A multiplex RT-PCR approach to detect aflatoxigenic strains of Aspergillus flavus

Aflatoxin profiles of Aspergillus flavus isolates in Sudanese fungal rhinosinusitis

Aspergillus flavus is a commonly encountered pathogen responsible for fungal rhinosinusitis (FRS) in arid regions. The species is known to produce aflatoxins, posing a significant risk to human health. This study aimed to investigate the aflatoxin profiles of A. flavus isolates causing FRS in Sudan. A total of 93 clinical and 34 environmental A. flavus isolates were studied. Aflatoxin profiles were evaluated by phenotypic (thin-layer and high-performance chromatography) and genotypic methods at various temperatures and substrates. Gene expression of aflD and aflR was also analyzed. A total of 42/93 (45%) isolates were positive for aflatoxin B1 and AFB2 by HPLC. When the incubation temperature changed from 28°C to 36°C, the number of positive isolates decreased to 41% (38/93). Genetic analysis revealed that 85% (79/93) of clinical isolates possessed all seven aflatoxin biosynthesis-associated genes, while 27% (14/51) of non-producing isolates lacked specific genes (aflD/aflR/aflS). Mutations were observed in aflS and aflR genes across both aflatoxin-producers and non-producers. Gene expression of aflD and aflR showed the highest expression between the 4th and 6th days of incubation on the Sabouraud medium and on the 9th day of incubation on the RPMI (Roswell Park Memorial Institute) medium. Aspergillus flavus clinical isolates demonstrated aflatoxigenic capabilities, influenced by incubation temperature and substrate. Dynamic aflD and aflR gene expression patterns over time enriched our understanding of aflatoxin production regulation. The overall findings underscored the health risks of Sudanese patients infected by this species, emphasizing the importance of monitoring aflatoxin exposure.

Control of aflatoxin biosynthesis by sulfur containing benzimidazole derivatives: In-silico interaction, biological activity, and gene regulation of Aspergillus flavus

Aspergillus flavus producing aflatoxins is one of the potent contaminants of raw food commodities during pre-and post-harvest crops. Aflatoxins are the group of secondary metabolites a subset of natural polyketides. Our major focus is on the inhibition of the biosynthesis pathway of aflatoxin by targeting the enzymes involved. Benzimidazoles are known antimicrobial compounds. In this study the sulfur containing benzimidazole derivatives were tested for their antifungal and antiaflatoxigenic activity. The fungal growth and aflatoxin production was analysed in culture medium as well as in the rice. Inhibition of specific genes was studied in terms of mRNA expression and the interaction of test compound with polyketide synthases by in-silico molecular docking. Substitution at the 6th position of 2-(2-thienyl) benzimidazole (2-TBD) reduced the antifungal property of benzimidazole but effectively inhibited the aflatoxin synthesis in the culture medium as well as in the rice from the toxigenic strain of A. flavus. Among the derivatives tested, the methyl group containing 2-(2-thienyl)- 6-methylbenzimidazole (6-MTBD) inhibited aflatoxin B1 most effectively followed by carboxylic group containing 2-(2-thienyl) benzimidazole-6-carboxylic acid (6-TBCA) with IC50 value of 12.36 and 18.25 µg/mL respectively. Molecular docking study shows that 2-(2-thienyl) benzimidazole-6-carbonitrile (6-CTBD) and 6-MTBD occupy same pocket on TE domain of PksA with similar range of binding energy, however the experimental data show a different effect on the biosynthesis of AFB1. 6-MTBD effectively inhibited the AFB1 synthesis (97%) while 6-CTBD could not (39.5%). Data obtained from the expression study also supports the experimental observations. These compounds are non-toxic to mammalian cells. These benzimidazole derivatives inhibit toxic secondary metabolites without affecting the growth of the fungi hence can be used during fermentation to avoid mycotoxin contamination.

Development of a real-time PCR and multiplex PCR assay for the detection and identification of mycotoxigenic fungi in stored maize grains

This study aimed to identify important mycotoxigenic fungi and accurate detection of mycotoxin in stored maize grains using molecular methods. The current study also optimised the real-time PCR (RT-PCR) assay. The melting curve was established to identify isolated fungal species of Aspergillus (4), Fusarium (3), Penicillium (3), and Alternaria (one). A multiplex polymerase chain reaction (mPCR) technique was developed for the detection and characterisation of mycotoxin producing fungi, mycotoxin metabolic pathway genes, and the determination of eleven mycotoxins in stored maize grains using high-performance liquid chromatography (HPLC). The mPCR results indicated positive signals for potentially mycotoxigenic fungal species tested of Aspergillus, Fusarium, Penicillium, and Alternaria. A protocol for multiplex reverse transcription-polymerase chain reaction (mRT-PCR) was tested to distinguish between free and contaminated, stored maize with aflatoxin B1 (AFB1). The expression pattern of four aflatoxin biosynthetic pathway genes, AFB1 (aflQ, aflP, aflO, and aflD), was a good marker for contaminated, stored maize grains. HPLC analysis showed that maize grain samples were contaminated with mycotoxins, and the concentration was above the detection level. The results indicate that the polyphasic approach might provide a sensitive, rapid, and accurate method for detecting and identifying mycotoxigenic fungal species and mycotoxins in stored maize grains.

Prospects for fungal bioremediation of unburied waste packages from the Goiânia radiological accident

Goiânia, the Goiás State capital, starred in 1987, where one of the largest radiological accidents in the world happened. A teletherapy machine was subtracted from a derelict radiotherapy clinic and disassembled by scavengers who distributed fragments of the 50 TBq ¹³⁷CsCl source among relatives and acquaintances, enchanted by the blue shine of the substance. During the 15 days before the accident was acknowledged, contaminated recycling materials were delivered to recycling factories in four cities in the state of São Paulo, Brazil, in the form of recycling paper bales. The contaminated bales were spotted, collected, and stored in fifty 1.6 m³ steel boxes at the interim storage facility of the Nuclear and Energy Research Institute (IPEN). In 2017, a check of the content was performed in a few boxes and the presence of high moisture content was observed even though the bales were dry when conditioned and the packages were kept sealed since then. The main objective of this work was to report the fungi found in the radioactive waste after they evolved for 30 years in isolation inside the waste boxes and their role in the decay of the waste. Examination of the microbiome showed the presence of nematodes and fungal communities. The fungi species isolated were Aspergillus quadricinctus, Fusarium oxysporum, Lecanicillium coprophilumi, Scedosporium boydii, Scytalidium lignicola, Xenoacremonium recifei, and Pleurostoma richardsiae. These microorganisms showed a significant capacity to digest cellulose in our trials, which could be one of the ways they survive in such a harsh environment, reducing the volume of radioactive paper waste. These metabolic abilities give us a future perspective of using these fungi in biotechnology to remediate radioactively contaminated materials, particularly cellulose-based waste.

Aflatoxin Contamination, Its Impact and Management Strategies: An Updated Review

Aflatoxin, a type of mycotoxin, is mostly produced by Aspergillus flavus and Aspergillus parasiticus. It is responsible for the loss of billions of dollars to the world economy, by contaminating different crops such as cotton, groundnut, maize, and chilies, and causing immense effects on the health of humans and animals. More than eighteen different types of aflatoxins have been reported to date, and among them, aflatoxins B1, B2, G1, and G2 are the most prevalent and lethal. Early detection of fungal infection plays a key role in the control of aflatoxin contamination. Therefore, different methods, including culture, chromatographic techniques, and molecular assays, are used to determine aflatoxin contamination in crops and food products. Many countries have set a maximum limit of aflatoxin contamination (2-20 ppb) in their food and agriculture commodities for human or animal consumption, and the use of different methods to combat this menace is essential. Fungal infection mostly takes place during the pre- and post-harvest stage of crops, and most of the methods to control aflatoxin are employed for the latter phase. Studies have shown that if correct measures are adopted during the crop development phase, aflatoxin contamination can be reduced by a significant level. Currently, the use of bio-pesticides is the intervention employed in many countries, whereby atoxigenic strains competitively reduce the burden of toxigenic strains in the field, thereby helping to mitigate this problem. This updated review on aflatoxins sheds light on the sources of contamination, and the on occurrence, impact, detection techniques, and management strategies, with a special emphasis on bio-pesticides to control aflatoxins.

Analysis of the competitiveness between a non-aflatoxigenic and an aflatoxigenic Aspergillus flavus strain on maize kernels by droplet digital PCR

Non-aflatoxigenic Aspergillus flavus strains are used as a biocontrol system on maize fields to decrease the aflatoxin biosynthesis of aflatoxigenic A. flavus strains. A. flavus strain AF36 was the first commercially available biocontrol strain and is authorized for use on maize fields by the US Environmental Protection Agency, e.g., in Texas and Arizona. A droplet digital PCR (ddPCR) assay was developed to analyze the mechanisms of competition and interaction of aflatoxigenic and non-aflatoxigenic A. flavus strains. This assay enables the parallel identification and quantification of the biocontrol strain A. flavus AF36 and the aflatoxigenic A. flavus strain MRI19. To test the assay, spores of both strains were mixed in varying ratios and were incubated on maize-based agar or maize kernels for up to 20 days. Genomic equivalent ratios (genome copy numbers) of both strains were determined by ddPCR at certain times after incubation and were compared to the spore ratios used for inoculation. The aflatoxin biosynthesis was also measured. In general, A. flavus MRI19 had higher competitiveness in the tested habitats compared to the non-aflatoxigenic strain, as indicated by higher final genomic equivalent ratios of this strain compared to the spore ratios used for inoculation. Nevertheless, A. flavus AF36 effectively controlled aflatoxin biosynthesis of A. flavus MRI19, as a clear aflatoxin inhibition was already seen by the inoculation of 10% spores of the biocontrol strain mixed with 90% spores of the aflatoxigenic strain compared to samples inoculated with only spores of the aflatoxigenic A. flavus MRI19.

Molecular identification of aflatoxigenic Aspergillus species in dried nuts and grains collected from Tehran, Iran

INTRODUCTION

Agricultural commodities contaminated by molds and mycotoxins can be considered as public health problems in less developed countries, particularly in Iran. Hence the main purpose of this study was to identify mold fungi and molecular analysis of the most important species of aflatoxin-B1-producing Aspergillus species in some dried nuts and grains in local markets in Tehran.

MATERIALS AND METHODS

Two hundred fifty samples of wheat, rice, corn, pistachios, and peanuts were collected from the five different locations of Tehran between January 2018 and January 2019. The samples were analyzed by using direct seed inoculation method and grain crushing method. Fungal strains were identified as Aspergillus spp. on the basis of morphological characters and further confirmed by using of β-tubulin gene sequencing. To differentiate between aflatoxigenic and non-aflatoxigenic Aspergillus spp., the isolates were screened for the presence of aflatoxigenic genes (nor-1, ver-1, omtA, and aflR).

RESULTS

One-handed forty-eight aflatoxigenic Aspergillus isolates (144 A. flavus and 4 A. parasiticus) were identified and aflR gene was the most frequent gene in these species. Five isolates (4 A. flavus, 1 A. parasiticus) had quadruplet pattern, 64 isolates (63 A. flavus, 1 A. parasiticus) had more than 1 gene and 39 isolates (38 A. flavus,1 A. parasiticus) did not have any genes.

CONCLUSION

According to the contamination of dried nuts and grains by some aflatoxigenic fungi, an extensive surveillance is necessary to provide a wider view on these products. Moreover, effective and efficient aflatoxin control program requires identifying and managing key elements that are effective in reducing mycotoxin production at farm level or in storage conditions.

Current Practices for Reference Gene Selection in RT-qPCR of Aspergillus: Outlook and Recommendations for the Future

Aspergillus is a genus of filamentous fungi with vast geographic and ecological distributions. Species within this genus are clinically, agriculturally and biotechnologically relevant, leading to increasing interest in elucidating gene expression dynamics of key metabolic and physiological processes. Reverse-transcription quantitative Polymerase Chain Reaction (RT-qPCR) is a sensitive and specific method of quantifying gene expression. A crucial step for comparing RT-qPCR results between strains and experimental conditions is normalisation to experimentally validated reference gene(s). In this review, we provide a critical analysis of current reference gene selection and validation practices for RT-qPCR gene expression analyses of Aspergillus. Of 90 primary research articles obtained through our PubMed query, 17 experimentally validated the reference gene(s) used. Twenty reference genes were used across the 90 studies, with beta-tubulin being the most used reference gene, followed by actin, 18S rRNA and glyceraldehyde 3-phosphate dehydrogenase. Sixteen of the 90 studies used multiple reference genes for normalisation. Failing to experimentally validate the stability of reference genes can lead to conflicting results, as was the case for four studies. Overall, our review highlights the need to experimentally validate reference genes in RT-qPCR studies of Aspergillus.

Biodiversity of Aflatoxigenic Aspergillus Species in Dairy Feeds in Bulawayo, Zimbabwe

The presence of molds, especially certain species of Aspergillus, in food commodities may contribute to aflatoxin contamination. The aim of this study was to determine the biodiversity of Aspergillus species in dairy feeds from farms in select locations in Zimbabwe and assess their aflatoxin production potential using a polyphasic approach. A total of 96 feed samples were collected, which consisted of dairy feed concentrate, mixed ration, brewers’ spent grain, and grass from 13 farms during the dry season (August–October, 2016) and the following rainy season (January–March, 2017). A total of 199 presumptive isolates representing four sections from genus Aspergillus (Nigri, Fumigati, Flavi, and Circumdati) were recovered from the feeds. Section Flavi, which includes several aflatoxin producers, constituted 23% (n = 46) of the isolates. Species from this section were A. flavus, A. nomius, A. oryzae, A. parasiticus, and A. parvisclerotigenus, and 39 (84.4%) of these showed evidence of aflatoxin production in plate assays. Of the 46 section Flavi isolates examined, some lacked one or more of the five targeted aflatoxin cluster genes (aflD, aflR, aflS, aflM, and aflP). The presence of the five genes was as follows: aflD (76.9%), aflR (48.7%), aflS (74.4%), aflM (64.1%), and aflP (79.5%). This study highlights the species diversity of aflatoxigenic fungi that have the potential to contaminate different types of feed for dairy cows. Our findings underscore the importance of preventing contamination of feedstuffs by these fungi so that aflatoxins do not end up in the diets of consumers.

Morphological and Molecular Characterization of Toxigenic Aspergillus flavus from Groundnut Kernels in Kenya

Pathogenesis of Aspergillus flavus on important agricultural products is a key concern on human health due to the synthesis and secretion of the hazardous secondary metabolite, aflatoxin. This study identified and further characterized aflatoxigenic A. flavus from groundnuts sampled from sundry shops in Kenya using integrated morphological and molecular approaches. The groundnuts were plated on potato dextrose agar for isolation and morphological observation of A. flavus based on macroscopic and microscopic features. Molecular characterization was done through amplification and comparison of the partial sequence of the ITS1-5.8S-ITS2 region. The expression analysis of aflR, aflS, aflD, aflP, and aflQ genes in the aflatoxin biosynthesis pathways was conducted to confirm the positive identification of A. flavus. The gene expression also aided to delineate toxigenic isolates of A. flavus from atoxigenic ones. Morphologically, 18 isolates suspected to be A. flavus were identified. Out of these, 14 isolates successfully amplified the 500 bp ITS region of A. flavus or Aspergillus oryzae, while 4 isolates were not amplified. All the remaining 14 isolates expressed at least one of the aflatoxigenic genes but only 5 had all the genes expressed. Partial sequencing revealed that isolates 5, 11, 12, 13, and 15 had 99.2%, 97.6%, 98.4%, 97.5%, and 100% homology, respectively, to the A. flavus isolate LUOHE, ITS-5.8S-ITS2, obtained from the NCBI database. The five isolates were accurate identification of atoxigenic A. flavus. Precise identification of toxigenic strains of A. flavus will be useful in establishing control strategies of the fungus in food products.

DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables

The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole‐genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing‐based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.

Molecular profile of non-aflatoxigenic phenotype in native strains of Aspergillus flavus

Aflatoxins are the most common mycotoxin contaminant reported in food and feed. Aflatoxin B₁, the most toxic among different aflatoxins, is known to cause hepatocellular carcinoma in animals. Aspergillus flavus and A. parasiticus are the main producers of aflatoxins and are widely distributed in tropical countries. Even though several robust strategies have been in use to control aflatoxin contamination, the control at the pre-harvest level is primitive and incompetent. Therefore, the aim of the study was to isolate and identify the non-aflatoxigenic A. flavus and to delineate the molecular mechanism for the loss of aflatoxin production by the non-aflatoxigenic isolates. Eighteen non-aflatoxigenic strains were isolated from various biological sources using cultural and analytical methods. Among the 18 isolates, 8 isolates produced sclerotia and 17 isolates had type I deletion in norB-cypA region. The isolates were confirmed as A. flavus using gene-specific PCR and sequencing of the ITS region. Later, aflatoxin gene-specific PCR revealed that the defect in one or more genes has led to non-aflatoxigenic phenotype. The strain R9 had maximum defect, and genes avnA and verB had the highest frequency of defect among the non-aflatoxigenic strains. Further, qRT-PCR confirmed that the non-aflatoxigenic strains had high frequency of defect or downregulation in the late pathway genes compared to early pathway genes. Thus, these non-aflatoxigenic strains can be the potential candidates for an effective and proficient strategy for the control of pre-harvest aflatoxin contamination.

Towards Managing and Controlling Aflatoxin Producers Within Aspergillus Species in Infested Rice Grains Collected from Local Markets in Kenya

Rice grains can be attacked by a range of pathogens, including Aspergillus species, which can cause the accumulation of aflatoxins and represent a serious threat to the consumers. Aflatoxins are secondary metabolites synthesized by Aspergillus species and naturally occur in various foodstuffs. In this study, we sought to analyze the prevalence of aflatoxin-producing Aspergillus spp. in rice grains currently sold in Kenyan local markets. We analyzed a total of 98 samples randomly collected and primarily analyzed to observe moisture content and fungal growth. We then isolated Aspergillus species, characterized them morphologically and using the Internal transcribed spacer (ITS) primers. Finally, we screened them for aflatoxin-producing isolates targeting Norsolorinic Acid (nor-1) and Versicolorin (ver-1) specific genes involved in aflatoxin biosynthesis. We observed that all tested samples were contaminated. The highest prevalence of Aspergillus species and aflatoxigenic fungal species, had values of 66% and 36.4% for nor-1 and ver-1, respectively. In total, 66% of all isolates were confirmed to be aflatoxin producers. The occurrence of high contamination levels of Aspergillus species points to the possibility of production of aflatoxins in rice grains. This work provides a baseline for future studies on the occurrence of mycotoxigenic fungal species in rice grains being sold in local markets and strategies to control these aflatoxigenic strains at pre- and post-harvest levels.

Analysis of the indoor environment of agricultural constructions in the context of sustainability

This research paper focuses on agricultural constructions, a special type of constructions with an important role in industry and agriculture. Food production is an important social factor that is vital to human survival, so its qualitative aspect is a key determinant of living standards and is also important in terms of sustainability. The need to create a suitable environment (welfare) for animals, as a factor in terms of health and productivity, is drawing increasing attention. The environment continuously and directly affects animals, so it is quickly reflected in their productivity and medical condition. The objective of this research paper is to present an analysis of the interactions between agricultural constructions' outdoor and indoor environment by monitoring an actual operational construction designed for animal rearing, from the point of view of animal welfare and sustainability, taking into account thermal protection and indoor climate.

Bioinformatics analysis of aflatoxins produced by Aspregillus sp. in basic consumer grain (corn and rice) in Saudi Arabia

The food contaminants by aflatoxins are inevitable even when all precautions and good agricultural practices are applied. Samples of white rice and corn (yellow, red) grains were collected from different local markets and houses. Three Aspergillus flavus strain isolated were identified using molecular characterization of AFLR (aflR) toxin gene. DNA genome of the three A. flavus isolates (namely A. flavus _ YC; A. flavus _ RC; A. flavus _ Rice) which corresponds to isolates from, yellow corn, red corn and white rice respectively were used as a template for PCR to amplify Aspergillus flavus AFLR (aflR) toxin gene. Partially sequenced was amplified using a specific primer set to confirm its identity, phylogenetic relationships between the three isolates as well as determination of the corresponding antigenic determinants. The epitope prediction analysis demonstrated that there were 1, 2, 3 and 4 epitopes whose score were equal 1 in A. flavus _ YC; A. flavus _ RC; A. flavus _ Rice, respectively. Interestingly, there were great dissimilarity in the epitope sequences among the three isolates except in RLQEGGDDAAGIPA, SPPPPVETQGLGGD, RPSESLPSARSEQG and PAHNTYSTPHAHTQ were found to be similar between all isolates. This work articulates that the molecular identification and characterization of three A. flavus using Aspergillus flavus AFLR (aflR) toxin gene and the unique antigenic determinants that could be used for design of a broad-spectrum antibody for rapid detection of A. flavus in foods and support quality system of food safety.

Assessment of Toxigenic Fusarium Species and Their Mycotoxins in Brewing Barley Grains

Fusarium species threaten yield and quality of cereals worldwide due to their ability to produce mycotoxins and cause plant diseases. Trichothecenes and zearalenone are the most economically significant mycotoxins and are of particular concern in barley, maize and wheat. For this reason, the aim of this study was to characterize the Fusarium isolates from brewing barley and to assess deoxynivalenol and zearalenone contamination in grains. Characterization of the Fusarium strains was carried out by the phylogeny based on two loci (EF-1α and RPB2). Mycotoxin detection and quantification were performed by LC-MS. The results show that Fusarium was the predominant genus. Phylogenetic study demonstrated that the majority of the strains clustered within the Fusarium sambucinum species complex followed by the Fusarium tricinctum species complex. The results revealed high incidence of deoxynivalenol (DON) and zearalenone (ZEA) contamination (90.6% and 87.5%, respectively). It was observed that 86% of the samples contaminated with ZEA were above the limits set by the EU and Brazilian regulations. These results may highlight the importance of controlling Fusarium toxins in barley, mainly because of its use in the brewing industry and the resistance of various mycotoxins to food processing treatments.

Molecular identification of aflatoxigenic Aspergillus species in feedstuff samples

Background and Purpose:

Aflatoxins are naturally produced by some species of Aspergillus, such as A.flavus and A.parasiticus. Aflatoxins reportedly have carcinogenic effects on human, poultry, and livestock, and therefore could be linked to severe human illnesses. Aflatoxin biosynthesis pathway involves different clustered genes, including structural, regular, and unassigned genes. The present study was conducted to detect aflR,aflP, and aflD as three important genes contributing to aflatoxin B1 production cycle in Aspergillus species isolated from the feedstuffs of animal husbandry.

Materials and Methods:

This study was conducted on 25 isolates of A. flavus, A. parasiticus, A. nomius, and A. nidulans, isolated from animal feedstuff as a test group. The test group was compared with two standard strains (i.e., A. flavus and A. parasiticus) as aflatoxigenic reference organisms and negative controls (i.e., A. fumigatus, A.fusarium, and A.penicillium) in terms of the presence of aflR, aflP, and aflD genes using polymerase chain reaction (PCR). The determination of the toxigenicity and aflatoxin production of isolated Aspergillus species was accomplished using thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC).

Results:

The results obtained by the amplification of the selected genes by PCR method for the detection of aflatoxigenic Asprgillus species were significantly correlated with TLC and HPLC results. Accordingly, all samples, having positive results for aflatoxin B1 production in TLC and HPLC, were able to show the amplification of three target genes. However, 4 cases out of 6 (66%) non-aflatoxigenic isolates were positive for three or two genes.

Conclusion:

Based on the findings, the molecular detection of aflatoxin biosynthesis genes (i.e., aflP, aflD, and aflR) could be considered as a quick and reliable method for the detection of aflatoxigenic Aspergillus. Furthermore, this method could be useful in planning and implementing strategies targeted toward improving the safety of human or animal food.

Targeting Aflatoxin Biosynthetic Genes

Chemical detoxification and physical destruction of aflatoxins in foods and feed commodities are mostly unattainable in a way that preserves the edibility of the food. Therefore, preventing mycotoxins in general and aflatoxins in particular from entering the food chain is a better approach. This requires early detection of the aflatoxin-causing organisms. Detection and quantification of aflatoxin-producing fungi has always been a challenge, especially within species of Aspergillus and Penicillium. Culture-based methods require a high level of expertise and a list of sophisticated equipment. Furthermore, even for a trained taxonomist, species that are identical in morphology, physiology, and nutritional aspects can be challenging to classify. Fungal taxonomy has changed over the past few decades; more species are being reclassified, and new species are being described due to advances in sequencing and genome assembly. These developments make the use of PCR-based approaches practical, rapid, and more reliable for the identification of fungi to the species level. This chapter presents a variety of protocols to detect and quantify aflatoxin-producing fungi using mycotoxin biosynthesis pathway genes.

Assessment and biomonitoring indoor environment of buildings

Ensuring hygiene and health protection is one of the basic construction requirements. Such requirements are examined when commissioning new constructions and examining defects in constructions already in use. One substantial defect is biocorrosion which represents a synergistic process with a complex variety of factors. It is caused by biochemical manifestations of various micro-organisms (micromycetes). Micromycetes producing mycotoxins therefore play an important role regarding the so-called 'Sick Building Syndrome' that has become a global problem nowadays. The case study presented here aims to demonstrate the effectiveness of the diagnostic methods used in assessing the presence of micromycetes in a building's internal atmosphere and on the internal surfaces of a construction built using traditional construction methods. The methodology of comparing methods is based on their effectiveness, taking into account the identification of type and intensity of micromycetes presence in the air and on the material surfaces in the monitored areas.

Rapid Detection and Identification of Mycotoxigenic Fungi and Mycotoxins in Stored Wheat Grain

This study aimed to assess the occurrence of toxigenic fungi and mycotoxin contamination in stored wheat grains by using advanced molecular and analytical techniques. A multiplex polymerase chain reaction (PCR) strategy was established for rapid identification of mycotoxigenic fungi, and an improved analytical method was developed for simultaneous multi-mycotoxin determination in wheat grains by liquid chromatography-tandem mass spectrometry (LC/MS/MS) without the need for any clean-up. The optimized multiplex PCR method was highly specific in detecting fungal species containing species-specific and mycotoxin metabolic pathway genes. The method was applied for evaluation of 34 wheat grain samples collected from storage warehouses for the presence of mycotoxin-producing fungi, and a few samples were found positive for Fusarium and Aspergillus species. Further chemical analysis revealed that 17 samples contained mycotoxins above the level of detection, but only six samples were found to be contaminated over the EU regulatory limits with at least one mycotoxin. Aflatoxin B₁, fumonisins, and deoxynivalenol were the most common toxins found in these samples. The results showed a strong correlation between the presence of mycotoxin biosynthesis genes as analyzed by multiplex PCR and mycotoxin detection by LC/MS/MS. The present findings indicate that a combined approach might provide rapid, accurate, and sensitive detection of mycotoxigenic species and mycotoxins in wheat grains.

Driver genes in non-small cell lung cancer: Characteristics, detection methods, and targeted therapies

Lung cancer is one of the most common causes of cancer-related death in the world. The large number of lung cancer cases is non-small cell lung cancer (NSCLC), which approximately accounting for 75% of lung cancer. Over the past years, our comprehensive knowledge about the molecular biology of NSCLC has been rapidly enriching, which has promoted the discovery of driver genes in NSCLC and directed FDA-approved targeted therapies. Of course, the targeted therapies based on driver genes provide a more exact option for advanced non-small cell lung cancer, improving the survival rate of patients. Now, we will review the landscape of driver genes in NSCLC including the characteristics, detection methods, the application of target therapy and challenges.

Fusarium verticillioides and fumonisin contamination in Bt and non-Bt maize cultivated in Brazil

Fusarium verticillioides is one of the main pathogens of maize, causing ear and stalk rots. This fungus is also able to produce high levels of fumonisins, which have been linked to various illnesses in humans and animals. Previous studies have shown that maize hybrids genetically modified with the cry genes from the bacterium Bacillus thuringiensis (Bt) presented lower incidence of F. verticillioides and fumonisin levels, presumably through the reduction of insects, which could act as vectors of fungi. The aim of this study was to assess the incidence of F. verticillioides and the concentration of fumonisins in Bt and isogenic non-Bt hybrids (2B710Hx, 30F35YG, 2B710, and 30F35, respectively). The samples of 2B710Hx and 30F35YG presented lower F. verticillioides frequency than 2B710 and 30F35 samples. However, there was no statistical difference between fumonisin contamination when Bt and non-Bt samples were compared (P > 0.05). The results suggest that other environmental parameters could possibly trigger fumonisin production during plant development in the field; consequently, other management strategies should be applied to aid controlling fumonisin contamination in maize.

Evaluating Aflatoxin Gene Expression in Aspergillus Section Flavi

The determination of aflatoxin production ability and differentiation of aflatoxigenic strains can be assessed by monitoring the expression of one or several key genes using reverse transcription polymerase chain reaction (RT-PCR). We herein describe the methods for RNA induction, extraction, and quality determination, and the RT-PCR conditions used to evaluate the ability of a given Aspergillus strain to produce aflatoxins.

Rapid detection of aflatoxigenic Aspergillus sp. in herbal specimens by a simple, bendable, paper-based lab-on-a-chip

Postharvest herbal product contamination with mycotoxins and mycotoxin-producing fungi represents a potentially carcinogenic hazard. Aspergillus flavus is a major cause of this issue. Available mold detection methods are PCR-based and rely heavily on laboratories; thus, they are unsuitable for on-site monitoring. In this study, a bendable, paper-based lab-on-a-chip platform was developed to rapidly detect toxigenic Aspergillus spp. DNA. The 3.0-4.0 cm(2) chip is fabricated using Whatman™ filter paper, fishing line and a simple plastic lamination process and has nucleic acid amplification and signal detection components. The Aspergillus assay specifically amplifies the aflatoxin biosynthesis gene, aflR, using loop-mediated isothermal amplification (LAMP); hybridization between target DNA and probes on blue silvernanoplates (AgNPls) yields colorimetric results. Positive results are indicated by the detection pad appearing blue due to dispersed blue AgNPls; negative results are indicated by the detection pad appearing colorless or pale yellow due to probe/target DNA hybridization and AgNPls aggregation. Assay completion requires less than 40 min, has a limit of detection (LOD) of 100 aflR copies, and has high specificity (94.47%)and sensitivity (100%). Contamination was identified in 14 of 32 herbal samples tested (43.75%). This work demonstrates the fabrication of a simple, low-cost, paper-based lab-on-a-chip platform suitable for rapid-detection applications.

Expression of Genes by Aflatoxigenic and Nonaflatoxigenic Strains of Aspergillus flavus Isolated from Brazil Nuts

The aims of the present study were to monitor the production of aflatoxin B1 (AFB1) and mycelial growth, and to evaluate the expression of genes directly and indirectly involved in the biosynthesis of aflatoxins by Aspergillus flavus isolated from Brazil nuts. Six previously identified A. flavus strains were grown on coconut agar at 25°C for up to 10 days. Mycotoxins were separated by high-performance liquid chromatography and fungal growth was measured daily using the diametric mycelial growth rate. Transcriptional analysis was performed by real-time polymerase chain reaction (PCR) after 2 and 7 d of incubation using specific primers (aflR, aflD, aflP, lipase, metalloprotease, and LaeA). Three (50%) of the six A. flavus isolates produced AFB1 (ICB-1, ICB-12, and ICB-54) and three (50%) were not aflatoxigenic (ICB-141, ICB-161, and ICB-198). Aflatoxin production was observed from d 2 of incubation (1.5 ng/g for ICB-54) and increased gradually with time of incubation until d 10 (15,803.6 ng/g for ICB-54). Almost all A. flavus isolates exhibited a similar gene expression pattern after 2 d of incubation (p > 0.10). After 7 d of incubation, the LaeA (p < 0.05) and metalloprotease (p < 0.05) genes were the most expressed by nonaflatoxigenic strains, whereas aflatoxigenic isolates exhibited higher expression of the aflR (p < 0.05) and aflD genes (p < 0.05). Our results suggest that the expression of aflR and aflD is correlated with aflatoxin production in A. flavus and that overexpression of aflR could affect the transcriptional and aflatoxigenic pattern (ICB-54). Elucidation of the molecular mechanisms that regulate the secondary metabolism of toxigenic fungi may permit the rational silencing of the genes involved and consequently the programmed inhibition of aflatoxin production. Knowledge of the conditions, under which aflatoxin genes are expressed, should contribute to the development of innovative and more cost-effective strategies to reduce and prevent aflatoxin contamination in Brazil nuts.

Detection of Aspergillus flavus in stored peanuts using real-time PCR and the expression of aflatoxin genes in toxigenic and atoxigenic A. flavus isolates

Aspergillus flavus is the main species from section Flavi responsible for aflatoxin accumulation in stored peanuts. Rapid methods to detect A. flavus could help to prevent aflatoxins from entering the food chain. A real-time polymerase chain reaction (RTi-PCR) assay was standardized for rapid, specific, and sensitive detection of A. flavus in stored peanuts. A. flavus was detected in 53.6% and 50% of peanut samples by RTi-PCR and A. flavus and Aspergillus parasiticus agar culture, respectively, with 95% agreement between them. Twenty-two A. flavus isolates were screened using high-performance liquid chromatography for their capacity to produce aflatoxin AFB1 (B1). B1 was produced by >72% of the isolates. Sixteen isolates produced B1 at concentrations ranging from 1.64 to 109.18 μg/mL. Four aflatoxin biosynthetic pathway genes (aflD, aflM, aflP, and aflQ) were evaluated using PCR and reverse-transcription PCR in 22 A. flavus isolates from peanut kernels with the aim of rapidly and accurately differentiating toxigenic and atoxigenic isolates. The PCR amplification of genes did not correlate with aflatoxin production capability. The expression of aflD and aflQ was a good marker for differentiating toxigenic from atoxigenic isolates.

Mycoflora dynamics analysis of Korean traditional wheat-based nuruk

The growing popularity of traditional Korean alcoholic beverages has led to a demand for quality enhancement of the traditional starter culture nuruk, which consists primarily of wheat. Therefore, this study focused on mycoflora characterization and the temporal variations in traditional wheat-based nuruks fermented at two representative traditional temperature conditions for 30 days. Nuruk A was fermented at a constant temperature of 36°C for 30 days and nuruk B was fermented at a high initial temperature of 45°C for 10 days followed by 35°C for 20 days. The average mycoflora load in the two different nuruk conditions did not vary significantly between the 0 and 30 day cultures, and a maximum load of 8.39 log CFU/g was observed for nuruk A on culture day 3 and 7.87 log CFU/g for nuruk B on culture day 30. Within two samples, pH was negatively correlated with temporal changes in mycoflora load. The pH of nuruk A was significantly lower than that of nuruk B at all of the time points evaluated. Culture-dependent characterization led to the identification of 55 fungal isolates belonging to 9 genera and 15 species, with the most prominent genera comprising Lichtheimia, Penicillium, Trametes, Aspergillus, Rhizomucor, and Mucor. A total of 25 yeast isolates were characterized belonging to 6 genera and 7 species, the most prominent among which were Rhodotorula, Pichia, Debaryomyces, Saccharomycopsis, and Torulospora. Mycofloral community dynamics analysis revealed that both samples A and B varied considerably with respect to the fungal communities over a span of 30 days.

Reconstruction of the original mycoflora in pelleted feed by PCR-SSCP and qPCR

Ground feeds for pigs were investigated for fungal contamination before and after pelleting (subsamples in total n = 24) by cultural and molecular biological methods. A fungal-specific primer pair ITS1/ITS5.8R was used to amplify fungal DNA; PCR products were processed for the PCR-SSCP method. In the resulting acrylamide gel, more than 85% of DNA bands of ground feeds were preserved after pelleting. Twenty-two DNA bands were sequenced; all represented fungal DNA. The level of fungal DNA in ground feed samples was equivalent to 4.77-5.69 log10  CFU g(-1) , calculated by qPCR using a standard curve of Aspergillus flavus. In pelleted feed, the level of fungal DNA was in average ± 0.07 log10 different from ground feed. Quantified by cultural methods, the fresh ground feeds contained up to 4.51 log10  CFU g(-1) culturable fungi, while there was < 2.83 log10  CFU g(-1) detected in pelleted feeds. This result shows that, while the process of pelleting reduced the amount of living fungi dramatically, it did not affect the total fungal DNA in feed. Thus, the described methodology was able to reconstruct the fungal microbiota in feeds and reflected a considerable fungal contamination of raw materials such as grains.

Real time PCR of Nor~1 (aflD) gene of aflatoxin producing fungi and its correlative quantization to aflatoxin levels in South African compound feeds

Aflatoxins (AFs) are naturally occurring secondary metabolites. This toxin is principally produced by Aspergillus flavus and Aspergillus parasiticus in compound feeds worldwide. Compound feeds are feeds blended from various raw materials and additives. Contaminations of these feeds by AFs and its possible transmission into edible materials like milk, egg and organs of the body, are a serious problem. Expression of the Nor~1 (aflD) gene is the main factor responsible for AFs production. For this reason, a study was carried out to establish a correlation between levels of AFs and determinant gene (Nor~1) in South African compound feeds. To achieve this, compound feeds (n=30) were analyzed for Nor~1 gene using real time polymerase chain reaction (RT-PCR), while AFs levels in similar samples were estimated using high-performance liquid chromatography (HPLC) after an immune-affinity clean-up extraction procedure. Results indicated that AFs levels in positive samples ranged from 0.7 to 33.0 ppb. These levels generally did not correlate (R(2)=0.093) with those of Nor~1 gene in similar samples. Consequently, Nor~1 gene levels established via RT-PCR cannot be used as a predicting model for AFs in compound feeds. Only four of the feeds analyzed, specifically poultry feeds, contained levels of AFs above the regulatory limits of 10 ppb established in South Africa (S.A.). This should be considered unsafe when consumed on a continuous basis and may pose some health related problems especially when AFs are found together with other significant mycotoxins such as ochratoxins (OTs) and/or fumonisins (FBs).

Molecular biodiversity of mycotoxigenic fungi that threaten food safety

Fungal biodiversity is one of the most important contributors to the occurrence and severity of mycotoxin contamination of crop plants. Phenotypic and metabolic plasticity has enabled mycotoxigenic fungi to colonize a broad range of agriculturally important crops and to adapt to a range of environmental conditions. New mycotoxin-commodity combinations provide evidence for the ability of fungi to adapt to changing conditions and the emergence of genotypes that confer enhanced aggressiveness toward plants and/or altered mycotoxin production profiles. Perhaps the most important contributor to qualitative differences in mycotoxin production among fungi is variation in mycotoxin biosynthetic genes. Molecular genetic and biochemical analyses of toxigenic fungi have elucidated specific differences in biosynthetic genes that are responsible for intra- and inter-specific differences in mycotoxin production. For Aspergillus and Fusarium, the mycotoxigenic genera of greatest concern, variation in biosynthetic genes responsible for production of individual families of mycotoxins appears to be the result of evolutionary adaptation. Examples of such variation have been reported for: a) aflatoxin biosynthetic genes in Aspergillus flavus and Aspergillus parasiticus; b) trichothecene biosynthetic genes within and among Fusarium species; and c) fumonisin biosynthetic genes in Aspergillus and Fusarium species. Understanding the variation in these biosynthetic genes and the basis for variation in mycotoxin production is important for accurate assessment of the risks that fungi pose to food safety and for prevention of mycotoxin contamination of crops in the field and in storage.

Expression of aflatoxin genes aflO (omtB) and aflQ (ordA) differentiates levels of aflatoxin production by Aspergillus flavus strains from soils of pistachio orchards

The expression of four aflatoxin (AF) biosynthetic pathway genes (aflD, aflO, aflP and aflQ) was evaluated in 24 Aspergillus flavus strains isolated from soils of pistachio orchards, with the aim of rapidly and accurately differentiating toxigenic from non-toxigenic strains. The amounts of AFB1 produced by 20 aflatoxigenic strains varied from 1.25 to 321.56 ng/mg fungal dry weights in YES medium. RT-PCR results showed that transcription of the four genes was not always correlated with AF production. The expression pattern of aflO and aflQ, however, was found to be well correlated with the amounts of AFB1 produced when strains were arbitrarily classified into two types: type I, comprised of strains producing ≥30 ng/mg; and type II, low (≤30 ng/mg) and non-AF producers. The present study suggests that, under specific growth conditions, the expression pattern of aflatoxin biosynthetic pathway genes such as aflO and aflQ can be used to infer the AF-producing capability of A. flavus strains.

Molecular phylogeny and phenotypic variability of clinical and environmental strains of Aspergillus flavus

Aspergillus flavus is the second most common cause of aspergillosis infection in immunocompromised patients and is responsible for the production of aflatoxins. Little is known about the population structure of A. flavus, although recent molecular and phenotypic data seem to demonstrate that different genetic lineages exist within this species. The aim of this study was to carry out a morphological, physiological, and molecular analysis of a set of clinical and environmental isolates to determine whether this variability is due to species divergence or intraspecific diversity, and to assess whether the clinical isolates form a separate group. The amdS and omtA genes were more phylogenetically informative than the other tested genes and their combined analysis inferred three main clades, with no clear distinction between clinical and environmental isolates. No important morphological and physiological differences were found between the members of the different clades, with the exception of the assimilation of d-glucosamine, which differentiates the members of the clade II from the others.

Development of a simple and high-throughput method for detecting aflatoxins production in culture media

AIMS

To develop a simple, high-throughput and inexpensive procedure to detect and quantify aflatoxins into the culture media of growing mycelia.

METHODS AND RESULTS

Fungal conidia (Aspergillus flavus) were inoculated into the wells of a microplate containing 200 μl of different formulations of coconut-derived liquid medium. Time-dependent production of aflatoxins in the culture media was evaluated by a procedure relying on the UV-induced fluorescence emission by the toxin, using a microplate reader. These data were validated by comparison with the outputs of a conventional HPLC-based procedure. Determinations of aflatoxin concentration, according to the fluorimetric procedure, were performed either by withdrawing samples from the plates or by direct 'in situ' readings, the latter method reinforcing the high-throughput feature of the procedure. Fluorescence enhancers (cyclodextrins) did not ameliorate the sensitivity of the procedure to low concentrations of the toxin into the medium. The efficacy of the procedure was also validated by testing the effect on toxin yield of adding an antioxidant agent (α-lipoic acid) to the medium.

CONCLUSIONS

We give evidence that our improved procedure is reliable and suitable to analyse aflatoxin accumulation time course in coconut-derived culture medium.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study shows that our procedure may profitably be used to give insights into the mechanisms of regulation of mycotoxin production and, consequently, to implement different strategies for the containment of aflatoxin contamination of food and feed commodities.

Complex microbiota of a Chinese "Fen" liquor fermentation starter (Fen-Daqu), revealed by culture-dependent and culture-independent methods

Daqu is a traditional fermentation starter that is used for Chinese liquor production. Although partly mechanized, its manufacturing process has remained traditional. We investigated the microbial diversity of Fen-Daqu, a starter for light-flavour liquor, using combined culture-dependent and culture-independent approaches (PCR-DGGE). A total of 190 microbial strains, comprising 109 bacteria and 81 yeasts and moulds, were isolated and identified on the basis of the sequences of their 16S rDNA (bacteria) and 26S rDNA and ITS regions (fungi). DGGE of DNA extracted from Daqu was used to complement the culture-dependent method in order to include non-culturable microbes. Both approaches revealed that Bacillus licheniformis was an abundant bacterial species, and Saccharomycopsis fibuligera, Wickerhamomyces anomalus, and Pichia kudriavzevii were the most common yeasts encountered in Fen-Daqu. Six genera of moulds (Absidia, Aspergillus, Mucor, Rhizopus, Rhizomucor and Penicillium) were found. The potential function of these microorganisms in starters for alcoholic fermentation is discussed. In general the culture-based findings overlapped with those obtained by DGGE by a large extent. However, Weissella cibaria, Weissella confusa, Staphylococcus saprophyticus, Enterobacter aerogenes, Lactobacillus sanfranciscensis, Lactobacillus lactis, and Bacillus megaterium were only revealed by DGGE.

Multiplex PCR assay for the detection of aflatoxigenic and non-aflatoxigenic fungi in meju, a Korean fermented soybean food starter

Aflatoxins are toxic secondary metabolites produced commonly by Aspergillus flavus and Aspergillus parasiticus. In this study, the possibility of using multiplex PCR was investigated to speed up and specify the detection of aflatoxigenic Aspergillus species in meju, a traditional Korean fermented soybean food starter. Two different sets of three primers were designed specifically for the omtB, ver-1, aflR, and omtA genes present in the aflatoxin biosynthesis cluster. The optimized multiplex PCR showed that only aflatoxigenic Aspergillus species gave three band patterns in both primer sets. The detection limits were determined as 125 pg/μl for genomic DNA from aflatoxigenic A. parasiticus KCCM 35078, and 10(5) spores/g of meju sample for DNA extracted directly from meju. A total of 65 Aspergillus isolates from meju were tested for the presence of aflatoxigenic fungi by the application of multiplex PCR, and were analyzed by TLC and HPLC for the aflatoxin production in the culture filtrates. Results showed a good correlation between the presence of the aflatoxin biosynthesis genes analyzed by multiplex PCR and aflatoxin production by TLC and HPLC. This suggests that this multiplex PCR method may provide an accurate and specific detection of aflatoxigenic Aspergillus species in fermented soybean foods.

Aspergillus novoparasiticus: a new clinical species of the section Flavi

During a survey on the incidence of Aspergillus in clinical environments, we found some interesting isolates that were morphologically similar to Aspergillus parasiticus, but differed in the color of the colonies and in the pattern of their conidial ornamentation. In the present study, those isolates were characterized using a polyphasic approach. A phylogenetic analysis was carried out, based on partial fragments of the acetamidase (amdS) and O-methyltransferase (omtS) genes and the internal transcribed spacer (ITS) region of rDNA. This information was combined with a detailed morphological and physiological study that included aflatoxin production and assimilation profiles of different carbon and nitrogen sources. The phenotypic and genotypic results support the proposal of a new species, Aspergillus novoparasiticus, phylogenetically placed in a distinct sister clade to that of A. parasiticus. The former has lobate-reticulate conidia and does not produce aspergillic acid on AFPA or organic acids on CREA, while A. parasiticus has echinulate conidia and produces aspergillic and organic acids. In addition, this new species, as well as A. parasiticus, produces aflatoxins B1, B2, G1 and G2.

Discrimination between aflatoxigenic and non-aflatoxigenic Aspergillus section Flavi strains from Egyptian peanuts using molecular and analytical techniques

A wide range of Aspergillus section Flavi strains were isolated from Egyptian peanut samples. Eighteen of these strains were compared with two type strains (Aspergillus flavus SRRC G1907 and Aspergillus parasiticus 2747) for aflatoxin production based on (a) qualitative fluorescence using a coconut cream agar medium (CAM), and (b) aflatoxin production on a conducive Yeast Extract-Sucrose (YES) medium using HPLC. These results were validated by using molecular approaches (the structural genes, aflD (nor-1), aflM (ver-1) and aflP (omt A) and the regulatory gene aflR) to discriminate between aflatoxigenic and non-aflatoxigenic strains of the Aspergillus section Flavi group in vitro and on peanut seeds. Overall, 13/18 strains producing aflatoxins B1 and B2 in the range 1.27-213.35 µg/g medium were identified. In addition, 5 non-aflatoxin producing strains were found. The expression of these four genes was assessed using PCR and RT-PCR. PCR showed that all strains contained the four aflatoxin genes examined, regardless of expression profiles. Our results also showed that aflD expression is a reliable marker to discriminate between aflatoxin and non-aflatoxin producers. Interestingly, when an aflatoxin producing strain and three non-aflatoxigenic strains were subsequently grown on peanuts at 0.95 water activity, two of the non-producers were able to initiate aflatoxin biosynthesis. This suggests that growth of strains on the natural food matrix is important for confirming aflatoxigenic production potential.