RNA-seq of Daphnia magna exposed to prochloraz in a 3-generation experiment
ABSTRACT: For most chemicals, environmental toxicity is only investigated for a single generation. In this study we investigate the effect of the fungicide prochloraz across generations in Daphnia magna. The study design included two exposure scenarios; one where all three generations were continuously exposed to prochloraz (100 ug/L) and one where only the first generation (F0) was exposed. We studied effects at different levels of biological organization combining key phenotypic effects, such as growth and reproduction, CYP enzyme activity, metabolomics and for generation F2 also transcriptomics
Project description:Study of the tetrapod limb has contributed a great deal to our understanding of developmental pathways and how changes to these pathways affect morphology. Most data on tetrapod limb development is known from amniotes, with far less known about genetic mechanisms of limb development in amphibians. To better understand the mechanisms of limb development in anuran amphibians, we use cyclopamine to inhibit Hedgehog signaling at various stages of limb development in Xenopus. We use transcriptomic analysis following cyclopamine exposure to understand the downstream effects of Hedgehog inhibition on gene expression. We find many aspects of Hedgehog function appear to be conserved with respect to amniotes, including the responses of ptc genes, gremlin, bmp2, and the autoregulatory property of shh. We show that, as was proposed based on experiments in chick, Sonic hedgehog plays two distinct roles in limb development – specification of digit number and specification of digit identity. In contrast to these points of conservation, we find that Hedgehog signaling is required for the maintenance of early limb bud outgrowth in Xenopus, a requirement not known for any other tetrapod. Experiment Overall Design: Eight microarray experiments were performed using RNA extracted from batches of hindlimbs dissected from Xenopus laevis tadpoles. Four of these were experimental groups exposed to cyclopamine at 1 µg/ml for 24 hours before animal fixation, and four were experimental groups exposed to the ethanol, the cyclopamine vehicle, at the same concentration used for cyclopamine vehicle for 24 hours. Each pool of RNA consisted of material from 18-22 hindlimb buds. Two experimental groups and two control groups were from one clutch of tadpoles, and the other four pools were from another clutch. Both samples within each of four paired groups (experimental vs. control) were exposed and processed simultaneously.
Project description:Custom D. magna gene expression microarray (Design ID: 023710, Agilent Technologies)were used to characterise gene expression profiles of Daphnia magna neoantes exposed to silver nanoparticles ( AgNPs ) or silver nitrate ( AgNO3 ) for 24 hours.
Project description:Variation in gene expression is known to be important for morphological evolution, however little is known about its general propensity. Here we examine a pair of frogs – Xenopus laevis and Xenopus tropicalis – with highly similar embryology, and ask how their transcriptomes compare. Despite separation for over ~30-90 million years we found a strong conservation in gene expression in the vast majority of the expressed orthologs. There were a significant number of changes in the level of expression of genes. Changes in timing of expression, heterochrony, were much less common, and were often found in genes and pathways that reflect responses to selective features of the environment. Differences in gene expression levels were concentrated in the earliest embryonic stages. We propose that different evolutionary rates across developmental stages may be explained by the stabilization of cell fate determination pathways in later stages. 96 microarrays, across developmental stages in Xenopus laevis and Xenopus tropicalis in wildtype embryos. For each of the two timecourse indepenent triplicates (clutches) were generated.
Project description:Pesticides are continuously released into the environment, with possible long-term consequences on aquatic organisms. One of the pesticides still applied in several crops in some countries is the fungicide carbendazim, ending up in surface waters with concentrations reaching 5 µg/L. Daphnia magna (clone k6) was used in this study as a model organism and it was exposed to a sub-lethal concentration of carbendazim (5 µg/L) for twelve generations. Gene expression alterations induced by this compound were assessed in the F0 and F12 generations using D. magna custom microarrays. Results revealed that carbendazim caused changes at the gene expression level in both generations. Genes involved in response to stress, DNA replication/repair, neurotransmission, protein biosynthesis, ATP production, lipids and carbohydrates metabolism were the most affected in both F0 and F12, although a lower number of differentially expressed genes were observed in the F12 generation exposed to carbendazim. The exposure of daphnids to carbendazim did not cause a stable change in gene expression from F0 to F12 generations. Effects at the gene expression level were early detected at the F0 generation after a short-time exposure (10 days), highlighting the advantages of using high throughput tools as early warning analysis but also providing information on chemical mode of action, which can add value in risk assessment procedures. For the microarray experiment, neonates with less than 24h were picked from the F0 and F12 generations from both clean medium and carbendazim. Three replicates per each treatment were used and consisted of 5 daphnids aging 10 days old. A total of three replicates per treatment were used and each biological replicate was individually hybridized on the array. A single-color design was used, using the Agilent one-color RNA Spike-In Kit (AgilentTechnologies, Santa Clara, CA, USA), following the manufacturers protocol.
Project description:Postharvest application of fungicides is commonly applied in order to reduce food loss. Prochloraz is currently the only postharvest fungicide registered in Israel and Europe in avocado fruits. Due to its unfavorable toxicological properties, prochloraz will be banned from the end of 2020 for future postharvest usage and therefore a substitute candidate is urgently warranted. Fludioxonil, a relatively safe, wide spectrum fungicide, is approved in Europe and Israel for postharvest use in various fruits, but not avocado. Hence, fludioxonil has been evaluated in the present study as a potential substitute for prochloraz in avocado. The objectives of the present study were to determine fludioxonil efficacy against common fungal infestations in avocado and distribution kinetics between peel and pulp in comparison to prochloraz. At the same concentration range (75-300 µg/L), fludioxonil was as effective as prochloraz in inhibiting postharvest decay, while in the early season cultivars, suffering mainly from stem-end rot, it exhibited a better decay control than prochloraz. Fludioxonil and prochloraz displayed negligible and undetected pulp levels, respectively, due to low peel penetrability. Taken altogether, fludioxonil was found to be a suitable candidate for replacing prochloraz as a postharvest fungicide in avocado.
Project description:Prochloraz is a fungicide that is widely used on vegetables to maintain freshness during storage. To ensure that prochloraz is used in a safe way that reduces the levels of residue on the product, we evaluated two treatment methods (soaking and spraying) that are commonly used for garlic sprouts. An ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) method was developed and validated for prochloraz residue on garlic sprouts. The linear range of the method was 5?500 ?g/kg and the correlation coefficient was 0.9983. The average recovery range was 88?94%, and the relative standard deviation range was 2.6?9.7%. Garlic sprout samples that had been soaked in or sprayed with prochloraz were collected from cold storage facilities in Laixi and Pingdu, China. For the soaked samples, the ranges for the levels of prochloraz residue on the whole garlic sprouts and stems (edible portion) were 15.76?25.14 mg/kg and 0.58?1.62 mg/kg, respectively. For the sprayed samples, the ranges for the levels of prochloraz residue on the whole garlic sprouts and stems were 1.85?7.89 mg/kg and 0.01?1.29 mg/kg, respectively. The results of this study provide a scientific basis for rationalizing the use of prochloraz and improving the safety of edible garlic sprouts.
Project description:Among numerous factors that contribute to honey bee colony losses and problems in beekeeping, pesticides and Nosema ceranae have been often reported. In contrast to insecticides, whose effects on bees have been widely studied, fungicides did not attract considerable attention. Prochloraz, an imidazole fungicide widely used in agriculture, was detected in honey and pollen stored inside hives and has been already proven to alter immune gene expression of honey bees at different developmental stages. The aim of this study was to simulate the realistic conditions of migratory beekeeping, where colonies, both uninfected and infected with N. ceranae, are frequently transported to the vicinity of crop fields treated with prochloraz. We investigated the combined effect of prochloraz and N. ceranae on honey bees that faced fungicide during the larval stage through food consumption and microsporidium infection afterwards. The most pronounced changes in gene expression were observed in newly emerged Nosema-free bees originating from colonies previously contaminated with prochloraz. As exclusively upregulation was registered, prochloraz alone most likely acts as a challenge that induces activation of immune pathways in newly emerged bees. The combination of both stressors (prochloraz and Nosema infection) exerted the greatest effect on six-day-old honey bees. Among ten genes with significantly altered expression, half were upregulated and half downregulated. N. ceranae as a sole stressor had the weakest effects on immune gene expression modulation with only three genes significantly dysregulated. In conclusion, food contaminated with prochloraz consumed in larval stage could present a threat to the development of immunity and detoxification mechanisms in honey bees.
Project description:The Larval Amphibian Growth and Development Assay (LAGDA) is an internationally harmonized testing guideline for evaluating effects of chronic chemical exposure in amphibians. In order to evaluate the effects of chronic exposure to an antiandrogenic chemical in an amphibian model, prochloraz was tested using a variation of the LAGDA design. Exposure was initiated with <1d post-fertilization embryos at nominal concentrations of 0, 6.7, 20, 60 and 180??g/L (0, 18, 53, 159, 478?nM) and continued in flow-through conditions until two months following the median time that controls completed metamorphosis. Growth, developmental rate, circulating thyroid hormone and thyroid gland histopathology were evaluated in a subsample at completion of metamorphosis. There were no effects on growth or development at this stage, but circulating thyroid hormone was elevated in the 20, 60 and 180??g/L treatments and minimal to mild thyroid follicular cell hypertrophy was observed histologically in the 180??g/L treatment. Growth, overt toxicity, and reproductive development were evaluated at test termination. There were no effects on growth in either gender, but livers and kidneys exhibited treatment-related pathologies consistent with organ toxicity related to metabolism and presumably impaired excretion of prochloraz metabolites. Histological assessments of female ovaries resulted in minimal pathologies only in the 180??g/L treatment while male testes exhibited numerous treatment-related pathologies that are consistent with previously reported antiandrogenic effects of prochloraz in other species. The most severe testis pathologies occurred in the 180??g/L treatment; however, incidences of treatment-related pathologies occurred in all prochloraz treatments. Müllerian duct regression in males was inhibited by prochloraz exposure while Müllerian duct maturation in females was accelerated, characteristic of a feminizing effect. Gene expression levels of potential biomarkers of testis function were also measured. Relative abundance of cyp17a1 transcripts was generally unaffected by prochloraz exposure whereas the Insl3 orthologue, rflcii, was elevated by 3 and >5-fold in the 60 and 180??g/L treatments, respectively, indicating impaired Leydig cell maturation and testosterone signaling. Overall, prochloraz exposure caused effects characteristic of an antiandrogenic mode of action, which is consistent with previously reported results in other species and supports the utility of the LAGDA design for chemical testing.
Project description:Recent studies have reported interspecific differences in how bee species respond to various stressors. Evaluating the exposure and responses of different bee species to plant protection products is considered an essential part of their risk assessment. This study was conducted to assess the impacts of thiacloprid-prochloraz mixture on buff-tailed bumblebees (Bombus terrestris) and red mason bees (Osmia bicornis) in a worst-case scenario under semi-field conditions. Bumblebee colonies or solitary bee trap nests were confined in tunnels with flowering oilseed rape. The recommended maximum application rates of 72 g thiacloprid/ha and 675 g prochloraz/ha were applied as a tank mixture during bee flight in full flowering oilseed rape. Several parameters such as flight and foraging activity, population parameters, and exposure level were investigated. Our results show adverse effects of the combination of thiacloprid and prochloraz on the reproductive performance of red mason bees. The number of cocoons produced by O. bicornis was significantly reduced in the treatment compared to the control group. Regarding bumblebees, we found no effects of the thiacloprid-prochloraz mixture on any observed parameters of colony development. The maximum detected concentrations of both active substances three days after application were higher in O. bicornis pollen mass compared to B. terrestris stored pollen. We conclude that this worst-case scenario of thiacloprid-prochloraz exposure poses a high risk to solitary bees and thus the use of such mixture should be restricted.
Project description:BACKGROUND:Penicillium italicum (blue mold) is one of citrus pathogens causing undesirable citrus fruit decay even at strictly-controlled low temperatures (<?10?°C) during shipping and storage. P. italicum isolates with considerably high resistance to sterol demethylation inhibitor (DMI) fungicides have emerged; however, mechanism(s) underlying such DMI-resistance remains unclear. In contrast to available elucidation on anti-DMI mechanism for P. digitatum (green mold), how P. italicum DMI-resistance develops has not yet been clarified. RESULTS:The present study prepared RNA-sequencing (RNA-seq) libraries for two P. italicum strains (highly resistant (Pi-R) versus highly sensitive (Pi-S) to DMI fungicides), with and without prochloraz treatment, to identify prochloraz-responsive genes facilitating DMI-resistance. After 6?h prochloraz-treatment, comparative transcriptome profiling showed more differentially expressed genes (DEGs) in Pi-R than Pi-S. Functional enrichments identified 15 DEGs in the prochloraz-induced Pi-R transcriptome, simultaneously up-regulated in P. italicum resistance. These included ATP-binding cassette (ABC) transporter-encoding genes, major facilitator superfamily (MFS) transporter-encoding genes, ergosterol (ERG) anabolism component genes ERG2, ERG6 and EGR11 (CYP51A), mitogen-activated protein kinase (MAPK) signaling-inducer genes Mkk1 and Hog1, and Ca2+/calmodulin-dependent kinase (CaMK) signaling-inducer genes CaMK1 and CaMK2. Fragments Per Kilobase per Million mapped reads (FPKM) analysis of Pi-R transcrtiptome showed that prochloraz induced mRNA increase of additional 4 unigenes, including the other two ERG11 isoforms CYP51B and CYP51C and the remaining kinase-encoding genes (i.e., Bck1 and Slt2) required for Slt2-MAPK signaling. The expression patterns of all the 19 prochloraz-responsive genes, obtained in our RNA-seq data sets, have been validated by quantitative real-time PCR (qRT-PCR). These lines of evidence in together draw a general portrait of anti-DMI mechanisms for P. italicum species. Intriguingly, some strategies adopted by the present Pi-R were not observed in the previously documented prochloraz-resistant P. digitatum transcrtiptomes. These included simultaneous induction of all major EGR11 isoforms (CYP51A/B/C), over-expression of ERG2 and ERG6 to modulate ergosterol anabolism, and concurrent mobilization of Slt2-MAPK and CaMK signaling processes to overcome fungicide-induced stresses. CONCLUSIONS:The present findings provided transcriptomic evidence on P. italicum DMI-resistance mechanisms and revealed some diversity in anti-DMI strategies between P. italicum and P. digitatum species, contributing to our knowledge on P. italicum DMI-resistance mechanisms.