Fungal Diversity – An Overview

Branco, Sara

doi:10.5772/23975

Cited by 4 publications

(2 citation statements)

References 68 publications

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“…Bootstrap analysis used a Python reimplementation of the Pvclust R package and was performed on unfiltered and filtered datasets to ensure stability and validity of the clusters obtained after filtering (Figure S3). NMDS was performed using the Bray–Curtis distance, since it can be applied to datasets with null values and unimodal relationships, which is particularly important for comparative metabolomics analyses. In MPACT, NMDS can be conducted with (Figure d) or without (Figure S4) averaging of technical replicates, although averaging technical replicates prevents pseudoreplication…”

Section: Methodsmentioning

confidence: 99%

Metabolomics Peak Analysis Computational Tool (MPACT): An Advanced Informatics Tool for Metabolomics and Data Visualization of Molecules from Complex Biological Samples

2023

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Untargeted metabolomics is a powerful tool for investigating chemistry of complex biological systems, but its utility is compromised by the presence of uninformative features and the limited efficiency of currently available prioritization tools. More effective filtering and prioritization tools are required to address the challenges of large untargeted metabolomics datasets. Here, we introduce Metabolomics Peak Analysis Computational Tool (MPACT), a new mass spectrometry data analysis platform employing filtering based on multiple modalities, statistical techniques incorporating multilevel replication, and interactive data visualization. We demonstrate application of MPACT to uncover hidden effects of the rare earth element cerium on tunicate-associated bacterium Streptomyces sp. PTY087I2, culminating in characterization of two thiolated compounds including a new cysteine derivative, granaticin C, and granaticin D, recently described as mycothiogranaticin A. While we demonstrate application of MPACT to microbial natural products discovery using an elicitation approach, the platform should be readily adaptable to investigation of multipartite interactions, biomarker detection, small molecules in the environment, and a wide range of other complex sample types.

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Section: Methodsmentioning

confidence: 99%

Metabolomics Peak Analysis Computational Tool (MPACT): An Advanced Informatics Tool for Metabolomics and Data Visualization of Molecules from Complex Biological Samples

2023

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“…Thus, care and safety measures should be applied by both users and consumers. For several plants, the active ingredients are well known, with solid evidence of relatively low toxicity, such as rotenoids, azadirachtin and pyrethrin (Branco, 2011;FRAC, 2018;Pavela, 2016;Singh, 2014;Tembo et al, 2018). Risks of toxicity are further mitigated in that the amount of active ingredients naturally found in parts of plants is often low and certainly not present in the artificially concentrated amounts found in synthetic pesticides.…”

Section: Safety Toxicity and Application Of Botanical Biopesticidesmentioning

confidence: 99%

Botanical Biopesticides and Critical Analysis of the Kenyan Legal Frameworks Regulating Biocontrol Agents: A Review

Alworah,

Gichuru,

Ogendo

et al. 2023

Preprint

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Before the green revolution, crude plant materials and plant-extracts were used for crop protection. However, their use was swiftly replaced by synthetic pesticides after World War II due to increased demand for more effective pesticides in intensified farming systems. The 20th century saw a steady increase in the use of synthetic pesticides until the mid-21st century when the world started to realize the negative impact of synthetic pesticides. The increased environmental awareness and the need for safe human food led to increased research and development of biopesticides as crop protection options in modern agriculture. This paper brings into perspective the global history of the application and use of botanical biopesticides in crop production. It also highlights the research progress, product development and registration challenges, and opportunities for business and adoption at the farm level in Kenya.

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Diversity of Marine-Derived Fungal Cultures Exposed by DNA Barcodes: The Algorithm Matters

et al. 2015

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Marine fungi are an understudied group of eukaryotic microorganisms characterized by unresolved genealogies and unstable classification. Whereas DNA barcoding via the nuclear ribosomal internal transcribed spacer (ITS) provides a robust and rapid tool for fungal species delineation, accurate classification of fungi is often arduous given the large number of partial or unknown barcodes and misidentified isolates deposited in public databases. This situation is perpetuated by a paucity of cultivable fungal strains available for phylogenetic research linked to these data sets. We analyze ITS barcodes produced from a subsample (290) of 1781 cultured isolates of marine-derived fungi in the Bioresources Library located at the Australian Institute of Marine Science (AIMS). Our analysis revealed high levels of under-explored fungal diversity. The majority of isolates were ascomycetes including representatives of the subclasses Eurotiomycetidae, Hypocreomycetidae, Sordariomycetidae, Pleosporomycetidae, Dothideomycetidae, Xylariomycetidae and Saccharomycetidae. The phylum Basidiomycota was represented by isolates affiliated with the genera Tritirachium and Tilletiopsis. BLAST searches revealed 26 unknown OTUs and 50 isolates corresponding to previously uncultured, unidentified fungal clones. This study makes a significant addition to the availability of barcoded, culturable marine-derived fungi for detailed future genomic and physiological studies. We also demonstrate the influence of commonly used alignment algorithms and genetic distance measures on the accuracy and comparability of estimating Operational Taxonomic Units (OTUs) by the automatic barcode gap finder (ABGD) method. Large scale biodiversity screening programs that combine datasets using algorithmic OTU delineation pipelines need to ensure compatible algorithms have been used because the algorithm matters.

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Fungal Diversity – An Overview

Cited by 4 publications

References 68 publications

Metabolomics Peak Analysis Computational Tool (MPACT): An Advanced Informatics Tool for Metabolomics and Data Visualization of Molecules from Complex Biological Samples

Metabolomics Peak Analysis Computational Tool (MPACT): An Advanced Informatics Tool for Metabolomics and Data Visualization of Molecules from Complex Biological Samples

Botanical Biopesticides and Critical Analysis of the Kenyan Legal Frameworks Regulating Biocontrol Agents: A Review

Diversity of Marine-Derived Fungal Cultures Exposed by DNA Barcodes: The Algorithm Matters

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