AgBase: a unified resource for functional analysis in agriculture

Analysis of functional genomics (transcriptomics and proteomics) datasets is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation. To facilitate systems biology in these species we have established the curated, web-accessible, public resource ‘AgBase’ (). We have improved the structural annotation of agriculturally important genomes by experimentally confirming the in vivo expression of electronically predicted proteins and by proteogenomic mapping. Proteogenomic data are available from the AgBase proteogenomics link. We contribute Gene Ontology (GO) annotations and we provide a two tier system of GO annotations for users. The ‘GO Consortium’ gene association file contains the most rigorous GO annotations based solely on experimental data. The ‘Community’ gene association file contains GO annotations based on expert community knowledge (annotations based directly from author statements and submitted annotations from the community) and annotations for predicted proteins. We have developed two tools for proteomics analysis and these are freely available on request. A suite of tools for analyzing functional genomics datasets using the GO is available online at the AgBase site. We encourage and publicly acknowledge GO annotations from researchers and provide an online mechanism for agricultural researchers to submit requests for GO annotations

Five-loop renormalisation of QCD in covariant gauges

We present the complete set of vertex, wave function and charge renormalisation constants in QCD in a general simple gauge group and with the complete dependence on the covariant gauge parameter $\xi$ in the minimal subtraction scheme of conventional dimensional regularisation. Our results confirm all already known results, which were obtained in the Feynman gauge, and allow the extraction of other useful gauges such as the Landau gauge. We use these results to extract the Landau gauge five-loop anomalous dimensions of the composite operator $A^2$ as well as the Landau gauge scheme independent gluon, ghost and fermion propagators at five loops.Comment: 17 pages; FORM and Mathematica result files available with the source; corrected minor typos, added references, journal ref, 1 remark, 1 note and 1 additional result fil

OPDA regulates maize defense against aphids

Copyright © 2019 American Society of Plant Biologists. DOI:10.1104/pp.18.0147

AgBase: a functional genomics resource for agriculture

BACKGROUND: Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals and biomedical models. Moreover, many agricultural microorganisms are human zoonoses. However, systems biology from functional genomics data is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation and agricultural research communities are smaller with limited funding compared to many model organism communities. DESCRIPTION: To facilitate systems biology in these traditionally agricultural species we have established "AgBase", a curated, web-accessible, public resource for structural and functional annotation of agricultural genomes. The AgBase database includes a suite of computational tools to use GO annotations. We use standardized nomenclature following the Human Genome Organization Gene Nomenclature guidelines and are currently functionally annotating chicken, cow and sheep gene products using the Gene Ontology (GO). The computational tools we have developed accept and batch process data derived from different public databases (with different accession codes), return all existing GO annotations, provide a list of products without GO annotation, identify potential orthologs, model functional genomics data using GO and assist proteomics analysis of ESTs and EST assemblies. Our journal database helps prevent redundant manual GO curation. We encourage and publicly acknowledge GO annotations from researchers and provide a service for researchers interested in GO and analysis of functional genomics data. CONCLUSION: The AgBase database is the first database dedicated to functional genomics and systems biology analysis for agriculturally important species and their pathogens. We use experimental data to improve structural annotation of genomes and to functionally characterize gene products. AgBase is also directly relevant for researchers in fields as diverse as agricultural production, cancer biology, biopharmaceuticals, human health and evolutionary biology. Moreover, the experimental methods and bioinformatics tools we provide are widely applicable to many other species including model organisms

Large scale analytic calculations in quantum field theories

We present a survey on the mathematical structure of zero- and single scale quantities and the associated calculation methods and function spaces in higher order perturbative calculations in relativistic renormalizable quantum field theories.Comment: 25 pages Latex, 1 style fil

Exploring the similarities and differences between medical assessments of competence and criminal responsibility

The medical assessments of criminal responsibility and competence to consent to treatment are performed, developed and debated in distinct domains. In this paper I try to connect these domains by exploring the similarities and differences between both assessments. In my view, in both assessments a decision-making process is evaluated in relation to the possible influence of a mental disorder on this process. I will argue that, in spite of the relevance of the differences, both practices could benefit from the recognition of this similarity. For cooperative research could be developed directed at elucidating exactly how various mental disturbances can affect decision-making processes

Free will and mental disorder: Exploring the relationship

A link between mental disorder and freedom is clearly present in the introduction of the fourth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV). It mentions “an important loss of freedom” as one of the possible defining features of mental disorder. Meanwhile, it remains unclear how “an important loss of freedom” should be understood. In order to get a clearer view on the relationship between mental disorder and (a loss of) freedom, in this article, I will explore the link between mental disorder and free will. I examine two domains in which a connection between mental disorder and free will is present: the philosophy of free will and forensic psychiatry. As it turns out, philosophers of free will frequently refer to mental disorders as conditions that compromise free will and reduce moral responsibility. In addition, in forensic psychiatry, the rationale for the assessment of criminal responsibility is often explained by referring to the fact that mental disorders can compromise free will. Yet, in both domains, it remains unclear in what way free will is compromised by mental disorders. Based on the philosophical debate, I discuss three senses of free will and explore their relevance to mental disorders. I conclude that in order to further clarify the relationship between free will and mental disorder, the accounts of people who have actually experienced the impact of a mental disorder should be included in future research

A Novel Approach for Sustainable Supplier Selection Using Differential Evolution: A Case on Pulp and Paper Industry

Abstract. Diverse sustainable supplier selection (SSS) methodologies have been suggested by the practitioners in earlier, to find a solution to the SSS prob-lem. A SSS problem fundamentally is a multi-criteria practice. It is a judgment of tactical significance to enterprises. The nature of this decision usually is dif-ficult and unstructured. Optimization practices might be useful tools for these types of decision-making difficulties. During last few years, Differential Evolu-tion has arisen as a dominating tool used for solving a variety of problems aris-ing in numerous fields. In the current study, we present an approach to find a solution to the SSS problem using Differential Evolution in pulp and paper in-dustry. Hence this paper presents a novel approach is to practice Differential Evolution to select the efficient sustainable suppliers providing the maximum fulfillment for the sustainable criteria determined. Finally, an illustrative exam-ple on pulp and paper industry validates the application of the present ap-proach

Salivary Glucose Oxidase from Caterpillars Mediates the Induction of Rapid and Delayed-Induced Defenses in the Tomato Plant

Caterpillars produce oral secretions that may serve as cues to elicit plant defenses, but in other cases these secretions have been shown to suppress plant defenses. Ongoing work in our laboratory has focused on the salivary secretions of the tomato fruitworm, Helicoverpa zea. In previous studies we have shown that saliva and its principal component glucose oxidase acts as an effector by suppressing defenses in tobacco. In this current study, we report that saliva elicits a burst of jasmonic acid (JA) and the induction of late responding defense genes such as proteinase inhibitor 2 (Pin2). Transcripts encoding early response genes associated with the JA pathway were not affected by saliva. We also observed a delayed response to saliva with increased densities of Type VI glandular trichomes in newly emerged leaves. Proteomic analysis of saliva revealed glucose oxidase (GOX) was the most abundant protein identified and we confirmed that it plays a primary role in the induction of defenses in tomato. These results suggest that the recognition of GOX in tomato may represent a case for effector-triggered immunity. Examination of saliva from other caterpillar species indicates that saliva from the noctuids Spodoptera exigua and Heliothis virescens also induced Pin2 transcripts