicinity of fault zones prior to earthquakes. However, operating permanent active seismic sources to monitor natural faults at seismogenic depth is found to be nearly impossible to achieve. We show that seismic noise generated by vehicle traffic, and especially heavy freight trains, can be turned into a powerful repetitive seismic source to continuously probe the Earth's crust at a few kilometers depth. Results of an exploratory seismic experiment in Southern California demonstrate that correlations of train-generated seismic signals allow daily reconstruction of direct P body waves probing the San Jacinto Fault down to 4-km depth. This new approach may facilitate monitoring most of the San Andreas Fault system using the railway and highway network of California.

Kinetics of CrPV and HCV IRES-mediated eukaryotic translation using single-molecule fluorescence microscopy

Protein synthesis is a complex multistep process involving many factors that need to interact in a coordinated manner to properly translate the messenger RNA. As translating ribosomes cannot be synchronized over many elongation cycles, single-molecule studies have been introduced to bring a deeper understanding of prokaryotic translation dynamics. Extending this approach to eukaryotic translation is very appealing, but initiation and specific labeling of the ribosomes are much more complicated. Here, we use a noncanonical translation initiation based on internal ribosome entry sites (IRES), and we monitor the passage of individual, unmodified mammalian ribosomes at specific fluorescent milestones along mRNA. We explore initiation by two types of IRES, the intergenic IRES of cricket paralysis virus (CrPV) and the hepatitis C (HCV) IRES, and show that they both strongly limit the rate of the first elongation steps compared to the following ones, suggesting that those first elongation cycles do not correspond to a canonical elongation. This new system opens the possibility of studying both IRES-mediated initiation and elongation kinetics of eukaryotic translation and will undoubtedly be a valuable tool to investigate the role of translation machinery modifications in human diseases.