Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1187060 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31380364_1.fastq.gz | Fastqsanger.gz | |||
| SRR31380364_2.fastq.gz | Fastqsanger.gz | |||
| SRR31380365_1.fastq.gz | Fastqsanger.gz | |||
| SRR31380365_2.fastq.gz | Fastqsanger.gz | |||
| SRR31380366_1.fastq.gz | Fastqsanger.gz |
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Project description:The goal of this study is to proactively assess the risk of insecticide resistance development by determining susceptibility of field-collected D. suzukii and their response to insecticide treatment at the transcriptome level using next-generation sequencing technology. Methods:LC50 values were calculated for zeta-cypermethrin, spinosad, malathion treated D. suzukii field-collected and lab-reared populations. LC50 dosage survived and untreated (10 individuals per replicate) field-collected and lab reared D.suzukii transcript profiles were generated by RNA sequencing, in triplicate, using Illumina NextSeq 500. The 24 samples (paired-end reads, including replicates) were independently mapped onto the D. suzukii genome (SpottedWingFlybase v.1) by using TopHat followed by Cufflinks to estimate the expression values of the transcripts in FPKM (Fragments Per Kilobase per Million mapped reads) with the Cuffdiff 2 default geometric normalization. Differentially expressed genes (FDR < 0.05 after Benjamini-Hochberg correction for multiple-testing) were identified for insecticide-treated or untreated control for either (1) lab-reared populations or (2) field-collected populations. Results: As an approach to proactively assess the risk of insecticide resistance development, we determined the LC50 (lethal concentration, 50%) values of commonly used insecticides zeta-cypermethrin, spinosad, and malathion against laboratory-reared and field-collected D. suzukii populations. The LC50 values were significantly higher in field-collected populations when compared to lab-reared populations, indicating that field populations are less susceptible to these insecticides. Furthermore, we used RNA sequencing to analyze the response of D. suzukii at the transcriptome level upon treatment with the same three insecticide classes that are used in our bioassays. We identified differentially expressed genes (DEGs) in D. suzukii that survived LD50 doses of zeta-cypermethrin, spinosad, and malathion and gene classes that are overrepresented in DEGs. We observed that a high number of significantly DEGs are involved in detoxification and reduced cuticular penetration, especially in field population, thus providing potential molecular mechanisms for the higher LC50 values for field-collected population. Conclusion: Our study identified a high number of metabolic detoxification genes that are induced in field-collected D. suzukii upon insecticide treatment and a high degree of overlap when examining the lists of genes that are induced when D. suzukii is treated with three commonly used insecticides. Based on our results, we conclude that there is a substantial risk of insecticide resistance and cross-resistance development in D. suzukii in the field.
2016-09-23 | GSE73595 | GEO
Project description:The presence of genetic groups of the entomopathogenic fungus Metarhizium anisopliae in soil is shaped by its adaptability to specific soil and habitat types, and by soil insect populations. Although the entomopathogenic life style of this fungus is well studied, its saprophytic life style has received little consideration. While a set of functionally related genes can be commonly expressed for the adaptability of this fungus to different environments (insect cuticle, insect blood and root exudates), a different subset of genes is also expected for each environment. In order to increase the knowledge of the potential use of M. anisopliae as a rhizosphere competent organism, in this study we evaluated the genetic expression of this fungus while growing on plant root exudates in laboratory conditions during a time course.
2010-12-29 | GSE16848 | GEO
Project description:The presence of genetic groups of the entomopathogenic fungus Metarhizium anisopliae in soil is shaped by its adaptability to specific soil and habitat types, and by soil insect populations. Although the entomopathogenic life style of this fungus is well studied, its saprophytic life style has received little consideration. While a set of functionally related genes can be commonly expressed for the adaptability of this fungus to different environments (insect cuticle, insect blood and root exudates), a different subset of genes is also expected for each environment. In order to increase the knowledge of the potential use of M. anisopliae as a rhizosphere competent organism, in this study we evaluated the genetic expression of this fungus while growing on plant root exudates in laboratory conditions during a time course. One fungal strain: Metarhizium anisopliae ARSEF 2575; Five time conditions: 0h, 1h, 4h, 8h, 12h; Five-condition experiment: Time0h vs. Time1h, Time1h vs. Time4h, Time4h vs. Time8h, Time8h vs. Time12h and Time12h vs. Time0h. Two Biological replicates: independently grown and harvested. Three replicates per array. Dye-swap was performed on replicate 2.
2010-12-29 | E-GEOD-16848 | biostudies-arrayexpress
Project description:The goal of the study was to investigate gene expression differences in Hyalella azteca exposed to pyrethroid insecticides and compare a laboratory strain to a wild population believed to be resistant to the pesticides. H. azteca reared in the laboratory at the University of CA, Berkeley (UCB) were exposed to cyfluthrin, a commerical pyrethroid insecticide for 96-h. A wild population collected from Grayson Creek (GC), CA was reared in the laboratory for several days and also exposed to cyfluthrin. Toxicity testing revealed that GC animals were two orders of magnitude less sensitive to cyfluthrin compared to the laboratory animals with the no observed effect concentration (NOEC) for UCB = 0.4 ng/L and GC= 170 ng/L. Unexposed, control animals and animals exposed to 0.4 ng/L (GC and UCB) or 170 ng/L cyfluthrin were collected following 96-h treatments. Differences in gene expression were measured using a custom Hyalella azteca microarray. Gene expression profiles revealed that laboratory H. azteca responded to cyfluthrin through differential expression of genes involved in neurological system processes. In contract, H. azteca from Grayson Creek showed a pattern of oxidative stress through the differential expression of glutathione-S-transferases, heat shock proteins, and other genes involved in oxidation-reduction processes.
2013-07-17 | GSE48943 | GEO
Project description:Methanol extractions of fecal pellets collected from laboratory-reared wood frogs that were selectively inoculated with the herptile gut fungus, Basidiobolus.
2024-08-07 | MSV000095547 | MassIVE
Project description:Methanol extractions of fecal pellets collected from laboratory-reared wood frogs that were selectively inoculated with the herptile gut fungus, Basidiobolus.
2024-08-07 | MSV000095549 | MassIVE
Project description:Background and Methods: High mercury (Hg) levels are a significant concern in many aquatic environments, and adverse effects of Hg exposure in fish can include altered behavior, reproduction, growth, and increased stress responses. In addition, human health concerns over Hg continue to warrant new research on its mechanisms of action. The objectives of this study were to investigate the impacts of Hg on the female largemouth bass (LMB) central nervous system transcriptome by conducting a laboratory injection experiment with 2.5 µg/g body weight in addition to sampling LMB from an environment that contains high levels of Hg (St. Mary’s River, Florida, USA). These animals were compared to LMB that inhibit river systems with lower Hg (Big Wekiva, Santa Fe and St. John’s Rivers Florida, USA). A LMB 8 x 15 K microarray was used for hypothalamic (laboratory) and whole brain (field) transcriptomics analysis. Results: Mercury in the blood of LMB collected from St Mary’s River was significantly elevated 3-fold (~ 0.1 ng Hg/ml blood) compared to LMB collected from the other three sites (~ 0.03 ng Hg/ml blood). In the hypothalamus of Hg injected LMB, there were 937 genes that showed differential expression (raw p = 0.05) but there were no probes that passed an FDR for multiple hypothesis correction. In contrast, in field collected LMB there were 2909 genes that that showed differential expression (raw p = 0.05) of which 38 were significant after correction for multiple hypothesis testing (FDR = 0.05). These included Hsp90 co-chaperone Cdc37, multicopper oxidase, mismatch repair protein Msh6, and 16 kDa heat shock protein A. Functional enrichment in whole brains of LMB collected from the field sites revealed that genes involved in the biological processes of protein folding and targeting, regulation of protein metabolic process, and protein degradation (i.e. ubiquitin cycle) were over-represented. Interestingly, gene set enrichment analysis identifed expression targets that were in common between the laboratory experiment (MeHg injected) and field collected LMB and these consisted of mainly homeobox transcription factors (PROP paired-like homeobox 1, LIM homeobox 3 and paired-like homeodomain 1 and 2). Lastly, prevalent themes emerged in the SNEA expression targets that included neuropeptide receptor signaling, steroid signaling, and structural components, such as beta-actin, integrins, and stress fibres. Conclusions: This study characterizes novel cell signaling pathways that underlie Hg toxicity in the teleostean central nervous system.
2012-08-31 | GSE38456 | GEO