Ontology highlight
ABSTRACT:
PROVIDER: PRJNA939966 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23697700_1.fastq.gz | Fastqsanger.gz | |||
| SRR23697700_2.fastq.gz | Fastqsanger.gz | |||
| SRR23697701_1.fastq.gz | Fastqsanger.gz | |||
| SRR23697701_2.fastq.gz | Fastqsanger.gz | |||
| SRR23697702_1.fastq.gz | Fastqsanger.gz |
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Project description:Native host plant insect resistance in the maize inbred line Mp708 was developed by traditional plant breeding. Resistant Mp708 thwarts feeding by fall armyworm (Spodoptera frugiperda [J.E. Smith]; Lepidoptera: Noctuidae), numerous other lepidopteran pests, and the coleopteran western corn rootworm. This broad resistance makes it an excellent model for studying native host plant resistance mechanisms. In response to caterpillar feeding, Mp708 rapidly mobilizes Mir1-CP, a unique cysteine protease that appears to translocate from roots to the maize midwhorl where it accumulates. This accumulation correlates with a significant reduction in caterpillar growth resulting from diminished food utilization. In addition, the peritrophic membrane (PM) that surrounds the food bolus in the mudgut (MG) is severely damaged in caterpillars fed on sweet corn callus transformed to express the gene encoding Mir1-CP or on midwhorl tissue from resistant Mp708 maize. Functions of the PM include assisting digestion and protecting the epithelium of the caterpillar MG from physical and chemical damage. Consequently, the reduced growth of caterpillars that feed on Mp708 is probably due to the action of Mir1-CP on PM physiology. In fact, previous in vitro studies indicated that Mir1-CP was capable of permeabilizing the PM. The present study used both targeted (qRT-PCR) and global (mRNA-seq) transcriptome analyses to explore the effect of eating Mir1-CP expressing Mp708 maize on abundance of transcripts in the MG of fall armyworm larvae in comparison to MGs from larvae fed on susceptible Tx601 maize that does not express Mir1-CP. Expression of genes encoding proteins involved in PM production is upregulated in MGs from fall armyworm fed on Mp708. Also, several digestive enzymes (endopeptidases, aminopeptidases, lipases, amylase) were more highly expressed in MGs from larvae fed on Mp708 than MGs from larvae fed on Tx601. Impaired growth of larvae fed on Mp708 probably results from metabolic costs associated with higher production of PM constituents and digestive enzymes in a compensatory attempt to maintain MG function.
2012-12-01 | GSE42659 | GEO
Project description:Background: More than 100 million Americans are living with metabolic syndrome, increasing their propensity to develop heart disease– the leading cause of death worldwide. A major contributing factor to this epidemic is caloric excess, often a result of consuming low cost, high calorie fast food. Several recent seminal studies have demonstrated the pivotal role of gut microbes contributing to cardiovascular disease in a diet-dependent manner. Given the central contributions of diet and gut microbiota to cardiometabolic disease, we hypothesized that novel microbial metabolites originating postprandially after fast food consumption may contribute to cardiometabolic disease progression. Methods: To test this hypothesis, we gave conventionally raised or antibiotic-treated mice a single oral gavage of a fast food slurry or a control rodent chow diet slurry and sacrificed the mice four hours later. Here, we coupled untargeted metabolomics in portal and peripheral blood, 16S rRNA gene sequencing, targeted liver metabolomics, and host liver RNA sequencing to identify novel fast food-derived microbial metabolites. Results: We successfully identified several metabolites that were enriched in portal blood, increased by fast food feeding, and essentially absent in antibiotic-treated mice. Strikingly, just four hours post-gavage, we found that fast food consumption resulted in rapid reorganization of the gut microbial community structure and drastically altered hepatic gene expression. Importantly, diet-driven reshaping of the microbiome and liver transcriptome was dependent on a non-antibiotic ablated gut microbial community. Conclusions: Collectively, these data suggest that single fast food meal is sufficient to reshape the gut microbial community yielding a unique signature of food-derived microbial metabolites. Future studies are warranted to determine if these metabolites are causally linked to cardiometabolic disease.
2021-11-14 | GSE165756 | GEO
Project description:Native host plant insect resistance in the maize inbred line Mp708 was developed by traditional plant breeding. Resistant Mp708 thwarts feeding by fall armyworm (Spodoptera frugiperda [J.E. Smith]; Lepidoptera: Noctuidae), numerous other lepidopteran pests, and the coleopteran western corn rootworm. This broad resistance makes it an excellent model for studying native host plant resistance mechanisms. In response to caterpillar feeding, Mp708 rapidly mobilizes Mir1-CP, a unique cysteine protease that appears to translocate from roots to the maize midwhorl where it accumulates. This accumulation correlates with a significant reduction in caterpillar growth resulting from diminished food utilization. In addition, the peritrophic membrane (PM) that surrounds the food bolus in the mudgut (MG) is severely damaged in caterpillars fed on sweet corn callus transformed to express the gene encoding Mir1-CP or on midwhorl tissue from resistant Mp708 maize. Functions of the PM include assisting digestion and protecting the epithelium of the caterpillar MG from physical and chemical damage. Consequently, the reduced growth of caterpillars that feed on Mp708 is probably due to the action of Mir1-CP on PM physiology. In fact, previous in vitro studies indicated that Mir1-CP was capable of permeabilizing the PM. The present study used both targeted (qRT-PCR) and global (mRNA-seq) transcriptome analyses to explore the effect of eating Mir1-CP expressing Mp708 maize on abundance of transcripts in the MG of fall armyworm larvae in comparison to MGs from larvae fed on susceptible Tx601 maize that does not express Mir1-CP. Expression of genes encoding proteins involved in PM production is upregulated in MGs from fall armyworm fed on Mp708. Also, several digestive enzymes (endopeptidases, aminopeptidases, lipases, amylase) were more highly expressed in MGs from larvae fed on Mp708 than MGs from larvae fed on Tx601. Impaired growth of larvae fed on Mp708 probably results from metabolic costs associated with higher production of PM constituents and digestive enzymes in a compensatory attempt to maintain MG function. Beginning as neonates, fall armyworm larvae used in the mRNA-seq experiment were reared on yellow-green midwhorl foliage from resistant Mp708 maize or susceptible Tx601 maize. Old foliage and frass were removed every other day and replaced with fresh foliage. Larvae were reared in an environmental chamber at 27M-BM-0C, 14:10 (light:dark) photoperiod, and 70% relative humidity. Midguts were dissected from larvae 2 d after molting to the last instar with masses between 300 and 400 mg. Dissections were done with cold anesthetized larvae submerged in Bombyx saline. After removing Malpighian tubules, foregut anterior to the stomodial valve, hindgut and food bolus, the MG was transferred from the body cavity, rinsed well with cold saline, and preserved in RNAlaterM-BM-.. Equal amounts (3 M-BM-5g) of total RNA from an individual MG were randomly pooled into three replicates per treatment (i.e., Mp708 or Tx601) such that each treatment replicate derived from 12-13 MGs. Each pool of total RNA was separately enriched for poly(A+) RNA and submitted to the Penn State Genomics Core Facility (University Park, PA) where barcoded cDNA libraries were prepared and equimolar quantities of each library sequenced on the SOLiD 3 Plus System. Sequence reads were filtered to accept reads whose median score threshold was M-bM-^IM-%12, contained M-bM-^IM-%25 bases and contained one or more bases with a quality score M-bM-^IM-%14. The 138911 Sanger ESTs in SPODOBASE (http://bioweb.ensam.inra.fr/spodobase) were assembled into a reference transcriptome using SeqMan Pro version 8.0.2. Filtered reads from each library representing a replicate within a maize inbred treatment were mapped separately to the reference transcriptome using the Bowtie-like algorithm in NextGENeM-BM-. with the requirement that 85% of 12 or more nucleotides comprising a read must match the reference. A read was allowed to map only once (i.e., no ambiguous mapping). The number of mapped reads per contig (i.e., gene model) in each treatment replicate-library were summed by NextGENeM-BM-. as read counts per gene and subsequently used in differential expression analyses.
2012-12-01 | E-GEOD-42659 | biostudies-arrayexpress
Project description:Fall armyworm and corn earworm gut microbiome Metagenome
| PRJNA507591 | ENA
Project description:Impact of small molecules from different microbial gut community types on gene expression from preterm intestinal derived organoids
2022-07-18 | GSE208315 | GEO
Project description:Opioids such as morphine have many beneficial properties as analgesics, however, opioids may induce multiple adverse gastrointestinal symptoms. We have recently demonstrated that morphine treatment results in significant disruption in gut barrier function leading to increased translocation of gut commensal bacteria. However, it is unclear how opioids modulate the gut homeostasis. By using a mouse model of morphine treatment, we studied effects of morphine treatment on gut microbiome. We characterized phylogenetic profiles of gut microbes, and found a significant shift in the gut microbiome and increase of pathogenic bacteria following morphine treatment when compared to placebo. In the present study, wild type mice (C57BL/6J) were implanted with placebo, morphine pellets subcutaneously. Fecal matter were taken for bacterial 16s rDNA sequencing analysis at day 3 post treatment. A scatter plot based on an unweighted UniFrac distance matrics obtained from the sequences at OTU level with 97% similarity showed a distinct clustering of the community composition between the morphine and placebo treated groups. By using the chao1 index to evaluate alpha diversity (that is diversity within a group) and using unweighted UniFrac distance to evaluate beta diversity (that is diversity between groups, comparing microbial community based on compositional structures), we found that morphine treatment results in a significant decrease in alpha diversity and shift in fecal microbiome at day 3 post treatment compared to placebo treatment. Taxonomical analysis showed that morphine treatment results in a significant increase of potential pathogenic bacteria. Our study shed light on effects of morphine on the gut microbiome, and its role in the gut homeostasis.
2018-04-16 | E-MTAB-5546 | biostudies-arrayexpress