Evaluation de la faille alimentaire en algerie par un modele economico demographique?

La «faille alimentaire» est un concept assez proche de celui de «dépendance alimentaire», cependant, si le second terme renvoie plus à une idéologie, le premier se rapporte à une estimation en valeur de la dépendance alimentaire d’un pays. Aussi, l’appréciation de la faille et plus encore le suivi de son évolution nécessite des calculs astreignants. De plus elle est souvent sujette à des erreurs d’interprétations. Dans cette étude, nous avons procédé à une approche basée en partie sur un modèle de Louis Malassis, qui permettrait entre autres, d’évaluer les effets des politiques agricoles sur la sécurité alimentaire. Enfin les résultats auxquels nous avons abouti nous autorisent à conclure qu’il est inapproprié de quantifier la faille en termes de « valeur » parce que d’une part les variations des taux de change et des prix des denrées alimentaires conduisent à des conclusions erronées. D’autre part, les politiques agricoles, entreprises en Algérie et qui visent essentiellement le côté «offre», n’ont pas réussies à réduire la faille (bien au contraire).Mots clés: Autosuffisance, Dépendance alimentaire, Modèle de Malassis, Faille alimentaire, Politiques agricoles.Codes Jel : C51, Q11, Q18

In silico modelling of RNA-RNA dimer and its application for rational siRNA design and ncRNA target search

Non-protein coding region, which constitutes 98.5% of the human genome, were long depreciated as evolutive relict. It is only recently that the biological relevance of\ud the non-coding RNAs associated with these non-coding regions was recognized. The development of experimental and bioinformatical methods aimed at detecting these non-coding RNAs (ncRNAs) lead to the discovery of more than 29,000,000 sequences, grouped into more than 1300 families. More often than not these ncRNAs function by binding to other RNAs, either pro- tein coding or non-protein coding. Compared to the number of tools to detect and classify ncRNAs, the number of tools to search for putative RNA binding partners is negligible. This leads to the actual situation where the function of the majority of the annotated ncRNAs genes is completely unknown. The aim of this work is to assess the function of different families of ncRNAs by developing new algorithms and methods to study RNA-RNA interactions. These new methods are extensions of RNA-folding algorithms applied to the problem of RNA- RNA interactions. Depending on the class of ncRNA studied, different methods were developed and tested. This work shows that the development of RNA-folding algorithms to study RNA- RNA interactions is a promising way to functionally annotate ncRNAs. Still other factors like RNA-proteins interaction, RNA-concentration or RNA-expression, play an important role in the process of RNA hybridization and will have to be taken into account in future works in order to achieve reliable prediction of RNA binding partners.Non-protein coding region, which constitutes 98.5% of the human genome, were long depreciated as evolutive relict. It is only recently that the biological relevance of the non-coding RNAs associated with these non-coding regions was recognized. The development of experimental and bioinformatical methods aimed at detecting these non-coding RNAs (ncRNAs) lead to the discovery of more than 29,000,000 sequences, grouped into more than 1300 families. More often than not these ncRNAs function by binding to other RNAs, either pro- tein coding or non-protein coding. Compared to the number of tools to detect and classify ncRNAs, the number of tools to search for putative RNA binding partners is negligible. This leads to the actual situation where the function of the majority of the annotated ncRNAs genes is completely unknown. The aim of this work is to assess the function of different families of ncRNAs by developing new algorithms and methods to study RNA-RNA interactions. These new methods are extensions of RNA-folding algorithms applied to the problem of RNA- RNA interactions. Depending on the class of ncRNA studied, different methods were developed and tested. This work shows that the development of RNA-folding algorithms to study RNA- RNA interactions is a promising way to functionally annotate ncRNAs. Still other factors like RNA-proteins interaction, RNA-concentration or RNA-expression, play an important role in the process of RNA hybridization and will have to be taken into account in future works in order to achieve reliable prediction of RNA binding partners

RNApredator: fast accessibility-based prediction of sRNA targets

Bacterial genomes encode a plethora of small RNAs (sRNAs), which are heterogeneous in size, structure and function. Most sRNAs act as post-transcriptional regulators by means of specific base pairing interactions with the 5′-untranslated region of mRNA transcripts, thereby modifying the stability of the target transcript and/or its ability to be translated. Here, we present RNApredator, a web server for the prediction of sRNA targets. The user can choose from a set of over 2155 genomes and plasmids from 1183 bacterial species. RNApredator then uses a dynamic programming approach, RNAplex, to compute putative targets. Compared to web servers with a similar task, RNApredator takes the accessibility of the target during the target search into account, improving the specificity of the predictions. Furthermore, enrichment in Gene Ontology terms, cellular pathways as well as changes in accessibilities along the target sequence can be done in fully automated post-processing steps. The predictive performance of the underlying dynamic programming approach RNAplex is similar to that of more complex methods, but needs at least three orders of magnitude less time to complete. RNApredator is available at http://rna.tbi.univie.ac.at/RNApredator

Nonrandom structure in the urea-unfolded Escherichia coli outer membrane protein X (OmpX)

On the basis of sequence-specific resonance assignments for the complete polypeptide backbone and most of the amino acid side chains by heteronuclear nuclear magnetic resonance (NMR) spectroscopy, the urea-unfolded form of the outer membrane protein X (OmpX) from Escherichia coli has been structurally characterized. (1)H-(1)H nuclear Overhauser effects (NOEs), dispersion of the chemical shifts, amide proton chemical shift temperature coefficients, amide proton exchange rates, and (15)N[(1)H]-NOEs show that OmpX in 8 M urea at pH 6.5 is globally unfolded, but adopts local nonrandom conformations in the polypeptide segments of residues 73-82 and 137-145. For these two regions, numerous medium-range and longer-range NOEs were observed, which were used as the input for structure calculations of these polypeptide segments with the program DYANA. The segment 73-82 forms a quite regular helical structure, with only loosely constrained amino acid side chains. In the segment 137-145, the tryptophan residue 140 forms the core of a small hydrophobic cluster. Both nonrandom structures are present with an abundance of about 25% of the protein molecules. The sequence-specific NMR assignment and the physicochemical characterization of urea-denatured OmpX presented in this paper are currently used as a platform for investigations of the folding mechanism of this integral membrane protein

RNA Accessibility in cubic time

<p>Abstract</p> <p>Background</p> <p>The accessibility of RNA binding motifs controls the efficacy of many biological processes. Examples are the binding of miRNA, siRNA or bacterial sRNA to their respective targets. Similarly, the accessibility of the Shine-Dalgarno sequence is essential for translation to start in prokaryotes. Furthermore, many classes of RNA binding proteins require the binding site to be single-stranded.</p> <p>Results</p> <p>We introduce a way to compute the accessibility of all intervals within an RNA sequence in <inline-formula><graphic file="1748-7188-6-3-i1.gif"/></inline-formula>(<it>n</it>³) time. This improves on previous implementations where only intervals of one defined length were computed in the same time. While the algorithm is in the same efficiency class as sampling approaches, the results, especially if the probabilities get small, are much more exact.</p> <p>Conclusions</p> <p>Our algorithm significantly speeds up methods for the prediction of RNA-RNA interactions and other applications that require the accessibility of RNA molecules. The algorithm is already available in the program RNAplfold of the ViennaRNA package.</p

Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics

The thermodynamics of RNA-RNA interaction consists of two components: the energy necessary to make a potential binding region accessible, i.e., unpaired, and the energy gained from the base pairing of the two interaction partners. We show here that both components can be efficiently computed using an improved variant of RNAup. The method is then applied to a set of bacterial small RNAs involved in translational control. In all cases of biologically active sRNA target interactions, the target sites predicted by RNAup is in perfect agreement with literature. In addition to prediction of target site location, RNAup can be also be used to determine the mode of sRNA action. Using information about target site location and the accessibility change resulting form sRNA binding we can discriminate between positive and negative regulators of translation

Transcriptome Study of an Exophiala dermatitidis PKS1 Mutant on an ex Vivo Skin Model: Is Melanin Important for Infection?

The black yeast Exophiala dermatitidis is a polyextremophilic human pathogen, especially known for growing in man-made extreme environments. Reported diseases caused by this fungus range from benign cutaneous to systemic infections with 40% fatality rate. While the number of cases steadily increases in both immunocompromised and immunocompetent people, detailed knowledge about infection mechanisms, virulence factors and host response are scarce. To understand the impact of the putative virulence factor melanin on the infection, we generated a polyketide synthase (PKS1) mutant using CRISPR/Cas9 resulting in a melanin deficient strain. The mutant and the wild-type fungus were inoculated onto skin explants using an ex vivo skin organ culture model to simulate in vivo cutaneous infection. The difference between the mutant and wild-type transcriptional landscapes, as assessed by whole RNA-sequencing, were small and were observed in pathways related to the copper homeostasis, cell wall genes and proteases. Seven days after inoculation the wild-type fungus completely colonized the stratum corneum, invaded the skin and infected keratinocytes while the mutant had only partially covered the skin and showed no invasiveness. Our results suggest that melanin dramatically improves the invasiveness and virulence of E. dermatitidis during the first days of the skin infection

About -rV ending verbs in the Sakhalin dialect of Ainu

Table S2. Abbreviations of peroxidase gene names used for the peroxidase-catalase superfamily. (XLSX 54 kb

Efficient use of accessibility in microRNA target prediction

Considering accessibility of the 3′UTR is believed to increase the precision of microRNA target predictions. We show that, contrary to common belief, ranking by the hybridization energy or by the sum of the opening and hybridization energies, used in currently available algorithms, is not an efficient way to rank predictions. Instead, we describe an algorithm which also considers only the accessible binding sites but which ranks predictions according to over-representation. When compared with experimentally validated and refuted targets in the fruit fly and human, our algorithm shows a remarkable improvement in precision while significantly reducing the computational cost in comparison with other free energy based methods. In the human genome, our algorithm has at least twice higher precision than other methods with their default parameters. In the fruit fly, we find five times more validated targets among the top 500 predictions than other methods with their default parameters. Furthermore, using a common statistical framework we demonstrate explicitly the advantages of using the canonical ensemble instead of using the minimum free energy structure alone. We also find that ‘naïve’ global folding sometimes outperforms the local folding approach