Genetic dissection of complex traits using hierarchical biological knowledge.

Despite the growing constellation of genetic loci linked to common traits, these loci have yet to account for most heritable variation, and most act through poorly understood mechanisms. Recent machine learning (ML) systems have used hierarchical biological knowledge to associate genetic mutations with phenotypic outcomes, yielding substantial predictive power and mechanistic insight. Here, we use an ontology-guided ML system to map single nucleotide variants (SNVs) focusing on 6 classic phenotypic traits in natural yeast populations. The 29 identified loci are largely novel and account for ~17% of the phenotypic variance, versus <3% for standard genetic analysis. Representative results show that sensitivity to hydroxyurea is linked to SNVs in two alternative purine biosynthesis pathways, and that sensitivity to copper arises through failure to detoxify reactive oxygen species in fatty acid metabolism. This work demonstrates a knowledge-based approach to amplifying and interpreting signals in population genetic studies.

Transcriptome analysis of Apis mellifera under benomyl stress to discriminate the gene expression in response to development and immune systems.

The health and safety of the honeybees are seriously threatened due to the abuse of chemical pesticides in modern agriculture and apiculture. In this study, the RNA Seq approach was used to assess the effects of the honeybees treated with benomyl. The results showed that there were a total of 11,902 differentially expressed genes (DEGs). Among them, 5,759 DEGs were up-regulated and involved in the functions of immunity, detoxification, biological metabolism, and regulation. The DEGs were clustered in the GO terms of epidermal structure and response to external stimuli, and most of the DEGs were enriched in 15 pathways, such as light conduction, MAPK, calcium ion pathway, and so on. Moreover, the pathway of the toll signal transduction was activated. The data investigated that the expression of functional genes involved in the growth, development, foraging, and immunity of honeybees were significantly affected by benomyl stress, which would seriously threaten the health of the honeybees. This study provided a theoretical basis for revealing the response mechanism of honeybees to pesticides stress.

Benomyl induced oxidative stress related DNA damage and apoptosis in H9c2 cardiomyoblast cells.

Benomyl, benzimidazole group pesticide, has been prohibited in Europe and USA since 2003 due to its toxic effects and it has been still determined as food and environmental contaminant. In the present study, the toxic effect mechanisms of benomyl were evaluated in rat cardiomyoblast (H9c2) cells. Cytotoxicity was determined by MTT and NRU assay and, oxidative stress potential was evaluated by reactive oxygen species (ROS) production and glutathione levels. DNA damage was assessed by alkaline comet assay. Relative expressions of apoptosis related genes were evaluated; furthermore, NF-κB and JNK protein levels were determined. At 4 µM concentration (at which cell viability was >70%), benomyl increased 2-fold of ROS production level and 2-fold of apoptosis as well as DNA damage. Benomyl down-regulated miR21, TNF-α and Akt1 ≥ 48.75 and ≥ 97.90; respectively. PTEN, JNK and NF-κB expressions were upregulated. The dramatic changes in JNK and NF-κB expression levels were not observed in protein levels. These findings showed the oxidative stress related DNA damage and apoptosis in cardiomyoblast cells exposed to benomyl. However, further mechanistic and in vivo studies are needed to understand the cardiotoxic effects of benomyl and benzimidazol fungucides.

Benomyl treatment decreases fecundity of ant queens.

Methyl benzimidazole carbamate fungicides, including benomyl, are widely used in agriculture, and to eliminate entomopathogenic infections. We treated queens of Myrmica rubra (Hymenoptera:Formicidae) infected or not by Rickia wasmannii (Laboulbeniales:Laboulbeniaceae) with benomyl, 1mg/ml p.o. for six weeks. Benomyl did not treat the infection, and the treatment alone caused strong decrease in the fecundity of control healthy queens from 18.0±8.4 to 3.7±5.2eggs per healthy queen. This is the first evidence on severe adverse effects of methyl benzimidazole carbamate fungicide on the fecundity of insects, which might be responsible for altered species composition of ant assemblages in the cultural landscape.

Influence of the carbamate fungicide benomyl on the gene expression and activity of aromatase in the human breast carcinoma cell line MCF-7.

The carbamate fungicide benomyl reportedly inhibited the growth of the human breast cancer cell line MCF-7 by inducing apoptosis. However, influence of benomyl on the expression and activity of aromatase of MCF-7 cells remains to be examined, since benomyl was identified as an endocrine disruptor. We here confirmed through cell cycle analysis and immunofluorescence staining that benomyl damaged microtubules and caused apoptosis. We also found that benomyl inhibited histone deacetylase (HDAC) 1 and accumulated acetylated histone H3 in MCF-7 cells. Additionally, benomyl enhanced the levels of aromatase protein and mRNA, albeit at high concentrations. It is thus likely that benomyl enhanced the promoter activity of the aromatase gene via acetylation of histone H3 as does the HDAC inhibitor Vorinostat. In conclusion, benomyl remains to be a risk factor as an endocrine disruptor for breast cancer.

Deleterious effects of benomyl and carbendazim on human placental trophoblast cells.

Benomyl and carbendazim are benzimidazole fungicides that are used throughout the world against a wide range of fungal diseases of agricultural products. There is as yet little information regarding the toxicity of benzimidazole fungicides to human placenta. In this study, we utilized human placental trophoblast cell line HTR-8/SVneo (HTR-8) to access the toxic effects of benomyl and carbendazim. Our data showed that these two fungicides decreased cell viability and the percentages of cells in G0/G1 phase, as well as induced apoptosis of HTR-8 cells. The invasion and migration of HTR-8 cells were significantly inhibited by benomyl and carbendazim. We further found that benomyl and carbendazim altered the expression of protease systems (MMPs/TIPMs and uPA/PAI-1) and adhesion molecules (integrin α5 and ß1) in HTR-8 cells. Our present study firstly shows the deleterious effects of benomyl and carbendazim on placental cells and suggests a potential risk of benzimidazole fungicides to human reproduction.

Combined effects of benomyl and environmental factors on growth and expression of the fumonisin biosynthetic genes FUM1 and FUM19 by Fusarium verticillioides.

Fusarium verticillioides is predominantly responsible of fumonisin contamination of maize and other cereals in Mediterranean climatic regions. This study examined the interaction of the fungicide benomyl, at ED50 and ED90 concentrations (effective doses of benomyl to reduce growth by 50% and 90%, respectively), with a range of temperatures (20-35 °C) and water potentials (-0.7, -2.8 and -7.0 MPa) compatible with current and foreseen climate change scenarios for these regions on growth and fumonisin biosynthesis in in vitro assays. The expression of fumonisin biosynthetic genes (FUM1 and FUM19) was quantified by real time RT-PCR. FUM1 encodes a polyketide synthase and FUM19 an ABC-type transporter, located both in the fumonisin biosynthetic cluster. The ED50 and ED90 concentrations obtained at 25 °C were 0.93 mg/L and 3.30 mg/L, respectively. Benomyl affected growth and fumonisin gene expression differently but it generally reduced fungal growth and fumonisin biosynthesis and both were significantly affected by temperature and water potential. This indicated that efficacy of benomyl might be compromised at certain conditions, although at similar or lower levels than other fungicides tested. Both fumonisin biosynthetic genes had similar expression patterns in all treatments and their correlation was positive and significant. The results suggested that Mediterranean climatic scenarios might suffer an additional negative impact of climate change by reducing the efficacy of antifungals used to control pathogens and toxigenic fungi.

Benomyl, aldehyde dehydrogenase, DOPAL, and the catecholaldehyde hypothesis for the pathogenesis of Parkinson's disease.

The dopamine metabolite 3,4-dihydroxyphenylacetaldehyde (DOPAL) is detoxified mainly by aldehyde dehydrogenase (ALDH). We find that the fungicide benomyl potently and rapidly inhibits ALDH and builds up DOPAL in vivo in mouse striatum and in vitro in PC12 cells and human cultured fibroblasts and glial cells. The in vivo results resemble those noted previously with knockouts of the genes encoding ALDH1A1 and 2, a mouse model of aging-related Parkinson's disease (PD). Exposure to pesticides that inhibit ALDH may therefore increase PD risk via DOPAL buildup. This study lends support to the "catecholaldehyde hypothesis" that the autotoxic dopamine metabolite DOPAL plays a pathogenic role in PD.

Aldehyde dehydrogenase inhibition as a pathogenic mechanism in Parkinson disease.

Parkinson disease (PD) is a neurodegenerative disorder particularly characterized by the loss of dopaminergic neurons in the substantia nigra. Pesticide exposure has been associated with PD occurrence, and we previously reported that the fungicide benomyl interferes with several cellular processes potentially relevant to PD pathogenesis. Here we propose that benomyl, via its bioactivated thiocarbamate sulfoxide metabolite, inhibits aldehyde dehydrogenase (ALDH), leading to accumulation of the reactive dopamine metabolite 3,4-dihydroxyphenylacetaldehyde (DOPAL), preferential degeneration of dopaminergic neurons, and development of PD. This hypothesis is supported by multiple lines of evidence. (i) We previously showed in mice the metabolism of benomyl to S-methyl N-butylthiocarbamate sulfoxide, which inhibits ALDH at nanomolar levels. We report here that benomyl exposure in primary mesencephalic neurons (ii) inhibits ALDH and (iii) alters dopamine homeostasis. It induces selective dopaminergic neuronal damage (iv) in vitro in primary mesencephalic cultures and (v) in vivo in a zebrafish system. (vi) In vitro cell loss was attenuated by reducing DOPAL formation. (vii) In our epidemiology study, higher exposure to benomyl was associated with increased PD risk. This ALDH model for PD etiology may help explain the selective vulnerability of dopaminergic neurons in PD and provide a potential mechanism through which environmental toxicants contribute to PD pathogenesis.

Potential of an in vitro toolbox combined with exposure data as a first step for the risk assessment of dietary chemical contaminants.

In vitro risk assessment of dietary contaminants has become a priority in human food safety. This paper proposes an in vitro approach associating different complementary tools in an original toolbox and aims to improve the assessment of the toxicological impact of dietary contaminants at realistic human exposure levels, with a special focus on the intestinal compartment. The system is based on the use of four complementary cellular tools, namely stress gene induction in transgenic strains of Escherichia coli, modulation of the activity of key biotransformation enzymes (cytochrome P-450 (CYP) 1A1 and 3A4) in a human intestinal cell line, and activation of aryl hydrocarbon receptor (AhR) and oestrogenic receptor (ER)-dependent genes in agonistic and antagonistic assays with luciferase reporter cells. It was applied to four chosen model molecules: ochratoxin A (OTA) and deoxynivalenol (DON), two common food-borne mycotoxins, and imazalil (IMA) and benomyl (BEN), two fungicides widely occurring in foodstuffs. All these assays were performed at or around a realistic intestinal concentration, determined through a deterministic approach based on the calculation of a theoretical maximum daily intake (TMDI). Using the four model molecules, it is clearly highlighted that induction of CYP1A1 activity and inhibition of CYP3A4 activity occurred in Caco-2 cells at a realistic intestinal concentration of IMA. Furthermore, some bacterial stress genes were induced in a range of realistic concentrations, following exposure to DON and IMA. In addition, BEN clearly provoked an ER agonistic activity in a human oestrogen sensitive reporter cell line. All these results are in accordance with the literature, suggesting that the in vitro toolbox constitutes an interesting approach in order to obtain a first 'fingerprint' of dietary contaminants at realistic human exposure for further risk assessment.

Effects of some pesticides on the vital organs of juvenile rainbow trout (Oncorhynchus mykiss).

Gill, trunk kidney, spleen, and liver of rainbow trout (Oncorhynchus mykiss) were examined after exposure to different sublethal concentrations of carbosulfan (25, 50 and 200 µgL(-1)), propineb (3, 6 and 24 mgL(-1)), and benomyl (2, 5 and 20 mgL(-1)) for 14 days. Lesions were observed in gill, trunk kidney, spleen, and liver of rainbow trout exposed to either concentration of pesticides. The most important lesions were determined in the highest concentrations of pesticides. Lamellar fusion, lamellar hyperplasia, epithelial lifting, vacuolization of epithelial tissue, epithelial necrosis, hypertrophy and sloughing of epithelium were observed on fish exposed to carbosulfan, propineb and benomyl. Fish had cell necrosis, degeneration and oedemas in liver, trunk kidney and spleen. None of these lesions were seen in control fish.

The budding yeast protein Sum1 functions independently of its binding partners Hst1 and Sir2 histone deacetylases to regulate microtubule assembly.

The budding yeast protein Sum1 is a transcription factor that associates with the histone deacetylase Hst1p or, in its absence, with Sir2p to form repressed chromatin. In this study, SUM1 has been identified as an allele-specific dosage suppressor of mutations in the major alpha-tubulin-coding gene TUB1. When cloned in a 2mu vector, SUM1 suppressed the cold-sensitive and benomyl-hypersensitive phenotypes associated with the tub1-1 mutation. The suppression was Hst1p- and Sir2p-independent, suggesting that it was not mediated by deacetylation events associated with Sum1p when it functions along with its known partner histone deacetylases. This protein was confined to the nucleus, but did not colocalize with the microtubules nor did it bind to alpha- or beta-tubulin. Cells deleted of SUM1 showed hypersensitivity to benomyl and cold-sensitive growth, phenotypes exhibited by mutants defective in microtubule function and cytoskeletal defects. These observations suggest that Sum1p is a novel regulator of microtubule function. We propose that as a dosage suppressor, Sum1p promotes the formation of microtubules by increasing the availability of the alphabeta-heterodimer containing the mutant alpha-tubulin subunit.

Deleterious effects of arsenic, benomyl and carbendazim on human endometrial cell proliferation in vitro.

OBJECTIVE: We aimed to investigate the effects of arsenic (As), benomyl (Ben), and carbendazim (Carb) on endometrial cells. MATERIALS AND METHODS: Human endometrial cells were obtained during diagnostic curettage. All cultured endometrial cells were divided into four groups: (1) 0 M (controls), (2) 10(-6) M, (3) 10(-5) M, (4) 10(-4) M for As, Ben and Carb. After 24 and 48 hours in culture, endometrial cell proliferations were assessed by diphenyltetrazolium bromide assay. The influences of different concentrations of As, Ben and Carb upon the endometrium were compared. RESULTS: During the first 24 hours, As, Ben and Carb appeared to have insignificant influences upon endometrial growth. After 48 hours in culture, all three agents significantly inhibited endometrial growth. In As groups, cell absorption after 48 hours culture were 100% (group 1), 82.1% (group 2), 43.6% (group 3) and 35.3% (group 4). In Ben groups, cell absorption was 100% (1), 75.9% (2), 66.4% (3) and 49. 6% (4). In the Carb groups, cell absorption was 100% (1), 70.4% (2), 73.0% (3) and 76.7% (4). CONCLUSION: The agents As, Ben and Carb appear to have inhibitory effects upon endometrial cells after 48 hours in culture.

Rhinitis associated with pesticide exposure among commercial pesticide applicators in the Agricultural Health Study.

OBJECTIVES: Rhinitis is common, but the risk factors are not well described. To investigate the association between current rhinitis and pesticide use, we used data from 2245 Iowa commercial pesticide applicators in the Agricultural Health Study. METHODS: Using logistic regression models adjusted for age, education and growing up on a farm, we evaluated the association between current rhinitis and 34 pesticides used in the past year. RESULTS: 74% of commercial pesticide applicators reported at least one episode of rhinitis in the past year (current rhinitis). Five pesticides used in the past year were significantly positively associated with current rhinitis: the herbicides 2,4-D, glyphosate and petroleum oil, the insecticide diazinon and the fungicide benomyl. The association for 2,4-D and glyphosate was limited to individuals who used both in the past year (OR 1.42, 95% CI 1.14 to 1.77). Both petroleum oil and diazinon showed consistent evidence of an association with rhinitis, based on both current use and exposure-response models. We saw no evidence of confounding by common agricultural rhinitis triggers such as handling grain or hay. CONCLUSIONS: Exposure to pesticides may increase the risk of rhinitis.

Benomyl induction of brain aromatase and toxic effects in the zebrafish embryo.

Benomyl is a benzimidazole fungicide that has been widely used on a variety of food crops and ornamental plants. It is known to cause adverse effects on reproductive systems, including decreased testicular and epididymal weights and reduced epididymal sperm counts and fertility. The brain aromatase gene is up-regulated by estrogens and estrogen mimics and considered a target gene to screen estrogen mimics. This study was designed to test the estrogenic potential and toxic effects of benomyl in the zebrafish system, and validated this system as a model that may correspond to the effect of benomyl in rodents. Concentrations of 20 x 10(-6), 40 x 10(-6) and 80 x 10(-6) M of benomyl-treated embryos showed decreased survival, hatching and heart rates, and increased incidence of malformations, such as pericardial edema, spinal lordosis, elongated heart, head edema, eye lens protrusion and caudal fin disappearance. Benomyl induced enhanced green fluorescent protein (EGFP) expression in the mediobasal hypothalamus (MBH) in transient zebrafish embryos with a brain aromatase-based reporter gene. In this study, we determined that benomyl has estrogenic potential based on zebrafish brain aromatase gene induction, and that benomyl is toxic at 20 x 10(-6) M concentration and higher. These results demonstrate the usefulness of zebrafish embryos as an in vivo system to examine the estrogenic and developmental toxic potential of unknown compounds.

A novel yeast-based tool to detect mutagenic and recombinogenic effects simultaneously.

In this work, we describe a new yeast-based assay to allow efficient detection of a comprehensive spectrum of genotoxicity events. The constructed diploid Saccharomyces cerevisiae strain allows the simultaneous monitoring of forward mutations, mitotic recombination events and chromosome loss or non-disjunction by direct selection in an easy and highly reproducible approach. The strain contains a DNA module consisting of a single functional copy of the URA3 gene and the kanMX4 gene inserted at the ADE2 locus on the right arm of chromosome XV. The changes of the genotype within the marker region were primarily selected on 5-fluoroorotic acid (5-FOA) agar plates. Further simple phenotypic tests of the 5-FOA-resistant ura3 clones make it possible to analyze the genetic configuration in detail (e.g. point mutations in URA3, gene conversion, crossing-over and chromosome loss). We demonstrate the successful application of our test system by studying the effects of well-known genotoxic agents (UV radiation, N-methyl-N'-nitro-N-nitrosoguanidine, aniline and benomyl). We found that the various agents induced mutations and recombination events with different relative frequencies. The integration of the module has generated a hot spot region of mutation and recombination at the borders of the artificially integrated URA3 kanMX4 cassette, which makes the system more sensitive towards DNA-damaging agents. Unlike other test systems, our S. cerevisiae strain is capable to detect a mutagenic effect caused by aniline.

Toxic effects of carbendazim and n-butyl isocyanate, metabolites of the fungicide benomyl, on early development in the African clawed frog, Xenopus laevis.

We investigated the toxic effects of carbendazim and n-butyl isocyanate (BIC), metabolites of the fungicide benomyl, on development in the African clawed frog, Xenopus laevis. To test the toxic effects, frog embryo teratogenesis assays using Xenopus were performed. Embryos were exposed to various concentrations of carbendazim (0-7 microM) and BIC (0-0.2 microM). LC(100) for carbendazim and BIC were 7 and 0.2 microM, respectively, and the corresponding LC(50), determined by probit analysis, were 5.606 and 0.135 microM. Exposure to carbendazim concentrations > or = 3 microM and BIC concentrations > or = 0.1 microM resulted in 10 different types of severe external malformation. Histological examinations revealed dysplasia of the brain, eyes, intestine, and somatic muscle, and swelling of the pronephric ducts. These phenomena were common in both test groups. The tissue-specific toxic effects were investigated with an animal cap assay. Neural tissues are normally induced at a high frequency by activin A, however, the induction of neural tissues was strongly inhibited by the addition of carbendazim. Conversely, the addition of BIC resulted in weak inhibition of neural tissues. Electron micrographs of animal cap explants revealed degeneration of cell junctions in the carbendazim-treated group, but not in the BIC-treated group. Numerous residual yolk platelets and mitochondrial degeneration were commonly observed in both test groups. The gene expression of cultivated animal cap explants was investigated by reverse transcriptase-polymerase chain reaction and revealed that expression of the neural-specific marker neural cell adhesion molecule was more strongly inhibited in the carbendazim-treated group than in the BIC-treated group.

Effects of three pesticides on the avoidance behavior of earthworms in laboratory tests performed under temperate and tropical conditions.

Little research has been performed on the impact of pesticides on earthworms under tropical conditions. Taking into consideration the often-limited resources in tropical countries, simple screening tests are needed. Therefore, it was investigated whether three pesticides relevant for the Brazilian Amazon (benomyl, carbendazim, lambda-cyhalothrin) affect the avoidance behavior of the earthworm Eisenia fetida. The tests were performed for two days according to ISO guideline 17512 but were adapted to tropical conditions (i.e. test substrate, test organism and temperature). The results indicate that this test gives reproducible and reliable results. Toxicity values (NOEC, EC50) are lower than those determined in 14 day-acute mortality tests and are approximately in the same range such as those found in 56 day-chronic reproduction tests with the same earthworm species, which were performed in parallel. Therefore, the use of the earthworm avoidance tests is recommended as a screening tool for the risk assessment of pesticides.

Avoidance tests with earthworms and springtails: defining the minimum exposure time to observe a significant response.

Based on the ability of organisms to avoid contaminated soils, avoidance tests have a great potential as early screening tools in lower tier levels of ERA schemes. Aiming at their standardization, the definition of the minimum exposure time necessary to observe an avoidance response to a contaminant is needed. To fill this gap, avoidance tests with earthworms (Eisenia andrei) and springtails (Folsomia candida), comparing distinct time periods (from 1-7 to 1-14 days, respectively), were performed using the artificial OECD soil and reference chemicals for each test organism. Results showed that for both organisms a clear response within 24 h of exposure can be obtained. This rapid response enhances the utility of the test for "on site" analysis to evaluate contaminated sites.

Effects of the fungicide benomyl on earthworms in laboratory tests under tropical and temperate conditions.

Soil organisms play a crucial role in the terrestrial ecosystem. Plant protection products (PPPs) are known to affect soil organisms and might have negative impacts on soil functions influenced by these organisms. Little research has been performed to date on the impact of PPPs on tropical soil ecosystems. Therefore, in this study it was investigated whether the effects of the fungicide benomyl (chosen as a model substance) differ between tropical and temperate regions and whether data generated under temperate conditions can be used for the Environmental Risk Assessment (ERA) in tropical regions. The effect of benomyl on earthworms was evaluated in acute and chronic laboratory tests modified for tropical conditions. These tests were performed at two temperatures (20 degrees C and 28 degrees C) and with two strains (temperate and tropical) of the compost worm Eisenia fetida. The fungicide was spiked in two natural and two artificial soils. In addition to the organization for economic cooperation and development (OECD) artificial soil, a tropical artificial soil (TAS), containing a tropical fern product (xaxim) instead of peat, was developed in this study. The results from the laboratory tests and a literature review showed that the effects of benomyl were, on average, lower under tropical conditions (LC(50): 450-630 mg active ingredient (a.i.)/kg; EC(50): 0.8-12.9 mg a.i./kg) than under temperate conditions (LC(5)0: 61-67 mg a.i./kg; EC(50): 1.0-1.6 mg a.i./kg) by a maximum factor of 10.3 (acute tests) and 12.9 (chronic tests). This result might be caused by an increased degradation of benomyl, and/or its first metabolite carbendazim, at higher temperatures, but a different sensitivity of the two worm strains cannot be ruled out. Despite the lower toxicity under tropical conditions and assuming comparable application rates, a preliminary assessment confirms the risk of benomyl to soil invertebrates under both conditions.