Importance, impacts de l’utilisation et gestion rationnelle du satrana ou Hyphaene coriacea Gaertn. (Arecaceae) près de la baie de Rigny, Antsiranana (Madagascar)

Hyphaene coriacea is a useful palm in tropical Africa which also grows in the grasslands of western  Madagascar. A study was conducted on the importance of this species in handcrafts and the ecological impacts in three Fokontany around the Baie de Rigny. Ethnobotanical surveys were conducted with  women aged between 14 and 70 years old who commonly created baskets, from the collection of leaves until the sale of the finished products. The evaluation of human activities on the production of H. coriacea leaves was conducted by counting leaves produced by 175 palm trees subjected to different sampling conditions during one year. On average, one person collects 120 to 160 leaves, produces 60 to 80 baskets and earns 43,200 Ariary per month. The collection of the leaves contributes to sustainable management by using special tools and practices during collection such as not completely cutting down palms. However, collection of leaves   negatively impacts production of leaves by reducing their number. Rotating leaf collection, restricting the number of leaves collected on each individual per year, and protection of the vegetation against brush fires are strongly advised while respecting the management techniques already in use. Hyphaene coriacea, un palmier d’Afrique tropicale, pousse dans les formations herbeuses de la partie occidentale de Madagascar. Une étude sur l’importance de cette espèce pour la vannerie ainsi que l’impact de son utilisation a été effectuée dans trois Fokontany à la périphérie de la baie de Rigny. Des enquêtes  ethnobotaniques ont été menées auprès de femmes âgées de 14 à 70 ans sur la pratique de la vannerie, de la collecte des feuilles à la vente des produits finis. Les impacts de l’activité humaine sur la production de feuilles de H. coriacea ont été mesurés à partir du nombre de feuilles produites par 175 palmiers soumis à des niveaux de prélèvement différents pendant une année. En moyenne, une personne collecte mensuellement de 120 à 160 feuilles, fabrique 60 à 80 paniers et génère un revenu de 43.200 Ariary. La collecte de ces feuilles de palmier est menée dans le cadre d’une gestion rationnelle car elle est réalisée avec un outil adapté et elle profite de l’interdiction d’abattre les palmiers. Le mode de collecte a cependant un impact négatif sur la production de feuilles en diminuant leur nombre. La rotation de la collecte de feuilles, la limitation du nombre de feuilles prélevées sur chaque individu pendant une année (28,4%) et la protection de la végétation contre les feux de brousses sont vivement recommandées, tout en respectant les techniques positives qui sont déjà pratiquées

PLoS Pathog

Viruses in the family Luteoviridae have positive-sense RNA genomes of around 5.2 to 6.3 kb, and they are limited to the phloem in infected plants. The Luteovirus and Polerovirus genera include all but one virus in the Luteoviridae. They share a common gene block, which encodes the coat protein (ORF3), a movement protein (ORF4), and a carboxy-terminal extension to the coat protein (ORF5). These three proteins all have been reported to participate in the phloem-specific movement of the virus in plants. All three are translated from one subgenomic RNA, sgRNA1. Here, we report the discovery of a novel short ORF, termed ORF3a, encoded near the 5' end of sgRNA1. Initially, this ORF was predicted by statistical analysis of sequence variation in large sets of aligned viral sequences. ORF3a is positioned upstream of ORF3 and its translation initiates at a non-AUG codon. Functional analysis of the ORF3a protein, P3a, was conducted with Turnip yellows virus (TuYV), a polerovirus, for which translation of ORF3a begins at an ACG codon. ORF3a was translated from a transcript corresponding to sgRNA1 in vitro, and immunodetection assays confirmed expression of P3a in infected protoplasts and in agroinoculated plants. Mutations that prevent expression of P3a, or which overexpress P3a, did not affect TuYV replication in protoplasts or inoculated Arabidopsis thaliana leaves, but prevented virus systemic infection (long-distance movement) in plants. Expression of P3a from a separate viral or plasmid vector complemented movement of a TuYV mutant lacking ORF3a. Subcellular localization studies with fluorescent protein fusions revealed that P3a is targeted to the Golgi apparatus and plasmodesmata, supporting an essential role for P3a in viral movement

MetWAMer: eukaryotic translation initiation site prediction

<p>Abstract</p> <p>Background</p> <p>Translation initiation site (TIS) identification is an important aspect of the gene annotation process, requisite for the accurate delineation of protein sequences from transcript data. We have developed the MetWAMer package for TIS prediction in eukaryotic open reading frames of non-viral origin. MetWAMer can be used as a stand-alone, third-party tool for post-processing gene structure annotations generated by external computational programs and/or pipelines, or directly integrated into gene structure prediction software implementations.</p> <p>Results</p> <p>MetWAMer currently implements five distinct methods for TIS prediction, the most accurate of which is a routine that combines weighted, signal-based translation initiation site scores and the contrast in coding potential of sequences flanking TISs using a perceptron. Also, our program implements clustering capabilities through use of the <it>k</it>-medoids algorithm, thereby enabling cluster-specific TIS parameter utilization. In practice, our static weight array matrix-based indexing method for parameter set lookup can be used with good results in data sets exhibiting moderate levels of 5'-complete coverage.</p> <p>Conclusion</p> <p>We demonstrate that improvements in statistically-based models for TIS prediction can be achieved by taking the class of each potential start-methionine into account pending certain testing conditions, and that our perceptron-based model is suitable for the TIS identification task. MetWAMer represents a well-documented, extensible, and freely available software system that can be readily re-trained for differing target applications and/or extended with existing and novel TIS prediction methods, to support further research efforts in this area.</p

Efficient Translation of Pelargonium line pattern virus RNAs Relies on a TED-Like 3 '-Translational Enhancer that Communicates with the Corresponding 5 '-Region through a Long-Distance RNA-RNA Interaction

[EN] Cap-independent translational enhancers (CITEs) have been identified at the 3'-terminal regions of distinct plant positive-strand RNA viruses belonging to families Tombusviridae and Luteoviridae. On the bases of their structural and/or functional requirements, at least six classes of CITEs have been defined whose distribution does not correlate with taxonomy. The so-called TED class has been relatively under-studied and its functionality only confirmed in the case of Satellite tobacco necrosis virus, a parasitic subviral agent. The 3' untranslated region of the monopartite genome of Pelargonium line pattern virus (PLPV), the recommended type member of a tentative new genus (Pelarspovirus) in the family Tombusviridae, was predicted to contain a TED-like CITE. Similar CITEs can be anticipated in some other related viruses though none has been experimentally verified. Here, in the first place, we have performed a reassessment of the structure of the putative PLPV-TED through in silico predictions and in vitro SHAPE analysis with the full-length PLPV genome, which has indicated that the presumed TED element is larger than previously proposed. The extended conformation of the TED is strongly supported by the pattern of natural sequence variation, thus providing comparative structural evidence in support of the structural data obtained by in silico and in vitro approaches. Next, we have obtained experimental evidence demonstrating the in vivo activity of the PLPV-TED in the genomic (g) RNA, and also in the subgenomic (sg) RNA that the virus produces to express 3'-proximal genes. Besides other structural features, the results have highlighted the key role of long-distance kissing-loop interactions between the 3'-CITE and 5'-proximal hairpins for gRNA and sgRNA translation. Bioassays of CITE mutants have confirmed the importance of the identified 5'-3' RNA communication for viral infectivity and, moreover, have underlined the strong evolutionary constraints that may operate on genome stretches with both regulatory and coding functions.This work was supported by grants BFU2009-11699 and BFU2012-36095 from the Ministerio de Investigacion, Ciencia e Innovacion (MICINN, Spain, www.micinn.es) and the Ministerio de Economia y Competitividad (MINECO, Spain, http://www.mineco.gob.es), respectively, and ACOMP/2012/100 from the Generalitat Valenciana (http://www.gva.es) (to C.H.). MBP and LR were the recipients of a predoctoral and postdoctoral (Juan de la Cierva program) contract, respectively, from MICINN, and MPC was the recipient of a predoctoral contract from MINECO.Blanco Pérez, M.; Pérez Cañamás, M.; Ruiz, L.; Hernandez Fort, C. (2016). Efficient Translation of Pelargonium line pattern virus RNAs Relies on a TED-Like 3 '-Translational Enhancer that Communicates with the Corresponding 5 '-Region through a Long-Distance RNA-RNA Interaction. PLoS ONE. 11(4):1-24. https://doi.org/10.1371/journal.pone.0152593S12411

Furoquinoline Alkaloids and Methoxyflavones from the Stem Bark of Melicope madagascariensis (Baker) T.G. Hartley

Abstract Melicope madagascariensis (Rutaceae) is an endemic plant species of Madagascar that was first classified as a member of the genus Euodia J. R. & G. Forst (Rutaceae) under the scientific name Euodia madagascariensis Baker. Based on morphological characteristics, Thomas Gordon Hartley taxonomically revised E. madagascariensis Baker to be M. madagascariensis (Baker) T.G. Hartley. Chemotaxonomical studies have long been used to help the identification and confirmation of taxonomical classification of plant species and botanicals. Aiming to find more evidences to support the taxonomical revision performed on E. madagascariensis, we carried out phytochemical investigation of two samples of the plant. Fractionation of the ethanol extracts prepared from two stem bark samples of M. madagascariensis (Baker) T.G. Hartley led to the isolation of seven known furoquinoline alkaloids 1–7 and two known methoxyflavones 8 and 9. The presence of furoquinoline alkaloids and methoxyflavones in the title species is in agreement with its taxonomic transfer from Euodia to Melicope. Antiprotozoal evaluation of the isolated compounds showed that 6-methoxy-7-hydroxydictamnine (heliparvifoline, 3) showed weak antimalarial activity (IC50 = 35 µM) against the chloroquine-resistant strain Dd2 of Plasmodium falciparum. Skimmianine (4) displayed moderate cytotoxicity with IC50 value of 1.5 µM against HT-29 colon cancer cell line whereas 3,5-dihydroxy-3′,4′,7-trimethoxyflavone (9) was weakly active in the same assay (IC50 = 13.9 µM). Graphical Abstrac

Implications of a molecular phylogenetic study of the Malagasy genus Cedrelopsis and its relatives (Ptaeroxylaceae).

International audiencePtaeroxylaceae is an Afro-Malagasy family containing three genera, Bottegoa, Cedrelopsis, and Ptaeroxylon. Although the family is morphologically well delimited, it is currently considered part of the subfamily Spathelioideae in a broadly circumscribed orange family (Rutaceae). The Malagasy Cedrelopsis has traditionally been associated with different families of the order Sapindales and its phylogenetic placement in Rutaceae sensu lato has yet to be tested with molecular data. The present molecular phylogenetic study reaffirms the monophyly of Ptaeroxylaceae and its placement in Spathelioideae. Therefore, molecules and morphology support close affinities between Bottegoa, Cedrelopsis, and Ptaeroxylon and also their current generic circumscriptions. We report a case of an evolutionary change from one-seeded to two-seeded carpels within the Harrisonia-Cneorum-Ptaeroxylaceae clade of Spathelioideae. Finally, the sister-group relationship between the African Bottegoa and the Afro-Malagasy Ptaeroxylon-Cedrelopsis clade suggests an African origin of Cedrelopsis