Comprehensive planning of natural resources: present situation and factors to consider

Problems of the ecology, conservation, management and utilisation of a nation's renewable natural resources deserve a high priority in scientific, social and economic planning. Using examples from Kenya and other parts of Eastern Africa, the value of various renewable natural resources is described as well as the threats to which they are subject. The importance of a coordinated approach to scientific research, management of the environment and national policy making is stressed. Planning should start with comprehensive land use surveys. National parks and reserves are also important, not only because they constitute wise land use in themselves, but because they provide a basis for comparison with regions which have been modified by man. These national parks and reserves should be located according to ecological criteria in order to create a network of representative ecosystems, biomes and habitats. The most basic factor causing environmental stress is the rapid growth of the human population. In Eastern Africa, this leads to stress on marginal grasslands by overstocking and inappropriate cultivation. It is suggested that wild animals could provide more protein for human diets without causing the same stress to the environment as domestic species. The importance of assuring continued genetic diversity is also emphasised. An even more serious consequence of the accelerating population growth is the increasing destruction of the remaining forests, particularly on mountains and hilly slopes, because forests are a key element as retainers of watersheds for vast areas and of soil stability. Finally, it is suggested that developing countries should formulate scientifically-based conservation, management and utilisation plans for all renewable natural resources, taking into account the importance of the vegetation cover for the maintenance of the water regime, the productivity of soils and the habitat requirements of wild animals, with particular attention to the control of bush fires in rangelands and forests, clearing for cultivation, forest destruction and control of livestock numbers

Prediction and validation of protein intermediate states from structurally rich ensembles and coarse grained simulations

Protein conformational changes are at the heart of cell functions, from signalling to ion transport. However, the transient nature of the intermediates along transition pathways hampers their experimental detection, making the underlying mechanisms elusive. Here we retrieve dynamic information on the actual transition routes from principal component analysis (PCA) of structurally-rich ensembles and, in combination with coarse-grained simulations, explore the conformational landscapes of five well-studied proteins. Modelling them as elastic networks in a hybrid elastic-network Brownian dynamics simulation (eBDIMS), we generate trajectories connecting stable end-states that spontaneously sample the crystallographic motions, predicting the structures of known intermediates along the paths. We also show that the explored non-linear routes can delimit the lowest energy passages between end-states sampled by atomistic molecular dynamics. The integrative methodology presented here provides a powerful framework to extract and expand dynamic pathway information from the Protein Data Bank, as well as to validate sampling methods in general

Analyzing ligation mixtures using a PCR based method

We have developed a simple and effective method (Lig-PCR) for monitoring ligation reactions using PCR and primers that are common to many cloning vectors. Ligation mixtures can directly be used as templates and the results can be analyzed by conventional gel electrophoresis. The PCR products are representative of the recombinant molecules created during ligation and the corresponding transformants. Orientation of inserts can also be determined using an internal primer. The usefulness of this method has been demonstrated using ligation mixtures of two cDNA’s derived from the salivary glands of Aedes aegypti mosquitoes. The method described here is sensitive and easy to perform compared to currently available methods

Normative Autonomy and Normative Co-ordination: Declarative Power, Representation, and Mandate

In this paper we provide a formal analysis of the idea of normative co-ordination. We argue that this idea is based on the assumption that agents can achieve flexible co-ordination by conferring normative positions to other agents. These positions include duties, permissions, and powers. In particular, we explain the idea of declarative power, which consists in the capacity of the power-holder of creating normative positions, involving other agents, simply by "proclaiming" such positions. In addition, we account also for the concepts of representation, namely the representative's capacity of acting in the name of his principal, and of mandate, which is the mandatee's duty to act as the mandator has requested. Finally, we show how the framework can be applied to represent the contract-net protocol. Some brief remarks on future research and applications conclude this contribution

Characterization of the Arabidopsis thaliana 2-Cys peroxiredoxin interactome

This document is the Accepted Manuscript of the following article: Delphine Cerveau, et al, ‘Characterization of the Arabidopsis thaliana 2-Cys peroxiredoxin interactome’, Plant Science, Vol. 252, pp. 30-41, July 2016, doi: https://doi.org/10.1016/j.plantsci.2016.07.003. This manuscript version is distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License CC BY NC-ND 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited, and is not altered, transformed, or built upon in any way.Peroxiredoxins are ubiquitous thiol-dependent peroxidases for which chaperone and signaling roles havebeen reported in various types of organisms in recent years. In plants, the peroxidase function of thetwo typical plastidial 2-Cys peroxiredoxins (2-Cys PRX A and B) has been highlighted while the otherfunctions, particularly in ROS-dependent signaling pathways, are still elusive notably due to the lack ofknowledge of interacting partners. Using an ex vivo approach based on co-immunoprecipitation of leafextracts from Arabidopsis thaliana wild-type and mutant plants lacking 2-Cys PRX expression followedby mass spectrometry-based proteomics, 158 proteins were found associated with 2-Cys PRXs. Alreadyknown partners like thioredoxin-related electron donors (Chloroplastic Drought-induced Stress Proteinof 32 kDa, Atypical Cysteine Histidine-rich Thioredoxin 2) and enzymes involved in chlorophyll synthe-sis (Protochlorophyllide OxidoReductase B) or carbon metabolism (Fructose-1,6-BisPhosphatase) wereidentified, validating the relevance of the approach. Bioinformatic and bibliographic analyses allowedthe functional classification of the identified proteins and revealed that more than 40% are localized inplastids. The possible roles of plant 2-Cys PRXs in redox signaling pathways are discussed in relation withthe functions of the potential partners notably those involved in redox homeostasis, carbon and aminoacid metabolisms as well as chlorophyll biosynthesis.Peer reviewe

Taxa-area relationship of aquatic fungi on deciduous leaves

One of the fundamental patterns in macroecology is the increase in the number of observed taxa with size of sampled area. For microbes, the shape of this relationship remains less clear. The current study assessed the diversity of aquatic fungi, by the traditional approach based on conidial morphology (captures reproducing aquatic hyphomycetes) and next generation sequencing (NGS; captures other fungi as well), on graded sizes of alder leaves (0.6 to 13.6 cm2). Leaves were submerged in two streams in geographically distant locations: the Oliveira Stream in Portugal and the Boss Brook in Canada. Decay rates of alder leaves and fungal sporulation rates did not differ between streams. Fungal biomass was higher in Boss Brook than in Oliveira Stream, and in both streams almost 100% of the reads belonged to active fungal taxa. In general, larger leaf areas tended to harbour more fungi, but these findings were not consistent between techniques. Morphospecies-based diversity increased with leaf area in Boss Brook, but not in Oliveira Stream; metabarcoding data showed an opposite trend. The higher resolution of metabarcoding resulted in steeper taxa-accumulation curves than morphospecies-based assessments (fungal conidia morphology). Fungal communities assessed by metabarcoding were spatially structured by leaf area in both streams. Metabarcoding promises greater resolution to assess biodiversity patterns in aquatic fungi and may be more accurate for assessing taxa-area relationships and local to global diversity ratios.This work was supported by the strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569), funded by national funds through the Portuguese Foundation for Science and Technology (FCT) I.P. (http://www.fct.pt/) and by the ERDF through the COMPETE2020 - Programa Operacional Competitividade e Internacionalizacao (POCI) and by the project PTDC/AAC-AMB/117068/2010, funded by national funds through FCT I.P. and the European Regional Development Funds through the Operational Competitiveness Program (FEDER-COMPETE). Support from FCT to SD (SFRH/BPD/47574/2008 and SFRH/BPD/109842/2015) and from NSERC Discovery grant program (http://www.nserc-crsng.gc.ca/index_eng.asp) to FB is also acknowledged. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.info:eu-repo/semantics/publishedVersio

Regulation of Bestrophins by Ca2+: A Theoretical and Experimental Study

Bestrophins are a recently discovered family of Cl− channels, for which no structural information is available. Some family members are activated by increased intracellular Ca2+ concentration. Bestrophins feature a well conserved Asp-rich tract in their COOH terminus (Asp-rich domain), which is homologous to Ca2+-binding motifs in human thrombospondins and in human big-conductance Ca2+- and voltage-gated K+ channels (BKCa). Consequently, the Asp-rich domain is also a candidate for Ca2+ binding in bestrophins. Based on these considerations, we constructed homology models of human bestrophin-1 (Best1) Asp-rich domain using human thrombospondin-1 X-ray structure as a template. Molecular dynamics simulations were used to identify Asp and Glu residues binding Ca2+ and to predict the effects of their mutations to alanine. We then proceeded to test selected mutations in the Asp-rich domain of the highly homologous mouse bestrophin-2. The mutants expressed in HEK-293 cells were investigated by electrophysiological experiments using the whole-cell voltage-clamp technique. Based on our molecular modeling results, we predicted that Asp-rich domain has two defined binding sites and that D301A and D304A mutations may impact the binding of the metal ions. The experiments confirmed that these mutations do actually affect the function of the protein causing a large decrease in the Ca2+-activated Cl− current, fully consistent with our predictions. In addition, other studied mutations (E306A, D312A) did not decrease Ca2+-activated Cl− current in agreement with modeling results