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Sporothrix spp.
Published in Rossana de Aguiar Cordeiro, Pocket Guide to Mycological Diagnosis, 2019
Anderson Messias Rodrigues, Rosane Orofino-Costa, Zoilo Pires de Camargo
Molecular phylogeny has revolutionized the taxonomy of Sporothrix species. The first amplification of Sporothrix DNA using polymerase chain reaction (PCR) was carried out just over 27 years ago (Berbee & Taylor, 1992). Later, a wave of significant phylogenetic studies provided understanding of the taxonomic relationship between pathogenic and non-pathogenic Sporothrix species (de Beer et al., 2003; de Meyer et al., 2008; Marimon et al., 2006, 2007; Rodrigues et al., 2016b), leading to the recognition of 51 species in the genus and splitting Sporothrix and Ophiostoma into different genera (de Beer et al., 2016).
Molecular Mycology and Emerging Fungal Pathogens
Published in Johan A. Maertens, Kieren A. Marr, Diagnosis of Fungal Infections, 2007
What makes a gene useful for molecular phylogeny? First, the gene should be present in all organisms under study, and this requirement forces one to select genes with essential cellular functions, such as ribosomal RNA genes. Second, the gene should serve as a molecular clock, with increasing evolutionary time since two organisms shared a common ancestor ticked off as accumulated nucleotide changes in the gene. If two organisms are close evolutionary cousins, then their genes should share a high degree of sequence similarity. If two organisms are distant evolutionary kin, then their genes should have been subjected to additional mutation and selection over this time period, witha resulting lower rate of sequence similarity noted. The application of molecular phylogenetic methods to some long-standing problems in mycology helps to illustrate this point.
Alternaria
Published in Dongyou Liu, Laboratory Models for Foodborne Infections, 2017
Alicia Rodríguez, Andrea Patriarca, Mar Rodríguez, María Jesús Andrade, Juan José Córdoba
As an alternative to traditional methods, nucleic-acid-based techniques are being increasingly applied to examine the taxonomic relationships among Alternaria species. Most of them have been focused on small-spored catenulate Alternaria, which show little resolution in their molecular phylogeny. However, cladistics analyses of “housekeeping genes” commonly used for other genera, such as the mitochondrial large subunit (mtLSU) ribosomal DNA, internal transcribed spacer (ITS), β-tubulin, translation elongation factor α, calmodulin, actin, chitin synthetase, etc., failed to discriminate among the small-spored species, except for the A. infectoria species group.42–45 There are also genomic techniques to detect, identify, and quantify toxigenic moulds in foodstuffs. So far, there are no molecular methods based on genes involved in the Alternaria mycotoxin biosynthesis pathways; however, some methods, which have used unique conserved genes that distinguish toxigenic and nontoxigenic Alternaria spp., have been developed successfully. Several molecular methods have been developed to detect the presence of Alternaria spores and biomass in foods, such as the one reported by Zur et al.,46 a polymerase chain reaction (PCR)-based method with primers specific to the ITS1 and ITS2 of the 5.8S rRNA gene of Alternaria to detect its presence in commercial tomato products. The main inconvenience of these methods is that viable and nonviable cells cannot be distinguished, thus resulting in an overestimation of the amount of spores that can actually produce mycotoxin in a food product. More recently, Crespo-Sempere et al.47 developed a method including a pretreatment of samples with nucleic-acid-intercalating dyes (propidium monoazide, PMA) prior to quantitative PCR. PMA selectively penetrates cells with a damaged membrane, inhibiting DNA amplification during PCR. The method, based on a primer pair (Alt4 and Alt5) specific to Alternaria spp., allowed quantifying a detection limit of 102 spores/g on tomatoes. Even though the tomato matrix had a protective effect on the cells against PMA toxicity, reducing the efficiency to distinguish between viable and nonviable cells, the method is still a suitable tool for quantifying viable Alternaria cells, which could be useful for estimating potential risks of mycotoxin contamination. The main drawback of these nucleic-acid-based methods as well as of the traditional identification of Alternaria followed by evaluation of mycotoxin production is that they only give information about the negative potential effect derived of the Alternaria presence in foods. Although the latter techniques allow taking corrective actions to avoid presence of mycotoxin-producing Alternaria on foods, for a more appropriate investigation of foodborne Alternaria it is necessary to use laboratory animals or cell system models in which the effect of Alternaria extracts or Alternaria mycotoxin contaminated foods can be evaluated. This could allow estimating the real risk of the presence of Alternaria in foods.
Identification, characterization, and molecular phylogeny of scorpion enolase (Androctonus crassicauda and Hemiscorpius lepturus)
Published in Toxin Reviews, 2023
Elham Pondehnezhadan, Atefeh Chamani, Fatemeh Salabi, Reihaneh Soleimani
The evolutionary origin and relevance of scorpions have been the subject of many studies in recent decades, especially recent pan-genome studies that support the Arachnopulmonata hypothesis: a sister-group relationship between scorpions and tetrapulmonates (i.e. spiders and allied orders) (Regier et al. 2010, Sharma et al. 2014, 2015). Previous morphological-based phylogenetic approaches are restricted to those scorpions exemplifying morphological stasis (Prendini and Wheeler 2005, Prendini et al. 2006). To address this challenge, however, phylogenetic relationships can be inferred more precisely using both molecular and morphological methods (Chippaux and Goyffon 2008). Molecular phylogeny compares homologous DNA or protein sequences to decide the relationships among organisms or genes. It constructs a hierarchical phylogenetic tree based on the genetic divergences of the similarity or dissimilarity of homologous molecules from different organisms, resulting from molecular evolution over time (Patwardhan et al. 2014).
Phylogenetic analysis of Uncaria species based on internal transcribed spacer (ITS) region and ITS2 secondary structure
Published in Pharmaceutical Biology, 2018
Shuang Zhu, Qiwei Li, Shanchong Chen, Yesheng Wang, Lin Zhou, Changqing Zeng, Jun Dong
A comprehensive phylogenetic analysis including all the 12 species of Uncaria recorded in the Flora of China were concluded. Firstly, all Uncaria medicinal species could be clustered clearly in the molecular phylogeny tree. Secondly, we established the ITS database with all of obtained sequences and found that ITS sequences have appropriate variable sites for discrimination most of species in Uncaria. Finally, the ITS2 secondary structure can be used as candidate method for distinguishing the two closely related species U. yunnanensis and U. lanosa.
The predictive utility of the plant phylogeny in identifying sources of cardiovascular drugs
Published in Pharmaceutical Biology, 2018
Emily Guzman, Jeanmaire Molina
In the present study, we aimed to identify potential new sources of CV drugs from phylogenetic and pharmacological analyses of plant species that have CV applications in the literature based on traditional and experimental evidence. We reconstructed the molecular phylogeny of these plants and map their pharmacological mechanisms of action to determine if there are common mechanisms within families, as would be expected due to common ancestry. This produced a phylogenetic scaffold that may guide CV drug discovery in related plant species that have not been tested experimentally.