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Studies suggest that ketogenic diets (KD) may improve memory in mouse models of aging and Alzheimer's disease (AD). This study determined whether a continuous or intermittent KD (IKD) enhanced cognitive behavior in the TgF344-AD rat model of AD. At 6 months-old, TgF344-AD and wild-type (WT) littermates were placed on a control (CD), KD, or IKD (morning CD and afternoon KD) provided as two meals per day for 2 or 6 months. Cognitive and motor behavior and circulating β-hydroxybutyrate (BHB), AD biomarkers and blood lipids were assessed. Animals on a KD diet had elevated circulating BHB, with IKD levels intermediate to CD and KD. TgF344-AD rats displayed impaired spatial learning memory in the Barnes maze at 8 and 12 months of age and impaired motor coordination at 12 months of age. Neither KD nor IKD improved performance compared to CD. At 12 months of age, TgF344-AD animals had elevated blood lipids. IKD reduced lipids to WT levels with KD further reducing cholesterol below WT levels. This study shows that at 8 or 12 months of age, KD or IKD intervention did not improve measures of cognitive or motor behavior in TgF344-AD rats; however, both IKD and KD positively impacted circulating lipids.

Sustainable intensification schemes such as integrated soil fertility management (ISFM) are a proposed strategy to close yield gaps, increase soil fertility, and achieve food security in sub-Saharan Africa. Biogeochemical models such as DayCent can assess their potential at larger scales, but these models need to be calibrated to new environments and rigorously tested for accuracy. Here, we present a Bayesian calibration of DayCent, using data from four long-term field experiments in Kenya in a leave-one-site-out cross-validation approach. The experimental treatments consisted of the addition of low- to high-quality organic resources, with and without mineral nitrogen fertilizer. We assessed the potential of DayCent to accurately simulate the key elements of sustainable intensification, including (1) yield, (2) the changes in soil organic carbon (SOC), and (3) the greenhouse gas (GHG) balance of CO2 and N2O combined. Compared to the initial parameters, the cross-validation showed improved DayCent simulations of maize grain yield (with the Nash–Sutcliffe model efficiency (EF) increasing from 0.36 to 0.50) and of SOC stock changes (with EF increasing from 0.36 to 0.55). The simulations of maize yield and those of SOC stock changes also improved by site (with site-specific EF ranging between 0.15 and 0.38 for maize yield and between −0.9 and 0.58 for SOC stock changes). The four cross-validation-derived posterior parameter distributions (leaving out one site each) were similar in all but one parameter. Together with the model performance for the different sites in cross-validation, this indicated the robustness of the DayCent model parameterization and its reliability for the conditions in Kenya. While DayCent poorly reproduced daily N2O emissions (with EF ranging between −0.44 and −0.03 by site), cumulative seasonal N2O emissions were simulated more accurately (EF ranging between 0.06 and 0.69 by site). The simulated yield-scaled GHG balance was highest in control treatments without N addition (between 0.8 and 1.8 kg CO2 equivalent per kg grain yield across sites) and was about 30 % to 40 % lower in the treatment that combined the application of mineral N and of manure at a rate of 1.2 t C ha−1 yr−1. In conclusion, our results indicate that DayCent is well suited for estimating the impact of ISFM on maize yield and SOC changes. They also indicate that the trade-off between maize yield and GHG balance is stronger in low-fertility sites and that preventing SOC losses, while difficult to achieve through the addition of external organic resources, is a priority for the sustainable intensification of maize production in Kenya.

We present results of simulations performed with a physical–biogeochemical ocean model of the Mediterranean Sea for the Last Glacial Maximum (LGM) and analyse the differences in physical and biochemical states between the historical period and the LGM. Long-term simulations with an Earth system model based on ice sheet reconstructions provide the necessary atmospheric forcing data, oceanic boundary conditions at the entrance to the Mediterranean Sea, and river discharge to the entire basin. Our regional model accounts for changes in bathymetry due to ice sheet volume changes, reduction in atmospheric CO2 concentration, and an adjusted aeolian dust and iron deposition. The physical ocean state of the Mediterranean during the LGM shows a reduced baroclinic water exchange at the Strait of Gibraltar, a more sluggish zonal overturning circulation, and the relocation of intermediate and deep-water-formation areas – all in line with estimates from palaeo-sediment records or previous modelling efforts. Most striking features of the biogeochemical realm are a reduction in the net primary production, an accumulation of nutrients below the euphotic zone, and an increase in the organic matter deposition at the seafloor. This seeming contradiction of increased organic matter deposition and decreased net primary production challenges our view of possible changes in surface biological processes during the LGM. We attribute the origin of a reduced net primary production to the interplay of increased stability of the upper water column, changed zonal water transport at intermediate depths, and lower water temperatures, which slow down all biological processes during the LGM. Cold water temperatures also affect the remineralisation rates of organic material, which explains the simulated increase in the organic matter deposition, which is in good agreement with sediment proxy records. In addition, we discuss changes in an artificial tracer which captures the surface ocean temperature signal during organic matter production. A shifted seasonality of the biological production in the LGM leads to a difference in the recording of the climate signal by this artificial tracer of up to 1 K. This could be of relevance for the interpretation of proxy records like, e.g., alkenones. Our study not only provides the first consistent insights into the biogeochemistry of the glacial Mediterranean Sea but will also serve as the starting point for transient simulations of the last deglaciation.

Abstract Background Within the follicular fluid, extracellular vesicles (EVs) guide oocyte growth through their cargo microRNAs (miRNAs). Here, we investigated the role of EVs and their cargo miRNAs by linking the miRNAs found in EVs, derived from the fluid of an individual follicle, to the ability of its oocyte to become a blastocyst (competent) or not (non-competent). Methods Bovine antral follicles were dissected, categorized as small (2–4 mm) or large (5–8 mm) and the corresponding oocytes were subjected to individual maturation, fertilization and embryo culture to the blastocyst stage. Follicular fluid was pooled in 4 groups (4 replicates) based on follicle size and competence of the corresponding oocyte to produce a blastocyst. Follicular fluid-derived EVs were isolated, characterized, and subjected to miRNA-sequencing (Illumina Miseq) to assess differential expression (DE) in the 4 groups. Functional validation of the effect of miR-34c on embryo development was performed by supplementation of mimics and inhibitors during in vitro maturation (IVM). Results We identified 16 DE miRNAs linked to oocyte competence when follicular size was not considered. Within the large and small follicles, 46 DE miRNAs were driving blastocyst formation in each group. Comparison of EVs from competent small and large follicles revealed 90 DE miRNAs. Cell regulation, cell differentiation, cell cycle, and metabolic process regulation were the most enriched pathways targeted by the DE miRNAs from competent oocytes. We identified bta-miR-34c as the most abundant in follicular fluid containing competent oocytes. Supplementation of miR-34c mimic and inhibitor during IVM did not affect embryo development. However, blastocyst quality, as evidenced by higher cell numbers, was significantly improved following oocyte IVM in the presence of miR-34c mimics, while miR-34c inhibitors resulted in the opposite effect. Conclusion This study demonstrates the regulatory effect of miRNAs from follicular fluid-derived EVs on oocyte competence acquisition, providing a further basis for understanding the significance of miRNAs in oocyte maturation and embryonic development. Up-regulation of miR-34c in EVs from follicular fluid containing competent oocytes and the positive impact of miR-34c mimics added during IVM on the resulting blastocysts indicate its pivotal role in oocyte competence.

Abstract Background Prioritisation of chemical pollutants is a major challenge for environmental managers and decision-makers alike, which is essential to help focus the limited resources available for monitoring and mitigation actions on the most relevant chemicals. This study extends the original NORMAN prioritisation scheme beyond target chemicals, presenting the integration of semi-quantitative data from retrospective suspect screening and expansion of existing exposure and risk indicators. The scheme utilises data retrieved automatically from the NORMAN Database System (NDS), including candidate substances for prioritisation, target and suspect screening data, ecotoxicological effect data, physico-chemical data and other properties. Two complementary workflows using target and suspect screening monitoring data are applied to first group the substances into six action categories and then rank the substances using exposure, hazard and risk indicators. The results from the ‘target’ and ‘suspect screening’ workflows can then be combined as multiple lines of evidence to support decision-making on regulatory and research actions. Results As a proof-of-concept, the new scheme was applied to a combined dataset of target and suspect screening data. To this end, > 65,000 substances on the NDS, of which 2579 substances supported by target wastewater monitoring data, were retrospectively screened in 84 effluent wastewater samples, totalling > 11 million data points. The final prioritisation results identified 677 substances as high priority for further actions, 7455 as medium priority and 326 with potentially lower priority for actions. Among the remaining substances, ca. 37,000 substances should be considered of medium priority with uncertainty, while it was not possible to conclude for 19,000 substances due to insufficient information from target monitoring and uncertainty in the identification from suspect screening. A high degree of agreement was observed between the categories assigned via target analysis and suspect screening-based prioritisation. Suspect screening was a valuable complementary approach to target analysis, helping to prioritise thousands of substances that are insufficiently investigated in current monitoring programmes. Conclusions This updated prioritisation workflow responds to the increasing use of suspect screening techniques. It can be adapted to different environmental compartments and can support regulatory obligations, including the identification of specific pollutants in river basins and the marine environments, as well as the confirmation of environmental occurrence levels predicted by modelling tools. Graphical Abstract

Predicting the quantity of soil organic carbon (SOC) requires understanding how different factors control the amount of SOC. Land use has a major influence on the function of the soil as a carbon sink, as shown by substantial organic carbon (OC) losses from the soil upon deforestation. However, predicting the degree to which land use change affects the OC content in soils and the depth down to which this occurs requires context-specific information related to, for example, climate, geochemistry, and land use history. In this study, 266 samples from forests and agricultural fields were collected from 94 soil profiles down to 300 cm depth in a subtropical region (Arvorezinha, southern Brazil) to study the impact of land use on the amount of stabilized OC along the soil profile. We found that the stabilized OC content was not affected by land use below a depth of 90 cm. Along the soil profile, the amount of stabilized OC was predominantly controlled by land use and depth in addition to the silt and clay content and aluminium ion concentrations. Below 100 cm, none of the soil profiles reached a concentration of stabilized OC above 50 % of the stabilized OC saturation point (i.e. the maximum OC concentration that can physically be stabilized in these soils). Based on these results, we argue that it is unlikely that deeper soil layers can serve as an OC sink over a timescale relevant to global climate change due to the limited OC input in these deeper layers. Furthermore, we found that the soil weathering degree was not a relevant control on the amount of stabilized OC in our profiles because of the high weathering degree of the studied soils. It is therefore suggested that, while the soil weathering degree might be an effective controlling factor of OC stabilization over a large spatial scale, it is not an informative measure for this process at regional and local scales (with similar climate, bedrock, and weathering history) in highly weathered soils.

Abstract The presence of Salmonella in dry fermented sausages is source of recalls and outbreaks. The genomic diversity of 173 Salmonella isolates from the dry fermented sausage production chains (pig carcasses, pork, and sausages) from France and Spain were investigated through their core phylogenomic relationships and accessory genome profiles. Ten different serovars and thirteen sequence type profiles were identified. The most frequent serovar from sausages was the monophasic variant of S. Typhimurium (1,4,[5],12:i:-, 72%) while S. Derby was in pig carcasses (51%). Phylogenomic clusters found in S. 1,4,[5],12:i:-, S. Derby, S. Rissen and S. Typhimurium serovars identified closely related isolates, with less than 10 alleles and 20 SNPs of difference, displaying Salmonella persistence along the pork production chain. Most of the S. 1,4,[5],12:i:- contained the Salmonella genomic island-4 (SGI-4), Tn21 and IncFIB plasmid. More than half of S. Derby strains contained the SGI-1 and Tn7. S. 1,4,[5],12:i:- genomes carried the most multidrug resistance genes (91% of the strains), whereas extended-spectrum β-lactamase genes were found in Typhimurium and Derby serovars. Salmonella monitoring and characterization in the pork production chains, specially S. 1,4,[5],12:i:- serovar, is of special importance due to its multidrug resistance capacity and persistence in dry fermented sausages.

Abstract Hematopoietic stem cell gene therapy (GT) using a γ-retroviral vector (γ-RV) is an effective treatment for Severe Combined Immunodeficiency due to Adenosine Deaminase deficiency. Here, we describe a case of GT-related T-cell acute lymphoblastic leukemia (T-ALL) that developed 4.7 years after treatment. The patient underwent chemotherapy and haploidentical transplantation and is currently in remission. Blast cells contain a single vector insertion activating the LIM-only protein 2 (LMO2) proto-oncogene, confirmed by physical interaction, and low Adenosine Deaminase (ADA) activity resulting from methylation of viral promoter. The insertion is detected years before T-ALL in multiple lineages, suggesting that further hits occurred in a thymic progenitor. Blast cells contain known and novel somatic mutations as well as germline mutations which may have contributed to transformation. Before T-ALL onset, the insertion profile is similar to those of other ADA-deficient patients. The limited incidence of vector-related adverse events in ADA-deficiency compared to other γ-RV GT trials could be explained by differences in transgenes, background disease and patient’s specific factors.

The concept of soil organic carbon (SOC) saturation emerged a bit more than 2 decades ago as our mechanistic understanding of SOC stabilization increased. Recently, the further testing of the concept across a wide range of soil types and environments has led some people to challenge the fundamentals of soil C saturation. Here, we argue that, to test this concept, one should pay attention to six fundamental principles or “rights” (R's): the right measures, the right units, the right dispersive energy and application, the right soil type, the right clay type, and the right saturation level. Once we take care of those six rights across studies, we find a maximum of C stabilized by minerals and estimate based on current data available that this maximum stabilization is around 82 ± 4 g C kg−1 silt + clay for 2 : 1-clay-dominated soils while most likely being only around 46 ± 4 g C kg−1 silt + clay for 1 : 1-clay-dominated soils. These estimates can be further improved using more data, especially for different clay types across varying environmental conditions. However, the bigger challenge is a matter of which C sequestration strategies to implement and how to implement them in order to effectively reach this 82/46 g C kg−1 silt + clay in soils across the globe.

MicroRNAs (miRNA) are important regulators of oocyte maturation, playing a key role in modulating gene expression both in a temporal- and spatial-specific manner. These small non-coding RNAs are involved in important processes during oocyte maturation, acting as messengers between the oocyte and its surrounding cumulus cells. Despite its significance, the bidirectional communication mechanism is still unknown. To test miRNA communication between oocyte and surrounding cumulus cells through the gap junctions the gap junctions were either blocked with carbenoxolone or not. MiRNA sequencing of oocytes at 1, 6, and 22 h of in vitro maturation was then performed. Among the differentially expressed miRNAs, bta-miR-21-5p, a regulator of cumulus cell viability and oocyte maturation, was the only previously known miRNA. Furthermore, by labeling a bta-miR-21-5p mimic with FAM, crossing of this miRNA through the gap junctions within the cumulus-oocyte complex could be visualized and internalization in the oocyte was confirmed by RT-qPCR. In conclusion, this study provides, for the first time, evidence that miRNA communication within the bovine cumulus-oocyte complex is enabled through the gap junctional network.

Conservation agriculture (CA), combining reduced or no tillage, permanent soil cover, and improved rotations, is often promoted as a climate-smart practice. However, our understanding of the impact of CA and its respective three principles on top- and subsoil organic carbon stocks in the low-input cropping systems of sub-Saharan Africa is rather limited. This study was conducted at two long-term experimental sites established in Zimbabwe in 2013. The soil types were abruptic Lixisols at Domboshava Training Centre (DTC) and xanthic Ferralsol at the University of Zimbabwe farm (UZF). The following six treatments, which were replicated four times, were investigated: conventional tillage (CT), conventional tillage with rotation (CTR), no tillage (NT), no tillage with mulch (NTM), no tillage with rotation (NTR), and no tillage with mulch and rotation (NTMR). Maize (Zea mays L.) was the main crop, and treatments with rotation included cowpea (Vigna unguiculata L. Walp.). The soil organic carbon (SOC) concentration and soil bulk density were determined for samples taken from depths of 0–5, 5–10, 10–15, 15–20, 20–30, 30–40, 40–50, 50–75 and 75–100 cm. Cumulative organic inputs to the soil were also estimated for all treatments. SOC stocks at equivalent soil mass were significantly (p) higher in the NTM, NTR and NTMR treatments compared with the NT and CT treatments in the top 5 cm and top 10 cm layers at UZF, while SOC stocks were only significantly higher in the NTM and NTMR treatments compared with the NT and CT treatments in the top 5 cm at DTC. NT alone had a slightly negative impact on the top SOC stocks. Cumulative SOC stocks were not significantly different between treatments when considering the whole 100 cm soil profile. Our results show the overarching role of crop residue mulching in CA cropping systems with respect to enhancing SOC stocks but also that this effect is limited to the topsoil. The highest cumulative organic carbon inputs to the soil were observed in NTM treatments at the two sites, and this could probably explain the positive effect on SOC stocks. Moreover, our results show that the combination of at least two CA principles including mulch is required to increase SOC stocks in these low-nitrogen-input cropping systems.

Maintaining soil organic matter (SOM) is crucial for healthy and productive agricultural soils and requires understanding at the process level, including the role of SOM protection by soil aggregates and the connection between microbial growth and aggregate formation. We developed the Soil Aggregation through Microbial Mediation (SAMM) model, to represent this important connection. The pools of SAMM are fully measurable, and we calibrated and evaluated it against data from a long-term bare fallow experiment in a tropical sandy soil. This experiment received additions of plant litter of different compositions, which resulted in twice the soil carbon stocks in the best treatment compared to the control (about 8 vs. 4 t C ha−1 in 0–15 cm soil depth) after 25 years. As hypothesized, the SAMM model effectively represented the microbial growth response after the addition of litter and the subsequent formation and later destabilization of aggregates. The low correlations between different calibrated model parameters (r for all parameters; r>0.4 for only 4 of 22) showed that SAMM is parsimonious. SAMM was able to capture differences between treatments in soil organic carbon (Nash–Sutcliffe modeling efficiency (EF) of 0.68), microbial nitrogen (EF of 0.24), and litter carbon (EF of 0.80). The amount of carbon within the aggregates (EF of 0.60) and in the free silt and clay fraction (EF of 0.24) was also simulated very well to satisfactorily. Our model results suggested that in spite of the sandy soil, up to 50 % of carbon stocks were stabilized through aggregate protection mechanisms; and that microbial and physical aggregate formation coexists. A version of the SAMM model without aggregate protection (SAMMnoAgg) initially failed to stabilize soil organic carbon (EF decreased to −3.68) and the simulation of microbial nitrogen worsened (EF of 0.13). By recalibrating SAMMnoAgg, it was possible to partially correct for the lack of aggregate protection by reducing the rate of mineral-attached carbon decomposition by about 85 % (EF of 0.68, 0.75, and 0.18 for SOC, litter carbon, and microbial nitrogen, respectively). However, the slightly better evaluation statistics of SAMM (e.g., Akaike information criterion of 5351 vs. 5554) suggest that representing aggregate dynamics in SOM models can be beneficial and necessary to understand the mechanism behind SOM dynamics. Our results indicate that current models without aggregate formation partly compensate for the absence of aggregate protection by lowering the turnover rates of other pools. Thus, they remain suitable options where data on aggregate associated carbon are not available.

Study region: Flanders (Belgium) Study focus: Stormwater infiltration for managed aquifer recharge is increasingly recognized as a drought adaptation measure. Given the high degree of urbanization and imperviousness, stormwater infiltration has significant potential in Flanders (Belgium). This research presents a novel approach to quantify stormwater availability and its potential to enhance groundwater recharge. Stormwater volumes available for recharge are calculated based on the imperviousness level, yearly average precipitation volumes, and runoff coefficients. This study focuses on groundwater protection zones around drinking water wells to assess the role of increased infiltration for sustainable drinking water production. Calculated potential stormwater volumes for recharge are compared to natural groundwater recharge and pumping volumes for drinking water production to quantify the potential significance of stormwater infiltration for aquifer recharge. New hydrological insights for the region: Results show a high potential for stormwater infiltration in Flemish protection zones with an average of 17% (7%-33%) additional groundwater recharge from stormwater infiltration. Additionally, stormwater recharge could potentially compensate for 19% (8%-37%) of abstracted drinking water production from phreatic aquifers. Locally, higher groundwater recharge potentials were calculated, especially in protection zones around the city of Leuven. Therefore, stormwater harvesting for infiltration and groundwater recharge should be further encouraged throughout the region, with special attention to urban areas. However, further research is needed on stormwater quality to assess groundwater quality risks in this water quantity-quality balancing exercise.