Ontology highlight
ABSTRACT:
PROVIDER: PRJNA546259 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9204460_1.fastq.gz | Fastqsanger.gz | |||
| SRR9204460_2.fastq.gz | Fastqsanger.gz | |||
| SRR9204470_1.fastq.gz | Fastqsanger.gz | |||
| SRR9204470_2.fastq.gz | Fastqsanger.gz | |||
| SRR9204480_1.fastq.gz | Fastqsanger.gz |
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Project description:Head smut of maize, which is caused by the Sporisorium reilianum f. sp. Zeae (Kühn), has been a serious disease in maize. In order to find head smut resistant candidate genes, microarrays were used to monitor the gene expression profiles between disease resistant near isogenic lines (NIL) L282 and L43, highly resistant inbred line Q319 and highly susceptible inbred line Huangzao4 after 0 to7 days post inoculation of S.reiliana by artificial inoculation method.
2012-08-16 | GSE40052 | GEO
Project description:Disease resistance is one of the most complicated yet important plant traits. The potential functions of long noncoding RNAs (lncRNAs) in response to pathogenic fungi remain unclear. In this study, we sequenced the transcriptomes of four different sea-island cotton (Gossypium barbadense) recombinant inbred lines (RILs) with susceptible, highly susceptible, highly resistant, or super highly resistant phenotypes and compared their responses to Fusarium oxysporum f. sp. vasinfectum (Fov) infection with those of their susceptible and resistant parents. Infection-induced protein coding genes were highly enriched in similar disease resistance-related pathways regardless of fungal susceptibility. In contrast, we found that the expression of a large number of Fov infection-induced lncRNAs was positively correlated with plant susceptibility. Bioinformatics analysis of potential target mRNAs of lncRNAs with both trans-acting and cis-acting mechanisms showed that mRNAs co-expressed or co-located with Fov-regulated lncRNAs were highly enriched in disease resistance-related pathways, including glutathione metabolism, glycolysis, plant hormone signal transduction, anthocyanin biosynthesis, and butanoate metabolism. Together these results suggest that lncRNAs could play a significant role in the response to pathogenic fungal infection and the establishment of disease resistance. The transcriptional regulation of these infection-susceptible lncRNAs could be coordinated with infection-susceptible mRNAs and integrated into a regulatory network to modulate plant-pathogen interactions and disease resistance. Fov-susceptible lncRNAs represent a novel class of molecular markers for breeding of Fov-resistant cotton cultivars.
2019-03-12 | GSE95288 | GEO
Project description:Head smut of maize, which is caused by the Sporisorium reilianum f. sp. Zeae (Kühn), has been a serious disease in maize. In order to find head smut resistant candidate genes, microarrays were used to monitor the gene expression profiles between disease resistant near isogenic lines (NIL) L282 and L43, highly resistant inbred line Q319 and highly susceptible inbred line Huangzao4 after 0 to7 days post inoculation of S.reiliana by artificial inoculation method. Maize leaves were selected at 0d, 1d, 2d, 4d, 7d post inoculation for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain different expression genes of different varieties at each inoculation stage in order to find head smut resistant candidate genes.
2012-08-16 | E-GEOD-40052 | biostudies-arrayexpress
Project description:The preferential localization of some neoplasms, such as serrated polyps, in specific areas of the intestine suggests that non-genetic factors may be important for their development. To test this hypothesis, we took advantage of transgenic mice that expressed HB-EGF throughout the intestine, but develop serrated polyps only in the cecum. Here we show that a host-specific microbiome was associated with serrated polyps, and that alterations of the microbiota induced by antibiotic treatment or by embryo-transfer rederivation markedly inhibited the formation of serrated polyps in the cecum. Mechanistically, development of serrated polyps was associated with a local decrease in epithelial barrier-function, bacterial invasion, production of antimicrobials, and increased expression of several inflammatory factors such as IL-17, Cxcl2, Tnf-α, and IL-1. Increased number of neutrophils were found within the serrated polyps, and their depletion significantly reduced polyp growth. Together these results indicate that non-genetic factors contribute to the development of serrated polyps and suggest that the development of these intestinal neoplasms in the cecum is driven by the interplay between genetic changes in the host, an inflammatory response, and a host-specific microbiota. SUMMARY: Serrated polyps (SP) are a heterogeneous group of neoplasms found in particular areas of the gut. To define the factors contributing to their specific localization, we analyzed a strain of transgenic mice that carry a genetic alteration throughout the intestinal epithelium, but only develop SP in the cecum. Transcriptome and immunostaining analyses showed increased expression of antimicrobial genes, inflammatory factors, and the presence of bacteria within SP. Alteration of the cecal microbiota by antibiotic treatment or by embryo-transfer rederivation dramatically reduced SP incidence. Microbiome analysis implicated a limited set of bacteria in the development of SP. Together, these results point to a crucial role for the microbiota in the localized development of SP in a genetically susceptible host. We obtained serrated polyp (SP) and surrounding normal (NM) tissue from the ceca of three affected mice (paired design) and assessed expression differences by RNA-Seq.
2014-02-12 | E-GEOD-47735 | biostudies-arrayexpress
Project description:<p>Malaria is a major public health problem, but many of the factors underlying the pathogenesis of this disease are not well understood. Here, we demonstrate in Malian children that susceptibility to febrile malaria following infection with <em>Plasmodium falciparum</em> is associated with the composition of the gut microbiome prior to the malaria season. Gnotobiotic mice colonized with the fecal samples of malaria-susceptible children had a significantly higher parasite burden following <em>Plasmodium</em> infection compared to gnotobiotic mice colonized with the fecal samples of malaria-resistant children. Shotgun metagenomics analysis revealed that the fecal microbiome of the susceptible children was enriched for bacteria associated with inflammation, mucin degradation, gut permeability and inflammatory bowel disorders (e.g., <em>Ruminococcus gauvreauii</em>, <em>Ruminococcus torques</em>, <em>Dorea formicigenerans</em>, <em>Dorea longicatena</em>, <em>Lachnoclostridium phocaeense</em> and <em>Lachnoclostridium sp.</em> YL32). However, the susceptible children also had a greater abundance of bacteria known to produce anti-inflammatory short-chain fatty acids and those associated with favorable prognosis and remission following dysbiotic intestinal events (e.g., <em>Anaerobutyricum hallii</em>, <em>Blautia producta</em> and <em>Sellimonas intestinalis</em>). Metabolomics analysis of the human fecal samples corroborated the existence of inflammatory and recovery-associated features within the gut microbiome of the susceptible children. There was an enrichment of nitric oxide-derived DNA adducts (deoxyinosine and deoxyuridine) and long-chain fatty acids, the absorption of which has been shown to be inhibited by inflamed intestinal epithelial cells, and a decrease in the abundance of mucus phospholipids. Nevertheless, there were also increased levels of pseudouridine and hypoxanthine, which have been shown to be regulated in response to cellular stress and to promote recovery following injury or hypoxia. Overall, these results indicate that the gut microbiome may contribute malaria pathogenesis and suggest that therapies targeting intestinal inflammation could decrease malaria susceptibility.</p>
2024-09-13 | MTBLS2247 | MetaboLights
Project description:We explore whether a low-energy diet intervention for Metabolic dysfunction-associated steatohepatitis (MASH) improves liver disease by means of modulating the gut microbiome. 16 individuals were given a low-energy diet (880 kcal, consisting of bars, soups, and shakes) for 12 weeks, followed by a stepped re-introduction to whole for an additional 12 weeks. Stool samples were obtained at 0, 12, and 24 weeks for microbiome analysis. Fecal microbiome were measured using 16S rRNA gene sequencing. Positive control (Zymo DNA standard D6305) and negative control (PBS extraction) were included in the sequencing. We found that low-energy diet improved MASH disease without lasting alterations to the gut microbiome.
2024-12-31 | E-MTAB-14061 | biostudies-arrayexpress
Project description:Whirling disease, caused by the pathogen Myxobolus cerebralis, afflicts several salmonid species. Rainbow trout are particularly susceptible and suffer high mortality rates. The disease is persistent and spreading in hatcheries and natural waters of several countries, including the U.S., and the economic losses associated with whirling disease have been extremely large. In this study, gene expression profiling was conducted for resistant and susceptible rainbow trout strains following pathogen exposure with the primary objective of identifying specific genes associated with whirling disease resistance. Several genes were significantly up-regulated in skin following pathogen exposure for both the resistant Hofer and susceptible Trout Lodge rainbow trout strains. For both strains, response to infection appears to be associated with the interferon system. Metallothionein is differentially expressed between the resistant and susceptible strains and is a good candidate for future studies due to its diverse functional roles in inflammation and immune response. The present study has provided the first examination into the genetic basis underlying rainbow trout’s immune response and resistance to the whirling disease pathogen. The identified genes have allowed us to gain initial insight into the molecular mechanisms associated with a salmonid host’s immune response and resistance to whirling disease infection. Keywords: Disease state comparison. 1st comparison: exposed vs control. 2nd comparison: resistant vs susceptible strains Resistant (Hofer) and susceptible (Trout Lodge) rainbow trout strains were exposed to 2,000 triactinomyxons (whirling disease pathogen) per fish. Unexposed controls for each strain were treated identically to exposed other than their lack of pathogen exposure. After twenty-four hours, caudal fin tissue was collected for RNA extraction. Amplified RNA was competitively hybridized (exposed versus control) for each strain. Four biological replicates were used for each experimental condition and a balanced block design was incorporated.
2008-02-20 | E-GEOD-8631 | biostudies-arrayexpress
Project description:The maize smut fungus, Sporisorium reilianum f. sp. zeae, which is an important biotrophic pathogen responsible for extensive crop losses, infects maize by invading the root during the early seedling stage. In order to investigate disease-resistance mechanisms at this early seedling stage, digital gene expression (DGE) analysis, which applies a dual-enzyme approach (DpnII and NlaIII), was used to identify the transcriptional changes in roots of Huangzao4 (susceptible) and Mo17 (resistant) after inoculation with teliospores of S. reilianum. Before and after inoculation, pathogenesis-related genes were differentially regulated and enzymes involved in controlling reactive oxygen species (ROS) levels showed different activity between Huangzao4 and Mo17, which can potentially lead to changes in the growth of S. reilianum and ROS production in maize. Moreover, lignin depositions of roots were also changed differentially during root colonization of hyphae between Huangzao4 and Mo17. These results suggest that the interplays between S. reilianum and maize during the early infection stage involve many interesting transcriptional and physiological changes, which offer several novel insights for understanding the mechanisms of resistance to the fungal infection. Examination of control stage (ck), post-inoculation stage1 (P1) and post-inoculation stage2 (P2) in Huangzao4 (susceptible) and Mo17 (resistant)
2012-12-03 | E-GEOD-40952 | biostudies-arrayexpress