Analysis of the CtrA Pathway in Magnetospirillum Reveals an Ancestral Role in Motility in Alphaproteobacteria

Developmental events across the prokaryotic life cycle are highly regulated at the transcriptional and posttranslational levels. Key elements of a few regulatory networks are conserved among phylogenetic groups of bacteria, although the features controlled by these conserved systems are as diverse as the organisms encoding them. In this work, we probed the role of the CtrA regulatory network, conserved throughout the Alphaproteobacteria, in the magnetotactic bacterium Magnetospirillum magneticum strain AMB-1, which possesses unique intracellular organization and compartmentalization. While we have shown that CtrA in AMB-1 is not essential for viability, it is required for motility, and its putative phosphorylation state dictates the ability of CtrA to activate the flagellar biosynthesis gene cascade. Gene expression analysis of strains expressing active and inactive CtrA alleles points to the composition of the extended CtrA regulon, including both direct and indirect targets. These results, combined with a bioinformatic study of the AMB-1 genome, enabled the prediction of an AMB-1-specific CtrA binding site. Further, phylogenetic studies comparing CtrA sequences from alphaproteobacteria in which the role of CtrA has been experimentally examined reveal an ancestral role of CtrA in the regulation of motility and suggest that its essential functions in other alphaproteobacteria were acquired subsequently

Cholesterol-lowering action of a novel nutraceutical combination in uremic rats: Insights into the molecular mechanism in a hepatoma cell line

Appropriate nutraceutical combinations may represent a valid approach to prevent vascular calcification associated with chronic kidney disease (CKD). In the present study, we tested the effect of a new nutraceutical combination named RenaTris®, containing MK-7, magnesium carbonate, and Sucrosomial® Iron, on vascular calcification in uremic rats. Rats were randomly divided into three groups, i.e. control (high-phosphate diet), uremic (high-phosphate diet containing 0.5% adenine), and supplemented uremic diet (0.5% adenine, MK-7, magnesium carbonate, and Sucrosomial® Iron). After six weeks, sera and vascular calcification were examined. The uremic diet increased creatinine and phosphate levels and induced extensive vascular calcification. The uremic condition also induced a mild hypercholesterolemic condition (+52% of total cholesterol; p < 0.05). The supplemented uremic diet did not reduce creatinine, phosphate levels, or vascular calcification, however, we observed a significant hypocholesterolemic effect (−18.9% in supplemental uremic vs. uremic diet; p < 0.05). Similar to simvastatin, incubation of cultured human hepatoma cells (Huh7) with MK-7 significantly reduced cholesterol biosynthesis (−38%) and induced 3-hydroxy-3-methyl-glutaryl-CoA (HMG-CoA) reductase and low-density lipoprotein receptor (LDLR) at both mRNA and protein levels. The effect of MK-7 on LDLR was counteracted by the co-incubation with squalene. Unlike simvastatin, MK-7 reduced PCSK9 in Huh7. These results indicated that the new nutraceutical combination significantly impacts cholesterol metabolism and its supplementation may help to control mild hypercholesterolemic conditions in CKD patients

Grape berry responses to sequential flooding and heatwave events: a physiological, transcriptional, and metabolic overview

Grapevine cultivation, such as the whole horticulture, is currently challenged by several factors, among which the extreme weather events occurring under the climate change scenario are the most relevant. Within this context, the present study aims at characterizing at the berry level the physiological response of Vitis vinifera cv. Sauvignon Blanc to sequential stresses simulated under a semi-controlled environment: flooding at bud-break followed by multiple summer stress (drought plus heatwave) occurring at pre-vèraison. Transcriptomic and metabolomic assessments were performed through RNASeq and NMR, respectively. A comprehensive hormone profiling was also carried out. Results pointed out a different response to the heatwave in the two situations. Flooding caused a developmental advance, determining a different physiological background in the berry, thus affecting its response to the summer stress at both transcriptional levels, with the upregulation of genes involved in oxidative stress responses, and metabolic level, with the increase in osmoprotectants, such as proline and other amino acids. In conclusion, sequential stress, including a flooding event at bud-break followed by a summer heatwave, may impact phenological development and berry ripening, with possible consequences on berry and wine quality. A berry physiological model is presented that may support the development of sustainable vineyard management solutions to improve the water use efficiency and adaptation capacity of actual viticultural systems to future scenario

Multimodel Evaluation of Nitrous Oxide Emissions From an Intensively Managed Grassland

Process‐based models are useful for assessing the impact of changing management practices and climate on yields and greenhouse gas (GHG) emissions from agricultural systems such as grasslands. They can be used to construct national GHG inventories using a Tier 3 approach. However, accurate simulations of nitrous oxide (N$_{2}$O) fluxes remain challenging. Models are limited by our understanding of soil‐plant‐microbe interactions and the impact of uncertainty in measured input parameters on simulated outputs. To improve model performance, thorough evaluations against in situ measurements are needed. Experimental data of N$_{2}$O emissions under two management practices (control with typical fertilization versus increased clover and no fertilization) were acquired in a Swiss field experiment. We conducted a multimodel evaluation with three commonly used biogeochemical models (DayCent in two variants, PaSim, APSIM in two variants) comparing four years of data. DayCent was the most accurate model for simulating N$_{2}$O fluxes on annual timescales, while APSIM was most accurate for daily N$_{2}$O fluxes. The multimodel ensemble average reduced the error in estimated annual fluxes by 41% compared to an estimate using the Intergovernmental Panel on Climate Change (IPCC)‐derived method for the Swiss agricultural GHG inventory (IPCC‐Swiss), but individual models were not systematically more accurate than IPCC‐Swiss. The model ensemble overestimated the N$_{2}$O mitigation effect of the clover‐based treatment (measured: 39–45%; ensemble: 52–57%) but was more accurate than IPCC‐Swiss (IPCC‐Swiss: 72–81%). These results suggest that multimodel ensembles are valuable for estimating the impact of climate and management on N$_{2}$O emissions

Modelling biological N fixation and grass-legume dynamics with process-based biogeochemical models of varying complexity

This work was conducted by the Models4Pastures consortium project under the auspices of FACCE-JPI. Funding was provided by: the New Zealand Government to support the objectives of the Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gases; AgResearch’s Strategic Science Investment Fund as a contribution to the Forages for Reduced Nitrate Leaching (FRNL) research programme; the input of UK partners was funded by DEFRA and also contributes to the RCUK-funded projects: N-Circle (BB/N013484/1), UGRASS (NE/M016900/1) and GREENHOUSE (NE/K002589/1). R.M. Rees and C.F.E. Topp also received funding from the Scottish Government Strategic Research Programme. Lutz Merbold and Kathrin Fuchs acknowledge funding received for the Swiss contribution to Models4Pastures (FACCE-JPI project, SNSF funded contract: 40FA40_154245/1) and for the Doc.Mobility fellowship (SNSF funded project: P1EZP2_172121). Lorenzo Brilli, Camilla Dibari and Marco Bindi acknowledge funding received from the Italian Ministry of Agricultural Food and Forestry Policies (MiPAAF).Peer reviewedPublisher PD

Exploring mobility in Italian Neolithic and Copper Age communities

As a means for investigating human mobility during late the Neolithic to the Copper Age in central and southern Italy, this study presents a novel dataset of enamel oxygen and carbon isotope values (delta (18)Oca and delta (13)Cca) from the carbonate fraction of biogenic apatite for one hundred and twenty-six individual teeth coming from two Neolithic and eight Copper Age communities. The measured delta (18)Oca values suggest a significant role of local sources in the water inputs to the body water, whereas delta (13)Cca values indicate food resources, principally based on C-3 plants. Both delta (13)Cca and delta (18)Oca ranges vary substantially when samples are broken down into local populations. Statistically defined thresholds, accounting for intra-site variability, allow the identification of only a few outliers in the eight Copper Age communities, suggesting that sedentary lifestyle rather than extensive mobility characterized the investigated populations. This seems to be also typical of the two studied Neolithic communities. Overall, this research shows that the investigated periods in peninsular Italy differed in mobility pattern from the following Bronze Age communities from more northern areas

Permanent draft genome sequences of the symbiotic nitrogen fixing Ensifer meliloti strains BO21CC and AK58

Ensifer (syn. Sinorhizobium) meliloti is an important symbiotic bacterial species that fixes nitrogen. Strains BO21CC and AK58 were previously investigated for their substrate utilization and their plant-growth promoting abilities showing interesting features. Here, we describe the complete genome sequence and annotation of these strains. BO21CC and AK58 genomes are 6,985,065 and 6,974,333 bp long with 6,746 and 6,992 genes predicted, respectively. © retained by original authors

Biogenic Volatile Organic Compound and Respiratory CO2 Emissions after 13C-Labeling: Online Tracing of C Translocation Dynamics in Poplar Plants

Globally plants are the primary sink of atmospheric CO(2), but are also the major contributor of a large spectrum of atmospheric reactive hydrocarbons such as terpenes (e.g. isoprene) and other biogenic volatile organic compounds (BVOC). The prediction of plant carbon (C) uptake and atmospheric oxidation capacity are crucial to define the trajectory and consequences of global environmental changes. To achieve this, the biosynthesis of BVOC and the dynamics of C allocation and translocation in both plants and ecosystems are important.We combined tunable diode laser absorption spectrometry (TDLAS) and proton transfer reaction mass spectrometry (PTR-MS) for studying isoprene biosynthesis and following C fluxes within grey poplar (Populus x canescens) saplings. This was achieved by feeding either (13)CO(2) to leaves or (13)C-glucose to shoots via xylem uptake. The translocation of (13)CO(2) from the source to other plant parts could be traced by (13)C-labeled isoprene and respiratory (13)CO(2) emission.In intact plants, assimilated (13)CO(2) was rapidly translocated via the phloem to the roots within 1 hour, with an average phloem transport velocity of 20.3±2.5 cm h(-1). (13)C label was stored in the roots and partially reallocated to the plants' apical part one day after labeling, particularly in the absence of photosynthesis. The daily C loss as BVOC ranged between 1.6% in mature leaves and 7.0% in young leaves. Non-isoprene BVOC accounted under light conditions for half of the BVOC C loss in young leaves and one-third in mature leaves. The C loss as isoprene originated mainly (76-78%) from recently fixed CO(2), to a minor extent from xylem-transported sugars (7-11%) and from photosynthetic intermediates with slower turnover rates (8-11%).We quantified the plants' C loss as respiratory CO(2) and BVOC emissions, allowing in tandem with metabolic analysis to deepen our understanding of ecosystem C flux