scholarly journals Ramf: An Open-Source R Package for Statistical Analysis and Display of Quantitative Root Colonization by Arbuscular Mycorrhiza Fungi

2019 ◽  
Vol 10 ◽  
Author(s):  
Marco Chiapello ◽  
Debatosh Das ◽  
Caroline Gutjahr
Author(s):  
Marne C Hagemeijer ◽  
Annelotte M Vonk ◽  
Nikhil T Awatade ◽  
Iris A L Silva ◽  
Christian Tischer ◽  
...  

Abstract Motivation The forskolin-induced swelling (FIS) assay has become the preferential assay to predict the efficacy of approved and investigational CFTR-modulating drugs for individuals with cystic fibrosis (CF). Currently, no standardized quantification method of FIS data exists thereby hampering inter-laboratory reproducibility. Results We developed a complete open-source workflow for standardized high-content analysis of CFTR function measurements in intestinal organoids using raw microscopy images as input. The workflow includes tools for (i) file and metadata handling; (ii) image quantification and (iii) statistical analysis. Our workflow reproduced results generated by published proprietary analysis protocols and enables standardized CFTR function measurements in CF organoids. Availability All workflow components are open-source and freely available: the htmrenamer R package for file handling https://github.com/hmbotelho/htmrenamer; CellProfiler and ImageJ analysis scripts/pipelines https://github.com/hmbotelho/FIS_image_analysis; the Organoid Analyst application for statistical analysis https://github.com/hmbotelho/organoid_analyst; detailed usage instructions and a demonstration dataset https://github.com/hmbotelho/FIS_analysis. Distributed under GPL v3.0. Supplementary information Supplementary information and a stepwise guide for software installation and data analysis for training purposes are available at Bioinformatics online.


2021 ◽  
Vol 20 (02) ◽  
pp. 10-16
Author(s):  
Huong N. D. Thai

The study was carried out to determine the distribution and presence of versicular-arbuscular mycorrhiza (VAM) fungi in rhizosphere soil and roots of Da Xanh pummelo in Phu My town, Ba Ria Vung Tau province. The rhizosphere soil and root samples were collected from 6 - 7 years old pummelo of two main soil types, on two soil layers at depths of 0 - 20 cm and 20 - 40 cm, at 2/3 and the edge of canopy. The results showed that the presence of VAM spore density was higher in red basaltic soil (ferralsols) than black soil (luvisols), and common exist on the topsoil layer (0 - 20 cm) as well as the edge of canopy. Glomus and Acaulospora were two most abundant genera in survey areas, and the proportion of mycorrhizal spores ranged from 53.18 ± 2.59% to 58.54 ± 0.46 and from 23.68 ± 2.96% to 29.33 ± 0.64%, respectively. Increasing the soil depth negatively affected on spore density of VAM fungi. The VAM fungi composition aslo changed with soil depth. The percentage of root colonization by VAM fungi ranged from 56.20 ± 3.11% to 62.00 ± 3.37%, and the highest percentage of root colonization by VAM fungi was detected in red basaltic soil.


Agrotek ◽  
2018 ◽  
Vol 2 (1) ◽  
Author(s):  
Antonius Suparno ◽  
Dwiana Wasgito Purnomo ◽  
Karyoto Sardi Amat

The research was conducted at Soroan, Ayamaru District, South Sorong, Papua. �The objective of the study was to observe the diversity of Arbuscular Mycorrhiza Fungi (AMF) that symbiosis with cultivated plants at the Ayamaru rock phosphates deposit. Based on the observation, there were four AMF associated with nine cultivated plants at the Ayamaru rock phosphates deposit, namely genus Glomus, Acaulospora, Sclerocystis and Gigaspora. Genus Glomus had the greatest diversity (13 types) followed by Acaulospora which comprised of seven types.� On the other hand, the diversity of genus Sclerocystis and Gigaspora only consisted of two types and one type, respectively.


2021 ◽  
Vol 39 ◽  
pp. 100284
Author(s):  
Joseph Molloy ◽  
Felix Becker ◽  
Basil Schmid ◽  
Kay W. Axhausen

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Charlie M. Carpenter ◽  
Daniel N. Frank ◽  
Kayla Williamson ◽  
Jaron Arbet ◽  
Brandie D. Wagner ◽  
...  

Abstract Background The drive to understand how microbial communities interact with their environments has inspired innovations across many fields. The data generated from sequence-based analyses of microbial communities typically are of high dimensionality and can involve multiple data tables consisting of taxonomic or functional gene/pathway counts. Merging multiple high dimensional tables with study-related metadata can be challenging. Existing microbiome pipelines available in R have created their own data structures to manage this problem. However, these data structures may be unfamiliar to analysts new to microbiome data or R and do not allow for deviations from internal workflows. Existing analysis tools also focus primarily on community-level analyses and exploratory visualizations, as opposed to analyses of individual taxa. Results We developed the R package “tidyMicro” to serve as a more complete microbiome analysis pipeline. This open source software provides all of the essential tools available in other popular packages (e.g., management of sequence count tables, standard exploratory visualizations, and diversity inference tools) supplemented with multiple options for regression modelling (e.g., negative binomial, beta binomial, and/or rank based testing) and novel visualizations to improve interpretability (e.g., Rocky Mountain plots, longitudinal ordination plots). This comprehensive pipeline for microbiome analysis also maintains data structures familiar to R users to improve analysts’ control over workflow. A complete vignette is provided to aid new users in analysis workflow. Conclusions tidyMicro provides a reliable alternative to popular microbiome analysis packages in R. We provide standard tools as well as novel extensions on standard analyses to improve interpretability results while maintaining object malleability to encourage open source collaboration. The simple examples and full workflow from the package are reproducible and applicable to external data sets.


2022 ◽  
Vol 171 ◽  
pp. 104325
Author(s):  
Jichen Wang ◽  
Jiang Wang ◽  
Ji-Zheng He ◽  
Zhongwang Jing ◽  
Yongli Xu ◽  
...  

2021 ◽  
Author(s):  
Jason Hunter ◽  
Mark Thyer ◽  
Dmitri Kavetski ◽  
David McInerney

<p>Probabilistic predictions provide crucial information regarding the uncertainty of hydrological predictions, which are a key input for risk-based decision-making. However, they are often excluded from hydrological modelling applications because suitable probabilistic error models can be both challenging to construct and interpret, and the quality of results are often reliant on the objective function used to calibrate the hydrological model.</p><p>We present an open-source R-package and an online web application that achieves the following two aims. Firstly, these resources are easy-to-use and accessible, so that users need not have specialised knowledge in probabilistic modelling to apply them. Secondly, the probabilistic error model that we describe provides high-quality probabilistic predictions for a wide range of commonly-used hydrological objective functions, which it is only able to do by including a new innovation that resolves a long-standing issue relating to model assumptions that previously prevented this broad application.  </p><p>We demonstrate our methods by comparing our new probabilistic error model with an existing reference error model in an empirical case study that uses 54 perennial Australian catchments, the hydrological model GR4J, 8 common objective functions and 4 performance metrics (reliability, precision, volumetric bias and errors in the flow duration curve). The existing reference error model introduces additional flow dependencies into the residual error structure when it is used with most of the study objective functions, which in turn leads to poor-quality probabilistic predictions. In contrast, the new probabilistic error model achieves high-quality probabilistic predictions for all objective functions used in this case study.</p><p>The new probabilistic error model and the open-source software and web application aims to facilitate the adoption of probabilistic predictions in the hydrological modelling community, and to improve the quality of predictions and decisions that are made using those predictions. In particular, our methods can be used to achieve high-quality probabilistic predictions from hydrological models that are calibrated with a wide range of common objective functions.</p>


Sign in / Sign up

Export Citation Format

Share Document