Editorial: Exploiting wheat biodiversity and agricultural practices for tackling the effects of climate change

Editorial: Exploiting wheat biodiversity and agricultural practices for tackling the effects of climate chang

Utilisation Des Caractères Biochimiques, Agronomiques Et Morphologiques Pour L’évaluation De La Diversité Génétique Des Variants D’orangers Dans La Région Du Gharb, Maroc

20 clones of orange trees, identified at the level of the collection of nucellar citrus varieties, have been the subject of several tests of behavior at the level of different citrus fruit sites in Morocco. Indeed, the present work aims to evaluate these variants on a clay soil at the Gharb region (INRA/Kenitra). The variants grafted on Citrange troyer were divided into three groups. Each group contains variants, genetically similar, from seedlings of the same parent variety. Clonal selection is based on the synthesis of the results of the study of the variability of the criteria of fruit quality and production. The average yield varies from 44.25 kg / tree to 217.30 kg / tree. While the average weight of a fruit varies from 95 g to 360 g. The results showed a predominance of juicy and medium-sized fruits with an equatorial diameter greater than 56 mm, acceptable for the fresh fruit market or the juice industry. The maturity coefficient study of the variants within each group, or between the three groups, showed that the harvest period extends over four months, from December to March. The final selection was focused on six productive and good quality variants. These promising variants have been described according to UPOV, and then presented for registration in the official catalog

Construction d'un graphe de connaissances à partir des annotations d'articles scientifiques et de leur contenu en sciences de la vie

National audienceIn this paper, we present an RDF knowledge graph to describe, structure and integrate annotations of named entities automatically extracted by the Alvis NLP tool from scientific publications on wheat genetics and phenotyping. These named entities refer to the names of genes, traits, phenotypes, markers and varieties involved in wheat breeding. However, once extracted, these annotations are stored ina raw format making it difficult for researchers to exploit?them. Hence, our interest in transforming (lifting) them into?a format compatible with linked data publication standardsin order to build a knowledge graph in which knowledge?coming from both genomic knowledge bases and scientific articles has been semantically described and integrated.Based on a set of competency questions formulated by a?domain expert, we validated the relevance of the proposed?model and consequently the generated knowledge graph.Dans ce papier, nous présentons un graphe de connaissances RDF permettant de décrire, structurer et intégrer des annotations d'entités nommées extraites automatiquement par l'outil Alvis NLP à partir de publications scientifiques portant sur la génétique et le phénotypage de blé. Ces entités nommées se réfèrent à la fois à des noms de gènes, traits, phénotypes, marqueurs et variétés impliqués dans la culture du blé. Cependant, une fois extraites, ces annotations sont stockées dans un format brut rendant difficile leur exploitation par les chercheurs. D'où, notre intérêt de les transformer (lifter) en un format compatible avec les standards de publication de données liées afin de construire un graphe de connaissances dans lequel des entités provenant à la fois de bases de connaissances génomiques et d'articles scientifiques ont été sémantiquement décrites et intégrées. Basé sur un ensemble de questions de compétence formulées par un expert du domaine, nous avons validé la pertinence du modèle proposé et par conséquent le graphe de connaissances généré

Emerging properties of financial time series in the “Game of Life”

We explore the spatial complexity of Conway’s “Game of Life,” a prototypical cellular automaton by means of a geometrical procedure generating a two-dimensional random walk from a bidimensional lattice with periodical boundaries. The one-dimensional projection of this process is analyzed and it turns out that some of its statistical properties resemble the so-called stylized facts observed in financial time series. The scope and meaning of this result are discussed from the viewpoint of complex systems. In particular, we stress how the supposed peculiarities of financial time series are, often, overrated in their importance

The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA

Threonylcarbamoyladenosine (t6A) is a universal modification found at position 37 of ANN decoding tRNAs, which imparts a unique structure to the anticodon loop enhancing its binding to ribosomes in vitro. Using a combination of bioinformatic, genetic, structural and biochemical approaches, the universal protein family YrdC/Sua5 (COG0009) was shown to be involved in the biosynthesis of this hypermodified base. Contradictory reports on the essentiality of both the yrdC wild-type gene of Escherichia coli and the SUA5 wild-type gene of Saccharomyces cerevisiae led us to reconstruct null alleles for both genes and prove that yrdC is essential in E. coli, whereas SUA5 is dispensable in yeast but results in severe growth phenotypes. Structural and biochemical analyses revealed that the E. coli YrdC protein binds ATP and preferentially binds RNAThr lacking only the t6A modification. This work lays the foundation for elucidating the function of a protein family found in every sequenced genome to date and understanding the role of t6A in vivo

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today's annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic models. To overcome these problems, we have developed the PlantSEED, an integrated, metabolism-centric database to support subsystems-based annotation and metabolic model reconstruction for plant genomes. PlantSEED combines SEED subsystems technology, first developed for microbial genomes, with refined protein families and biochemical data to assign fully consistent functional annotations to orthologous genes, particularly those encoding primary metabolic pathways. Seamless integration with its parent, the prokaryotic SEED database, makes PlantSEED a unique environment for cross-kingdom comparative analysis of plant and bacterial genomes. The consistent annotations imposed by PlantSEED permit rapid reconstruction and modeling of primary metabolism for all plant genomes in the database. This feature opens the unique possibility of model-based assessment of the completeness and accuracy of gene annotation and thus allows computational identification of genes and pathways that are restricted to certain genomes or need better curation. We demonstrate the PlantSEED system by producing consistent annotations for 10 reference genomes. We also produce a functioning metabolic model for each genome, gapfilling to identify missing annotations and proposing gene candidates for missing annotations. Models are built around an extended biomass composition representing the most comprehensive published to date. To our knowledge, our models are the first to be published for seven of the genomes analyzed

Pituitary Adenylate Cyclase Activating Peptide (1-38) and its analog (Acetyl-[Ala15, Ala20] PACAP 38-polyamide) reverse methacholine airway hyperresponsiveness in rats

O objetivo deste estudo foi investigar funcionalmente e estruturalmente efeito broncodilatador do peptídeo ativador da adenilato ciclase pituitária (PACAP1-38) e da acetil-[Ala15, Ala20]PACAP 38-poliamida, potente análogo do PACAP-38, nos ratos desafiados pelo metacolina (MeCh). Ratos Wistar machos foram aleatoriamente divididos em cinco grupos. Grupos 1 e 2, inalando aerossóis de solução salina ou doses crescentes de MeCh (0,5, 1, 2,12, 4,25, 8,5, 17, 34 e 68 mg/L). Os outros grupos recebendo terbutalina (Terb) (250 µg/rato) (10-6M), PACAP-38 (50 µg/rato) (0.1 mM) ou análogo do PACAP-38 (50 µg/rato) associados a MeCh na dose de 4,25 mg/L. A resistência pulmonar total (RL) foi registrada antes e 2 min após a administração de Mech pelo equipamento pneumomultiteste. A administração MeCh induziu aumento significativo e dose dependente (pThe aim of this study was to investigate both functionally and structurally bronchodilator effects of Pituitary adenylate cyclase activating peptide (PACAP38) and acetyl-[Ala15, Ala20] PACAP38-polyamide, a potent PACAP38 analog, in rats challenged by methacholine (MeCh). Male Wistar rats were divided randomly into five groups. Groups 1 and 2 inhaled respectively aerosols of saline or increasing doses of MeCh (0.5, 1, 2.12, 4.25, 8.5, 17, 34 and 68mg/L). The other groups received terbutaline (Terb) (250 µg/rat) (10-6 M), PACAP38 (50 µg/rat) (0.1 mM) or PACAP38 analog (50 µg/rat) associated to MeCh from the dose of 4.25 mg/L. Total lung resistances (RL) were recorded before and 2 min after MeCh administration by pneumomultitest equipment. MeCh administration induced a significant and a dose-dependent increase (

Evaluation of Spatially Targeted Strategies to Control Non-Domiciliated Triatoma dimidiata Vector of Chagas Disease

Chagas disease is one of the most important parasitic diseases in Latin America. Since the 1980's, many national and international initiatives have contributed to eliminate vectors developing inside human domiciles. Today's challenge is to control vectors that are non-adapted to the human domicile, but still able to transmit the parasite through regular short stay in the houses. Here, we assess the potential of different control strategies applied in specific spatial patterns using a mathematical model that reproduces the dynamic of dispersion of such ‘non-domiciliated’ vectors within a village of the Yucatan Peninsula, Mexico. We show that no single strategy applied in the periphery of the village, where the insects are more abundant, provides satisfying protection to the whole village. However, combining the use of insect screens in houses at the periphery of the village (to simultaneously fight insects dispersing from the garden and the forest), and the cleaning of the peri-domicile areas of the centre of the village (where sylvatic insects are absent), would provide a cost-effective control. This type of spatially mixed strategy offers a promising way to reduce the cost associated with the repeated interventions required to control non-domiciliated vectors that permanently attempt to infest houses

Characterization of the Dispersal of Non-Domiciliated Triatoma dimidiata through the Selection of Spatially Explicit Models

Chagas disease is one of the most important neglected diseases in Latin America. Although insecticides have been successfully sprayed to control domiciliated vector populations, this strategy has proven to be ineffective in areas where non-domiciliated vectors immigrating from peridomestic or sylvatic ecotopes can (re-)infest houses. The development of strategies for the control of non-domiciliated vectors has thus been identified by the World Health Organization as a major challenge. Such development primarily requires a description of the spatio-temporal dynamics of infestation by these vectors, and a good understanding of their dispersal. We combined for the first time extensive spatio-temporal data sets describing house infestation dynamics by Triatoma dimidiata inside one village, and spatially explicit population dynamics models. The models fitted and predicted remarkably the observed infestation dynamics. They thus provided both key insights into the dispersal of T. dimidiata in this area, and a suitable mathematical background to evaluate the efficacy of various control strategies. Interestingly, the observed and modelled patterns of infestation suggest that interventions could focus on the periphery of the village, where there is the highest risk of transmission. Such spatial optimization may allow for reducing the cost of control, compensating for repeated interventions necessary for non-domiciliated vectors