RNA recognition and cleavage by sequence-specific endoribonucleases

Inactivation of RNA molecules by sequence-specific endoribonucleolytic cleavage is a subtle mechanism by which cells regulate gene expression. Sequence-specific endoribonucleases can recognize and cleave particular phosphodiester bonds confined within hundreds/thousands of chemically similar bonds. Here, we present a comparative analysis of the mechanisms used by endoribonucleases to select and cleave their target RNA molecules. This analysis is based on the very recent molecular details obtained from the structural and/or biochemical studies of nine sequence-specific ribonucleases that target messenger, ribosomal, and transfer RNA molecules. This analysis shows that despite the absence of sequence homologies and the wide diversity of biological sources (prokaryotes, archaea and eukaryotes), the sequence-specific ribonucleases studied here adopt limited structural folds, catalyze their cleavage reactions using a common chemistry and involve a very limited set of amino acids for both RNA binding and processing.     

Contribution of cocoa plantations to the conservation of native ants (Insecta: Hymenoptera: Formicidae) with a special emphasis on the Atlantic Forest fauna of southern Bahia,Brazil

By maintaining a forest-like structure, shaded cocoa plantations contribute to the conservation of ants that usually live in the soil, leaf litter or canopy of tropical forests. Here we synthesize the available information on the diversity and community structure of ants in shaded cocoa plantations in the Atlantic forest region of Brazil, compare ant assemblages in cocoa agroforests with forests and other forms of agriculture, and discuss how these shaded plantations contribute to the conservation of the ants in the Atlantic Forest region. We also discuss ants of economical importance and of special interest, including Camponotus, Dolichoderus, Gnamptogenys, Pachycondyla, Pseudomyrmex and other litter dwelling genera. We discuss the situation of the tramp ant Wasmannia auropunctata in the Bahian cocoa-producing region where it is considered as native, and that of the two cryptobiotic genera Thaumatomyrmex and Typhlomyrmex, as well as that of proven and possible endangered army ant and Ponerini species. A total of 192 ant species from four strata were found in extensive sampling of a cocoa plantation with a relatively simple shade canopy (comprised primarily of Erythrina). Species richness in the cocoa plantations corresponded roughly to that of low diversity native forests, and species composition of cocoa plantations was most similar to native habitats (forest and mangroves) while ant composition in other agricultural habitats was most similar to that of urban areas. Although occurrences of Wasmannia auropunctata were similar in cocoa plantations and forests, abundance of Thaumatomyrmex and Typhlomyrmex, generally thought to be rare ants, was relatively high in cocoa plantations. These results, from cocoa plantations with relatively simple shade, demonstrate the importance of cocoa for ant conservation in the Atlantic forest region of Brazil. It is likely that cocoa plantations with a greater number of vegetation strata and higher tree species richness (such as traditional cabruca plantations) provide even more important habitat for ants generally and for ant species of conservation concern.     

Fast evolutionary response of house mice to anthropogenic disturbance on a Sub‐Antarctic island

Invasions and anthropogenic disturbances challenge species with rapid environmental changes. Understanding how organisms respond to these changes is of major concern for the future of biodiversity. The house mouse on a Sub‐Antarctic island (Guillou Island, Kerguelen Archipelago) had to face such challenges twice: first when invading the island two centuries ago; and nowadays when coping with an in‐depth remodeling of its habitat due to a cohort of anthropogenic changes. Morphometric and biomechanical results show that the initial invasion triggered the evolution of a jaw shape adapted to the local food resources. Contemporary changes are also associated to changes in jaw morphology, but are not directly functionally relevant. Here, a complex response integrating feeding behaviour, investment in feeding structure, and degree of mineralization, may provide the mice with a better tool to benefit of wider resources utilization and/or better cope with intra‐specific competition in a changing habitat. These Sub‐Antarctic mice exemplify that success of invasive species rely on the capacity of facing rapidly varying environments through integrated, multi‐faceted responses involving behaviour to morphology through life‐history traits. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 513–526.     

ORCHIDEE‐STICS,a process‐based model of sugarcane biomass production: calibration of model parameters governing phenology

Agro‐Land Surface Models (agro‐LSM) combine detailed crop models and large‐scale vegetation models (DGVMs) to model the spatial and temporal distribution of energy, water, and carbon fluxes within the soil–vegetation–atmosphere continuum worldwide. In this study, we identify and optimize parameters controlling leaf area index (LAI) in the agro‐LSM ORCHIDEE‐STICS developed for sugarcane. Using the Morris method to identify the key parameters impacting LAI, at eight different sugarcane field trial sites, in Australia and La Reunion island, we determined that the three most important parameters for simulating LAI are (i) the maximum predefined rate of LAI increase during the early crop development phase, a parameter that defines a plant density threshold below which individual plants do not compete for growing their LAI, and a parameter defining a threshold for nitrogen stress on LAI. A multisite calibration of these three parameters is performed using three different scoring functions. The impact of the choice of a particular scoring function on the optimized parameter values is investigated by testing scoring functions defined from the model‐data RMSE, the figure of merit and a Bayesian quadratic model‐data misfit function. The robustness of the calibration is evaluated for each of the three scoring functions with a systematic cross‐validation method to find the most satisfactory one. Our results show that the figure of merit scoring function is the most robust metric for establishing the best parameter values controlling the LAI. The multisite average figure of merit scoring function is improved from 67% of agreement to 79%. The residual error in LAI simulation after the calibration is discussed.     

Tip-DC Development during Parasitic Infection Is Regulated by IL-10 and Requires CCL2/CCR2, IFN-γ and MyD88 Signaling

The development of classically activated monocytic cells (M1) is a prerequisite for effective elimination of parasites, including African trypanosomes. However, persistent activation of M1 that produce pathogenic molecules such as TNF and NO contributes to the development of trypanosome infection-associated tissue injury including liver cell necrosis in experimental mouse models. Aiming to identify mechanisms involved in regulation of M1 activity, we have recently documented that during Trypanosoma brucei infection, CD11b⁺Ly6C⁺CD11c⁺ TNF and iNOS producing DCs (Tip-DCs) represent the major pathogenic M1 liver subpopulation. By using gene expression analyses, KO mice and cytokine neutralizing antibodies, we show here that the conversion of CD11b⁺Ly6C⁺ monocytic cells to pathogenic Tip-DCs in the liver of T. brucei infected mice consists of a three-step process including (i) a CCR2-dependent but CCR5- and Mif-independent step crucial for emigration of CD11b⁺Ly6C⁺ monocytic cells from the bone marrow but dispensable for their blood to liver migration; (ii) a differentiation step of liver CD11b⁺Ly6C⁺ monocytic cells to immature inflammatory DCs (CD11c⁺ but CD80/CD86/MHC-II^low) which is IFN-γ and MyD88 signaling independent; and (iii) a maturation step of inflammatory DCs to functional (CD80/CD86/MHC-II^high) TNF and NO producing Tip-DCs which is IFN-γ and MyD88 signaling dependent. Moreover, IL-10 could limit CCR2-mediated egression of CD11b⁺Ly6C⁺ monocytic cells from the bone marrow by limiting Ccl2 expression by liver monocytic cells, as well as their differentiation and maturation to Tip-DCs in the liver, showing that IL-10 works at multiple levels to dampen Tip-DC mediated pathogenicity during T. brucei infection. A wide spectrum of liver diseases associates with alteration of monocyte recruitment, phenotype or function, which could be modulated by IL-10. Therefore, investigating the contribution of recruited monocytes to African trypanosome induced liver injury could potentially identify new targets to treat hepatic inflammation in general, and during parasite infection in particular.     

The aquatic macrophytes of an English lowland river system: assessing response to nutrient enrichment

Assessment of the effects of nutrients in running water upon macrophytes is compounded by the variety of additional environmental factors which influence their growth. Some classification schemes have been effective in detecting eutrophication on a national or regional scale, and also downstream changes in large single catchments. However, in lowland rivers with naturally nutrient-rich geologies, detection of change at smaller spatial scales has been difficult. This study examined the macrophyte community at 44 sites on the river Welland, a small lowland catchment rising below 150 m in Leicestershire, England. The community at 23 of these sites was adequate for further analysis. The data show that the clearest effect on community composition is caused by watercourse size. However, sites below sewage works, even small village works, did show a reduction in Mean Trophic Rank, (MTR – an assesment system introduced into the UK over the last three years using a 10–100 scale based upon scores and cover value of indicator species). Overall there was a slight but significant correlation of MTR with soluble phosphate and nitrate. The effectiveness of the MTR method is limited at full catchment scale by low numbers of the indicator taxa at small upstream sites. Catchment-scale assessment of the plant community is probably best served by more detailed phytosociological analysis and by the further development of the habitat templet approach.     

The Arabidopsis PsbO2 protein regulates dephosphorylation and turnover of the photosystem II reaction centre D1 protein

The extrinsic photosystem II (PSII) protein of 33 kDa (PsbO), which stabilizes the water-oxidizing complex, is represented in Arabidopsis thaliana (Arabidopsis) by two isoforms. Two T-DNA insertion mutant lines deficient in either the PsbO1 or the PsbO2 protein were retarded in growth in comparison with the wild type, while differing from each other phenotypically. Both PsbO proteins were able to support the oxygen evolution activity of PSII, although PsbO2 was less efficient than PsbO1 under photoinhibitory conditions. Prolonged high light stress led to reduced growth and fitness of the mutant lacking PsbO2 as compared with the wild type and the mutant lacking PsbO1. During a short period of treatment of detached leaves or isolated thylakoids at high light levels, inactivation of PSII electron transport in the PsbO2-deficient mutant was slowed down, and the subsequent degradation of the D1 protein was totally inhibited. The steady-state levels of in vivo phosphorylation of the PSII reaction centre proteins D1 and D2 were specifically reduced in the mutant containing only PsbO2, in comparison with the mutant containing only PsbO1 or with wild-type plants. Phosphorylation of PSII proteins in vitro proceeded similarly in thylakoid membranes from both mutants and wild-type plants. However, dephosphorylation of the D1 protein occurred much faster in the thylakoids containing only PsbO2. We conclude that the function of PsbO1 in Arabidopsis is mostly in support of PSII activity, whereas the interaction of PsbO2 with PSII regulates the turnover of the D1 protein, increasing its accessibility to the phosphatases and proteases involved in its degradation.