The -11A of promoter DNA and two conserved amino acids in the melting region of sigma70 both directly affect the rate limiting step in formation of the stable RNA polymerase-promoter complex, but they do not necessarily interact

Formation of the stable, strand separated, ‘open’ complex between RNA polymerase and a promoter involves DNA melting of approximately 14 base pairs. The likely nucleation site is the highly conserved −11A base in the non-template strand of the −10 promoter region. Amino acid residues Y430 and W433 on the σ⁷⁰ subunit of the RNA polymerase participate in the strand separation. The roles of −11A and of the Y430 and W433 were addressed by employing synthetic consensus promoters containing base analog and other substitutions at −11 in the non-template strand, and σ⁷⁰ variants bearing amino acid substitutions at positions 430 and 433. Substitutions for −11A and for Y430 and W433 in σ⁷⁰ have small or no effects on formation of the initial RNA polymerase-promoter complex, but exert their effects on subsequent steps on the way to formation of the open complex. As substitutions for Y430 and W433 also affect open complex formation on promoter DNA lacking the −11A base, it is concluded that these amino acid residues have other (or additional) roles, not involving the −11A. The effects of the substitutions at −11A of the promoter and Y430 and W433 of σ⁷⁰ are cumulative.     

Encapsulation in liposomal nanoparticles enhances the immunostimulatory,adjuvant and anti-tumor activity of subcutaneously administered CpG ODN

Immunostimulatory oligodeoxynucleotides (ODN) containing cytosine-guanine (CpG) motifs are powerful stimulators of innate as well as adaptive immune responses, exerting their activity through triggering of the Toll-like receptor 9. We have previously shown that encapsulation in liposomal nanoparticles (LN) enhances the immunostimulatory activity of CpG ODN (LN-CpG ODN) (Mui et al. in J Pharmacol Exp Ther 298:1185, 2001). In this work we investigate the effect of encapsulation on the immunopotency of subcutaneously (s.c.) administered CpG ODN with regard to activation of innate immune cells as well as its ability to act as a vaccine adjuvant with tumor-associated antigens (TAAs) to induce antigen (Ag)-specific, adaptive responses and anti-tumor activity in murine models. It is shown that encapsulation specifically targets CpG ODN for uptake by immune cells. This may provide the basis, at least in part, for the significantly enhanced immunostimulatory activity of LN-CpG ODN, inducing potent innate (as judged by immune cell activation and plasma cytokine/chemokine levels) and adaptive, Ag-specific (as judged by MHC tetramer positive T lymphocytes, IFN-γ secretion and cytotoxicity) immune responses. Finally, in efficacy studies, it is shown that liposomal encapsulation enhances the ability of CpG ODN to adjuvanate adaptive immune responses against co-administered TAAs after s.c. immunization, inducing effective anti-tumor activity against both model and syngeneic tumor Ags in murine tumor models of thymoma and melanoma.     

Testacean communities in perturbed soils: the influence of the wandering albatross

On Île de la Possession (Crozet Archipelago, sub-Antarctica), the testate amoebae (Protozoa, Rhizopoda) fauna in soils around abandoned and occupied nests of the wandering albatross (Diomedea exulans) was investigated. A comparison with control samples, a cluster analysis and several ordination techniques indicated that the presence of the breeding albatrosses induced modifications in physico-chemical soil characteristics and in the soil inhabiting testacean fauna. Only 11 testate species occurred frequently in the soils in the albatross’ zone. Soils around occupied nests had significantly higher moisture values, less acid pH values, an increased specific conductance and elevated phosphate and ammonium concentrations. Highly influenced testacean communities were characterised by high abundances of Difflugiella oviformis and extremely high abundances of Trinema lineare, resulting in a very low diversity and evenness within these communities. The intermediary situation of one abandoned nest indicated that soils around abandoned nests evolve gradually back to undisturbed soils. Although an overall negative influence on the testacean diversity, a limited albatross’ influence may increase the living fraction within the testacean soil communities.     

Evaluating spatial within plot crop variability for different management practices with an optical sensor?

Subsoil constraints to root growth exacerbate frequent water and nutrient limitations to crop yields in Mediterranean-type environments. Amelioration of subsoil constraints can relieve these limitations by opening root-access to subsoil water and nutrients. However, decisions in subsoil amelioration are hampered by seasonally variable yield responses in these environments. We used the APSIM model to analyse the impact of subsoil constraints on yield and yield variability. The simulated yield data were used to calculate the financial benefits of subsoil amelioration across several scenarios. There was a strong yield-dependence on accessible soil water governed by root depth. Root depth development was limited to a minimum of either the effect of subsoil constraints or the weather-dependent depth of the soil wetting front. Insufficient rainfall in dry years or in a drier region often resulted in shallow soil wetting fronts and correspondingly shallow roots even in the absence of subsoil compaction. In these situations, there is little response to subsoil amelioration. Positive yield responses and positive financial returns to subsoil amelioration are therefore greater in good rainfall years and are more likely in a wetter region. A yield response to amelioration is also greater in coarser textured sand than finer textured sandy loam in an average rainfall season because the same amount of rainfall results in a deeper wetting front in sand than in sandy loam. Hence, roots in a sand are required to grow deeper compared to a sandy loam to access the same amount of water and therefore benefited more from subsoil amelioration in an average rainfall year. In wet years, sands leach more nitrate than sandy loam, which decreases yields and the response to subsoil amelioration in sands is more than in the sandy loam. Environmental threats occur along with yield loss when roots cannot access subsoil water. These include increased nitrate leaching and deep drainage due to unused water remaining in the soil profile. By allowing roots to access deep soil water, ameliorating subsoil is expected to yield financial gains in average to good rainfall seasons and decrease the environmental risk of drainage and leaching loss. The financial gains are expected to offset potential financial losses in dry and dry finish seasons especially in coarser textured soils and wetter environment. Responsible Editor: Jan Vos.     

Competition for light between toxic and nontoxic strains of the harmful cyanobacterium Microcystis

The cyanobacterium Microcystis can produce microcystins, a family of toxins that are of major concern in water management. In several lakes, the average microcystin content per cell gradually declines from high levels at the onset of Microcystis blooms to low levels at the height of the bloom. Such seasonal dynamics might result from a succession of toxic to nontoxic strains. To investigate this hypothesis, we ran competition experiments with two toxic and two nontoxic Microcystis strains using light-limited chemostats. The population dynamics of these closely related strains were monitored by means of characteristic changes in light absorbance spectra and by PCR amplification of the rRNA internal transcribed spacer region in combination with denaturing gradient gel electrophoresis, which allowed identification and semiquantification of the competing strains. In all experiments, the toxic strains lost competition for light from nontoxic strains. As a consequence, the total microcystin concentrations in the competition experiments gradually declined. We did not find evidence for allelopathic interactions, as nontoxic strains became dominant even when toxic strains were given a major initial advantage. These findings show that, in our experiments, nontoxic strains of Microcystis were better competitors for light than toxic strains. The generality of this finding deserves further investigation with other Microcystis strains. The competitive replacement of toxic by nontoxic strains offers a plausible explanation for the gradual decrease in average toxicity per cell during the development of dense Microcystis blooms.     

Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15

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Global patterns of intraspecific leaf trait responses to elevation

Elevational gradients are often used to quantify how traits of plant species respond to abiotic and biotic environmental variations. Yet, such analyses are frequently restricted spatially and applied along single slopes or mountain ranges. Since we know little on the response of intraspecific leaf traits to elevation across the globe, we here perform a global meta‐analysis of leaf traits in 109 plant species located in 4 continents and reported in 71 studies published between 1983 and 2018. We quantified the intraspecific change in seven morpho‐ecophysiological leaf traits along global elevational gradients: specific leaf area (SLA), leaf mass per area (LMA), leaf area (LA), nitrogen concentration per unit of area (Narea), nitrogen concentration per unit mass (Nmass), phosphorous concentration per unit mass (Pmass) and carbon isotope composition (δ¹³C). We found LMA, Narea, Nmass and δ¹³C to significantly increase and SLA to decrease with increasing elevation. Conversely, LA and Pmass showed no significant pattern with elevation worldwide. We found significantly larger increase in Narea, Nmass, Pmass and δ¹³C with elevation in warmer regions. Larger responses to increasing elevation were apparent for SLA of herbaceous compared to woody species, but not for the other traits. Finally, we also detected evidences of covariation across morphological and physiological traits within the same elevational gradient. In sum, we demonstrate that there are common cross‐species patterns of intraspecific leaf trait variation across elevational gradients worldwide. Irrespective of whether such variation is genetically determined via local adaptation or attributed to phenotypic plasticity, the leaf trait patterns quantified here suggest that plant species are adapted to live on a range of temperature conditions. Since the distribution of mountain biota is predominantly shifting upslope in response to changes in environmental conditions, our results are important to further our understanding of how plants species of mountain ecosystems adapt to global environmental change.     

Ischaemia alters the effects of cardiomyocyte‐derived extracellular vesicles on macrophage activation

Myocardial ischaemia is associated with an exacerbated inflammatory response, as well as with a deregulation of intercellular communication systems. Macrophages have been implicated in the maintenance of heart homeostasis and in the progression and resolution of the ischaemic injury. Nevertheless, the mechanisms underlying the crosstalk between cardiomyocytes and macrophages remain largely underexplored. Extracellular vesicles (EVs) have emerged as key players of cell‐cell communication in cardiac health and disease. Hence, the main objective of this study was to characterize the impact of cardiomyocyte‐derived EVs upon macrophage activation. Results obtained demonstrate that EVs released by H9c2 cells induced a pro‐inflammatory profile in macrophages, via p38MAPK activation and increased expression of iNOS, IL‐1β and IL‐6, being these effects less pronounced with ischaemic EVs. EVs derived from neonatal cardiomyocytes, maintained either in control or ischaemia, induced a similar pattern of p38MAPK activation, expression of iNOS, IL‐1β, IL‐6, IL‐10 and TNFα. Importantly, adhesion of macrophages to fibronectin was enhanced by EVs released by cardiomyocytes under ischaemia, whereas phagocytic capacity and adhesion to cardiomyocytes were higher in macrophages incubated with control EVs. Additionally, serum‐circulating EVs isolated from human controls or acute myocardial infarction patients induce macrophage activation. According to our model, in basal conditions, cardiomyocyte‐derived EVs maintain a macrophage profile that ensure heart homeostasis, whereas during ischaemia, this crosstalk is affected, likely impacting healing and post‐infarction remodelling.