Search results for "modeling"

Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species.

2018

International audience; Chloroplast sequences are widely used for phylogenetic analysis due to their high degree of conservation in plants. Whole chloroplast genomes can now be readily obtained for plant species using new sequencing methods, giving invaluable data for plant evolution However new annotation methods are required for the efficient analysis of this data to deliver high quality phylogenetic analyses. In this study, the two main tools for chloroplast genome annotation were compared. More consistent detection and annotation of genes were produced with GeSeq when compared to the currently used Dogma. This suggests that the annotation of most of the previously annotated chloroplast …

Phosphinotripeptidic Inhibitors of Leucylaminopeptidases

2021

Phosphinate pseudopeptide are analogs of peptides containing phosphinate moiety in a place of the amide bond. Due to this, the organophosphorus fragment resembles the tetrahedral transition state of the amide bond hydrolysis. Additionally, it is also capable of coordinating metal ions, for example, zinc or magnesium ions. These two properties of phosphinate pseudopeptides make them an ideal candidate for metal-related protease inhibitors. This research investigates the influence of additional residue in the P2 position on the inhibitory properties of phosphinopeptides. The synthetic strategy is proposed, based on retrosynthetic analysis. The N-C-P bond formation in the desired compounds is …

paco: implementing Procrustean Approach to Cophylogeny in R

2017

Summary The concordance of evolutionary histories and extant species interactions provides a useful metric for addressing questions of how the structure of ecological communities is influenced by macro-evolutionary processes. We introduce paco (v0.3.1), an R package to perform Procrustean Approach to Cophylogeny. This method assesses the phylogenetic congruence, or evolutionary dependence, of two groups of interacting species using both ecological interaction networks and their phylogenetic history. We demonstrate the functionality of paco through its application to empirical host-parasite and plant-pollinator communities. Although the package is intended to assess the phylogenetic congruen…

Evidence for Succession and Putative Metabolic Roles of Fungi and Bacteria in the Farming Mutualism of the Ambrosia Beetle Xyleborus affinis.

2020

The bacterial and fungal community involved in ambrosia beetle fungiculture remains poorly studied compared to the famous fungus-farming ants and termites. Here we studied microbial community dynamics of laboratory nests, adults, and brood during the life cycle of the sugarcane shot hole borer, Xyleborus affinis. We identified a total of 40 fungal and 428 bacterial operational taxonomic units (OTUs), from which only five fungi (a Raffaelea fungus and four ascomycete yeasts) and four bacterial genera (Stenotrophomonas, Enterobacter, Burkholderia, and Ochrobactrum) can be considered the core community playing the most relevant symbiotic role. Both the fungal and bacterial populations varied s…

Impact of gas emboli and hyperbaric treatment on respiratory function of loggerhead sea turtles (Caretta caretta)

2018

We investigated lung function in bycaught sea turtles with and without gas emboli. Hyperbaric O2 treatment significantly improves lung function. Pulmonary function testing may be a useful diagnostic tool to assess fisheries induced trauma.

Molecular signatures of silencing suppression degeneracy from a complex RNA virus

2021

As genomic architectures become more complex, they begin to accumulate degenerate and redundant elements. However, analyses of the molecular mechanisms underlying these genetic architecture features remain scarce, especially in compact but sufficiently complex genomes. In the present study, we followed a proteomic approach together with a computational network analysis to reveal molecular signatures of protein function degeneracy from a plant virus (as virus-host protein-protein interactions). We employed affinity purification coupled to mass spectrometry to detect several host factors interacting with two proteins of Citrus tristeza virus (p20 and p25) that are known to function as RNA sil…

Energy intake functions and energy budgets of ectotherms and endotherms derived from their ontogenetic growth in body mass and timing of sexual matur…

2017

Abstract Ectothermic and endothermic vertebrates differ not only in their source of body temperature (environment vs. metabolism), but also in growth patterns, in timing of sexual maturation within life, and energy intake functions. Here, we present a mathematical model applicable to ectothermic and endothermic vertebrates. It is designed to test whether differences in the timing of sexual maturation within an animal's life (age at which sexual maturity is reached vs. longevity) together with its ontogenetic gain in body mass (growth curve) can predict the energy intake throughout the animal's life (food intake curve) and can explain differences in energy partitioning (between growth, repro…

Detailed information on fruiting phenology provides new insights on wood-inhabiting fungal detection

2017

Abstract Fruiting phenology traits may have a large effect on the detection of fungal species. Detailed studies considering these biologically important traits are, however, surprisingly scarce. We conducted a rigorous fruit body monitoring of wood-inhabiting fungal occurrences over one fruiting season. Taxon-specific longevity of the fruiting was different between different morphological groups. This was mainly due to agaric fruiting being shorter than other groups. Different number and timing of surveys are needed to detect the majority of the fruiting taxa of different wood-inhabiting fungal groups.

2022

Abstract The interest in studying wood-inhabiting fungal communities has grown in recent years. This interest has mainly been motivated by the important roles of wood-inhabiting fungi in ecosystem functioning (e.g. nutrient cycling) and conservation biology (e.g. their sensitivity to forest management). In this paper, I argue that another important, but yet largely unexplored motivation for studying wood-inhabiting fungal communities, is their potential to advance fundamental community ecology. One major advantage of wood-inhabiting fungi as model systems is that they are organized as spatially well-defined metacommunities, thus conforming to the assumptions of many theoretical frameworks. …

Co-Designing Social Simulation Models For Policy Advise: Lessons Learned From the INFSO-SKIN Study

2019

This paper describes a participatory approach to co-designing social simulation models with policymakers using a case study of modeling European Commission policy. Managing the collaboration of a wide range of individuals or organizations is challenging but increasingly important as policy making becomes more complex. A framework for a co-design process based on a participatory approach is proposed. The framework suggests that the collaborative design should go through the following phases: Identifying user questions, data provision, model discussion for validation, visualization of results and discussing scope and limitations with stakeholders. Key findings are that the co-design process r…