Action and semantics of time in agro-ecology

In the systemic approach, the system is perceived as an action or a collection of overlapping actions expressed in reference to Time, Space, and Morphology (or Energy). When the system is studied by different disciplines, the referentials differ, as well as the semantics of terms used to describe the action. In order to establish the vocabulary of a collection of actions involving several disciplines, we propose a formal method for describing each action. The linguistic-based method enables (i) transcription of the literal description of an action in a semantic network, and (ii) building of a vocabulary in a formal setting. The method is illustrated through a complex biological system, i.e. the mutualistic relationship between two vine pests, while focusing particularly on temporality. The method provides a support for implementing multidisciplinary around a complex system. (Résumé d'auteur

Modélisation d'un système complexe - Une méthode déclarative

Dans le cadre de leurs travaux, les chercheurs peuvent être amenés à assembler des programmes de simulation préexistants. Le mode opératoire repose sur l'hypothèse que l'assemblage de programmes, chacun représentant un sous-système, permet d'accéder à la simulation du système global. Cette hypothèse n'est pas toujours vérifiée et la question se pose de l'identification des sous-systèmes manquants. La théorie du système général appréhende les systèmes sous la forme d'une collection d'actions enchevêtrées. L'objet de ce document est de présenter une méthode déclarative de description de système complexe reposant sur cette théorie et d'en montrer une application à un système biologique

Utilisation de connaissances expertes pour l'assemblage de programmes de simulation en agronomie

Soumis à la conférence INFORSIDThe work concerned the assembly of biological sub-systems to gain access to a functional representation of the overall system, in the case of complex biological interactions (symbiosis, etc.). The proposed method uses the statement of expert knowledge described in a literal way to establish the sub-system interface program. The use of interrogative pronouns and adverbs provides a formal framework to produce graphs from literal descriptions. In terms of results, the method enables (i) access to the vocabulary of the assembly program, (ii) identification of the transformation functions to be established, and (iii) an estimation of the valence required by programs to ensure assembly. From an operational perspective, the generic approach proposed is a theoretical construct that remains to be validated in concrete cases of application

Migration Revisited using the Categories Theory: Application to Biological Modelling Languages

N/

Diversity of fruit fly (Diptera: Tephritidae) species in French Guiana: their main host plants and associated parasitoids during the period 1994-2003 and prospects for management

Introduction. This study was carried out in French Guiana, over ten years (1994–2003) by three institutions (SPV, FDGPC and CIRAD); it updates the current state of knowledge of Tephritidae (both Dacini and Toxotrypanini tribes) species present in this country. Materials and methods. The work was mainly conducted in inhabited areas (from the Brazilian border to the Surinamese border) where cultivated fruit crops are located. Specimens were obtained by adult trapping and fruit sampling in nearby orchards and at the edge of the rainforest. Trapping was done consistently for 10 years, while fruit sampling was a discontinuous activity. We present only the results for fruit sampling from three consecutive years (2001–2003) in which a total of 880 kg from 45 fruit species in 22 plant families were collected. Results. Twenty-nine plant species from fourteen plant families were found to be hosts of twenty-one Anastrepha species and one Bactrocera species, Bactrocera carambolae Drew and Hancock. During this period, no specimen of Ceratitis capitata (Wiedemann) was collected in traps or fruit samples. We registered the main fruit trees which were hosts for B. carambolae and Anastrepha spp. Five hymenopterous parasitoid species were identified. Among them, Diachasmimorpha longicaudata (Ashmead) (Hymenoptera, Braconidae) is an exotic species and was introduced into French Guiana in collaboration with Brazilian authorities (EMBRAPA) in 2000 and 2001 within the framework of a classical biological control program. Conclusion. Our data provide baseline information about the tephritid species of economic importance present in French Guiana and assist in developing potential future control programs of both the B. carambolae and Anastrepha species in the Amazon Basin. These preliminary results are discussed in the light of their implication for rainforest conservation efforts and also evolutionary relationships between fruit flies and their hosts. (Résumé d'auteur

Convergent genetic and expression data implicate immunity in Alzheimer's disease

Background Late–onset Alzheimer's disease (AD) is heritable with 20 genes showing genome wide association in the International Genomics of Alzheimer's Project (IGAP). To identify the biology underlying the disease we extended these genetic data in a pathway analysis. Methods The ALIGATOR and GSEA algorithms were used in the IGAP data to identify associated functional pathways and correlated gene expression networks in human brain. Results ALIGATOR identified an excess of curated biological pathways showing enrichment of association. Enriched areas of biology included the immune response (p = 3.27×10-12 after multiple testing correction for pathways), regulation of endocytosis (p = 1.31×10-11), cholesterol transport (p = 2.96 × 10-9) and proteasome-ubiquitin activity (p = 1.34×10-6). Correlated gene expression analysis identified four significant network modules, all related to the immune response (corrected p 0.002 – 0.05). Conclusions The immune response, regulation of endocytosis, cholesterol transport and protein ubiquitination represent prime targets for AD therapeutics

Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease

We identified rare coding variants associated with Alzheimer’s disease (AD) in a 3-stage case-control study of 85,133 subjects. In stage 1, 34,174 samples were genotyped using a whole-exome microarray. In stage 2, we tested associated variants (P<1×10-4) in 35,962 independent samples using de novo genotyping and imputed genotypes. In stage 3, an additional 14,997 samples were used to test the most significant stage 2 associations (P<5×10-8) using imputed genotypes. We observed 3 novel genome-wide significant (GWS) AD associated non-synonymous variants; a protective variant in PLCG2 (rs72824905/p.P522R, P=5.38×10-10, OR=0.68, MAFcases=0.0059, MAFcontrols=0.0093), a risk variant in ABI3 (rs616338/p.S209F, P=4.56×10-10, OR=1.43, MAFcases=0.011, MAFcontrols=0.008), and a novel GWS variant in TREM2 (rs143332484/p.R62H, P=1.55×10-14, OR=1.67, MAFcases=0.0143, MAFcontrols=0.0089), a known AD susceptibility gene. These protein-coding changes are in genes highly expressed in microglia and highlight an immune-related protein-protein interaction network enriched for previously identified AD risk genes. These genetic findings provide additional evidence that the microglia-mediated innate immune response contributes directly to AD development

New insights into the genetic etiology of Alzheimer's disease and related dementias

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

Analysis of shared heritability in common disorders of the brain

ience, this issue p. eaap8757 Structured Abstract INTRODUCTION Brain disorders may exhibit shared symptoms and substantial epidemiological comorbidity, inciting debate about their etiologic overlap. However, detailed study of phenotypes with different ages of onset, severity, and presentation poses a considerable challenge. Recently developed heritability methods allow us to accurately measure correlation of genome-wide common variant risk between two phenotypes from pools of different individuals and assess how connected they, or at least their genetic risks, are on the genomic level. We used genome-wide association data for 265,218 patients and 784,643 control participants, as well as 17 phenotypes from a total of 1,191,588 individuals, to quantify the degree of overlap for genetic risk factors of 25 common brain disorders. RATIONALE Over the past century, the classification of brain disorders has evolved to reflect the medical and scientific communities' assessments of the presumed root causes of clinical phenomena such as behavioral change, loss of motor function, or alterations of consciousness. Directly observable phenomena (such as the presence of emboli, protein tangles, or unusual electrical activity patterns) generally define and separate neurological disorders from psychiatric disorders. Understanding the genetic underpinnings and categorical distinctions for brain disorders and related phenotypes may inform the search for their biological mechanisms. RESULTS Common variant risk for psychiatric disorders was shown to correlate significantly, especially among attention deficit hyperactivity disorder (ADHD), bipolar disorder, major depressive disorder (MDD), and schizophrenia. By contrast, neurological disorders appear more distinct from one another and from the psychiatric disorders, except for migraine, which was significantly correlated to ADHD, MDD, and Tourette syndrome. We demonstrate that, in the general population, the personality trait neuroticism is significantly correlated with almost every psychiatric disorder and migraine. We also identify significant genetic sharing between disorders and early life cognitive measures (e.g., years of education and college attainment) in the general population, demonstrating positive correlation with several psychiatric disorders (e.g., anorexia nervosa and bipolar disorder) and negative correlation with several neurological phenotypes (e.g., Alzheimer's disease and ischemic stroke), even though the latter are considered to result from specific processes that occur later in life. Extensive simulations were also performed to inform how statistical power, diagnostic misclassification, and phenotypic heterogeneity influence genetic correlations. CONCLUSION The high degree of genetic correlation among many of the psychiatric disorders adds further evidence that their current clinical boundaries do not reflect distinct underlying pathogenic processes, at least on the genetic level. This suggests a deeply interconnected nature for psychiatric disorders, in contrast to neurological disorders, and underscores the need to refine psychiatric diagnostics. Genetically informed analyses may provide important "scaffolding" to support such restructuring of psychiatric nosology, which likely requires incorporating many levels of information. By contrast, we find limited evidence for widespread common genetic risk sharing among neurological disorders or across neurological and psychiatric disorders. We show that both psychiatric and neurological disorders have robust correlations with cognitive and personality measures. Further study is needed to evaluate whether overlapping genetic contributions to psychiatric pathology may influence treatment choices. Ultimately, such developments may pave the way toward reduced heterogeneity and improved diagnosis and treatment of psychiatric disorders