A Multiplex High-Resolution Melting (HRM) assay to differentiate Fusarium graminearum chemotypes.

Fusarium graminearum is a primary cause of Fusarium head blight (FHB) on wheat and barley. The fungus produces trichothecene mycotoxins that render grain unsuitable for food, feed, or malt. Isolates of F.

Identification and Differentiation of the NX-2 Chemotype Using High-Resolution Melting (HRM).

Fusarium head blight causes significant yield losses in wheat and other cereals and contaminates grain products with trichothecene mycotoxins. isolates are classified into different chemotypes depending on the type of mycotoxin produced, including the type B trichothecenes 3-acetyl deoxynivalenol (3-ADON), 15-acetyl deoxynivalenol (15-ADON), nivalenol (NIV), and the recently identified type A trichothecene NX-2. Molecular tools to differentiate NX-2 producers from other chemotypes have remained relatively laborious and time consuming.

Mining for a new class of fungal natural products: the evolution, diversity, and distribution of isocyanide synthase biosynthetic gene clusters.

The products of non-canonical isocyanide synthase (ICS) biosynthetic gene clusters (BGCs) mediate pathogenesis, microbial competition, and metal-homeostasis through metal-associated chemistry. We sought to enable research into this class of compounds by characterizing the biosynthetic potential and evolutionary history of these BGCs across the Fungal Kingdom. We amalgamated a pipeline of tools to predict BGCs based on shared promoter motifs and located 3800 ICS BGCs in 3300 genomes, making ICS BGCs the fifth largest class of specialized metabolites compared to canonical classes found by antiSMASH.

Aneuploidy Formation in the Filamentous Fungus Aspergillus flavus in Response to Azole Stress.

Aspergillus flavus is a mycotoxigenic fungus that contaminates many important agricultural crops with aflatoxin B1, the most toxic and carcinogenic natural compound. This fungus is also the second leading cause of human invasive aspergillosis, after Aspergillus fumigatus, a disease that is particularly prevalent in immunocompromised individuals. Azole drugs are considered the most effective compounds in controlling Aspergillus infections both in clinical and agricultural settings.

Pangenomics of the death cap mushroom Amanita phalloides, and of Agaricales, reveals dynamic evolution of toxin genes in an invasive range.

The poisonous European mushroom Amanita phalloides (the "death cap") is invading California. Whether the death caps' toxic secondary metabolites are evolving as it invades is unknown. We developed a bioinformatic pipeline to identify the MSDIN genes underpinning toxicity and probed 88 death cap genomes from an invasive Californian population and from the European range, discovering a previously unsuspected diversity of MSDINs made up of both core and accessory elements.

LaeA-Regulated Fungal Traits Mediate Bacterial Community Assembly.

Potent antimicrobial metabolites are produced by filamentous fungi in pure culture, but their ecological functions in nature are often unknown. Using an antibacterial isolate and a cheese rind microbial community, we demonstrate that a fungal specialized metabolite can regulate the diversity of bacterial communities. Inactivation of the global regulator, LaeA, resulted in the loss of antibacterial activity in the isolate.

Mining for a New Class of Fungal Natural Products: The Evolution, Diversity, and Distribution of Isocyanide Synthase Biosynthetic Gene Clusters.

The products of non-canonical isocyanide synthase (ICS) biosynthetic gene clusters (BGCs) have notable bioactivities that mediate pathogenesis, microbial competition, and metal-homeostasis through metal-associated chemistry. We sought to enable research into this class of compounds by characterizing the biosynthetic potential and evolutionary history of these BGCs across the Fungal Kingdom. We developed the first genome-mining pipeline to identify ICS BGCs, locating 3,800 ICS BGCs in 3,300 genomes.

Congenital Nonprofound Bilateral Sensorineural Hearing Loss in Children: Comprehensive Characterization of Auditory Function and Hearing Aid Benefit.

A prospective cross-sectional design was used to characterize congenital bilateral sensorineural hearing loss (SNHL). The underlying material of >30,000 consecutively screened newborns comprised 11 subjects with nonprofound, alleged nonsyndromic, SNHL. Comprehensive audiological testing was performed at ≈11 years of age.

A Prospective Study of Etiology and Auditory Profiles in Infants with Congenital Unilateral Sensorineural Hearing Loss.

Congenital unilateral sensorineural hearing loss (uSNHL) is associated with speech-language delays and academic difficulties. Yet, controversy exists in the choice of diagnosis and intervention methods. A cross-sectional prospective design was used to study hearing loss cause in twenty infants with congenital uSNHL consecutively recruited from a universal neonatal hearing-screening program.

Why Do Plant-Pathogenic Fungi Produce Mycotoxins? Potential Roles for Mycotoxins in the Plant Ecosystem.

For many plant-pathogenic or endophytic fungi, production of mycotoxins, which are toxic to humans, may present a fitness gain. However, associations between mycotoxin production and plant pathogenicity or virulence is inconsistent and difficult due to the complexity of these host-pathogen interactions and the influences of environmental and insect factors. Aflatoxin receives a lot of attention due to its potent toxicity and carcinogenicity but the connection between aflatoxin production and pathogenicity is complicated by the pathogenic ability and prevalence of nonaflatoxigenic isolates in crops.

Bacterial hitchhikers derive benefits from fungal housing.

Fungi and bacteria are ubiquitous constituents of all microbiomes, yet mechanisms of microbial persistence in polymicrobial communities remain obscure. Here, we examined the hypothesis that specialized fungal survival structures, chlamydospores, induced by bacterial lipopeptides serve as bacterial reservoirs. We find that symbiotic and pathogenic gram-negative bacteria from non-endosymbiotic taxa enter and propagate in chlamydospores.

Inadvertent Selection of a Pathogenic Fungus Highlights Areas of Concern in Human Clinical Practices.

In studying the development of tolerance to common hospital cleaners (Oxivir and CaviCide™) in clinical isolate stocks of the emerging, multidrug-resistant yeast pathogen , we selected for a cleaner-tolerant subpopulation of a more common nosocomial pathogen, . Through the purification of each species and subsequent competition and other analyses, we determined that is capable of readily dominating mixed populations of and when exposed to hospital cleaners. This result suggests that exposure to antimicrobial compounds can preferentially select for low-level, stress-tolerant fungal pathogens.

Sex and self defense.

The fungus produces secondary metabolites during sexual development to protect itself from predators.

Transcription Factor Repurposing Offers Insights into Evolution of Biosynthetic Gene Cluster Regulation.

The fungal kingdom has provided advances in our ability to identify biosynthetic gene clusters (BGCs) and to examine how gene composition of BGCs evolves across species and genera. However, little is known about the evolution of specific BGC regulators that mediate how BGCs produce secondary metabolites (SMs). A bioinformatics search for conservation of the Aspergillus fumigatus xanthocillin BGC revealed an evolutionary trail of like BGCs across species.

Microevolution in the pansecondary metabolome of and its potential macroevolutionary implications for filamentous fungi.

Fungi produce a wealth of pharmacologically bioactive secondary metabolites (SMs) from biosynthetic gene clusters (BGCs). It is common practice for drug discovery efforts to treat species' secondary metabolomes as being well represented by a single or a small number of representative genomes. However, this approach misses the possibility that intraspecific population dynamics, such as adaptation to environmental conditions or local microbiomes, may harbor novel BGCs that contribute to the overall niche breadth of species.

An interpreted atlas of biosynthetic gene clusters from 1,000 fungal genomes.

Fungi are prolific producers of natural products, compounds which have had a large societal impact as pharmaceuticals, mycotoxins, and agrochemicals. Despite the availability of over 1,000 fungal genomes and several decades of compound discovery efforts from fungi, the biosynthetic gene clusters (BGCs) encoded by these genomes and the associated chemical space have yet to be analyzed systematically. Here, we provide detailed annotation and analyses of fungal biosynthetic and chemical space to enable genome mining and discovery of fungal natural products.

The Frequency of Sex: Population Genomics Reveals Differences in Recombination and Population Structure of the Aflatoxin-Producing Fungus Aspergillus flavus.

The apparent rarity of sex in many fungal species has raised questions about how much sex is needed to purge deleterious mutations and how differences in frequency of sex impact fungal evolution. We sought to determine how differences in the extent of recombination between populations of impact the evolution of genes associated with the synthesis of aflatoxin, a notoriously potent carcinogen. We sequenced the genomes of, and quantified aflatoxin production in, 94 isolates of sampled from seven states in eastern and central latitudinal transects of the United States.

Diversity of Secondary Metabolism in Aspergillus nidulans Clinical Isolates.

The filamentous fungus has been a primary workhorse used to understand fungal genetics. Much of this work has focused on elucidating the genetics of biosynthetic gene clusters (BGCs) and the secondary metabolites (SMs) they produce. SMs are both niche defining in fungi and of great economic importance to humans.

Functional Characterization of Clinical Isolates of the Opportunistic Fungal Pathogen Aspergillus nidulans.

is an opportunistic fungal pathogen in patients with immunodeficiency, and virulence of isolates has mainly been studied in the context of chronic granulomatous disease (CGD), with characterization of clinical isolates obtained from non-CGD patients remaining elusive. This study therefore carried out a detailed biological characterization of two clinical isolates (CIs), obtained from a patient with breast carcinoma and pneumonia and from a patient with cystic fibrosis that underwent lung transplantation, and compared them to the reference, nonclinical FGSC A4 strain. Both CIs presented increased growth in comparison to that of the reference strain in the presence of physiologically relevant carbon sources.

Fitness Cost of Aflatoxin Production in Aspergillus flavus When Competing with Soil Microbes Could Maintain Balancing Selection.

Selective forces that maintain the polymorphism for aflatoxigenic and nonaflatoxigenic individuals of are largely unknown. As soils are widely considered the natural habitat of , we hypothesized that aflatoxin production would confer a fitness advantage in the soil environment. To test this hypothesis, we used DNA quantified by quantitative PCR (qPCR) as a proxy for fitness of aflatoxigenic and nonaflatoxigenic field isolates grown in soil microcosms.

Population Subdivision and the Frequency of Aflatoxigenic Isolates in in the United States.

Consumption of food contaminated with aflatoxin, from crops infected by , is associated with acute toxicosis, cancer, and stunted growth. Although such contamination is more common in the lower latitudes of the United States, it is unclear whether this pattern is associated with differences in the relative frequencies of aflatoxigenic individuals of . To determine whether the frequency of the aflatoxin-producing ability of increases as latitude decreases, we sampled 281 isolates from field soils in two north-south transects in the United States and tested them for aflatoxin production.

Balancing selection at nonself recognition loci in the chestnut blight fungus, Cryphonectria parasitica, demonstrated by trans-species polymorphisms, positive selection, and even allele frequencies.

Balancing selection has been inferred in diverse organisms for nonself recognition genes, including those involved in immunity, mating compatibility, and vegetative incompatibility. Although selective forces maintaining polymorphisms are known for genes involved in immunity and mating, mechanisms of balancing selection for vegetative incompatibility genes in fungi are being debated. We hypothesized that allorecognition and its consequent inhibition of virus transmission contribute to the maintenance of polymorphisms in vegetative incompatibility loci (vic) in the chestnut blight fungus, Cryphonectria parasitica.