Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1181126 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We performed RNA-Seq based gene expression analysis of Arabidopsis Col-0 plants grown in presence of SynComCol-0 (eubiotic bacterial community), SynCommfec (dysbiotic bacterial community) and Axenic conditions in GnotoPot plant gnotobiotic growth system. SynCom preparation was done by mixing equal ratio of the each strain measured based on optical density of (OD600) in 10 mM MgCl2 and adjusting to the final combined OD600 of 0.04. Plants were grow in GnotoPots as described in (Chen et al, Nature 2020). We identified genes differentially enriched in response to presence of eubiotic and dysbiotic bacterial communities. Our results suggested that in presence of dysbiotic community there is over abundance of gene expression for immunity/defense-related genes in SynCommfec compared SynComCol-0 colonized plants.
2023-07-19 | GSE218962 | GEO
Project description:Background and study aims
Colorectal cancer (CRC) is one of the most commoncancers among humans worldwide. Recent studies demonstrated that the composition of the bacterial community in the human gut, as well as inflammation occurring in the gut, are some of the factors that modify the risk of an individual to develop CRC. The human gut is home to more than 1000 bacterial species, including health-promoting species and disease-causing species.
The consumption of rice bran, a by-product of rice milling, was previously shown to positively modify bacterial composition in the gut among healthy adults. The protective effect of a long-term rice bran consumption against CRC among individuals known to have higher risk of CRC, such as older individuals who are regular smokers and having a family history of CRC, needs to be established.
This study aims to investigate whether the implementation of a 24-week dietary programme involving rice bran consumption among adults at high risk of CRC is feasible, and whether it has any effect in inducing a health-promoting modification of the bacterial community, as well as a reduction of inflammation, in the gut of these individuals.
Who can participate?
Chinese adults of either gender, who are aged 50 or above and are categorised to be in the high risk CRC group by the Asian-Pacific Colorectal Screening tool, in which classification is based on age, smoking status and family history of CRC.
What does the study involve?
After the recruited subjects were screened for eligibility of study participation and written informed consent had been obtained from them, they were randomly assigned into either Group A or Group B. Participants in Group A were given packets of rice bran and were asked to consume 30 grams of the rice bran at 24-hour intervals for 24 weeks. Participants in Group B were given packets of rice powder that has similar appearance and colour as the rice bran, and were asked to consume 30 grams of the rice powder, also at 24-hour intervals for 24 weeks. All participants were asked to provide a stool sample and blood sample at various time points during the study, namely just before rice bran consumption, as well as 6 weeks, 12 weeks and 24 weeks after the start of rice bran consumption. Laboratory tests were conducted on these samples. All participants were also instructed to complete a log book, detailing the date and time of rice bran or rice powder intake each day, and the amount consumed. The participants also completed a faecal diary where they documented the frequency of egestion, and the shape and amount of stool egested each day, as well as the occurrence of any abdominal discomfort or pain.
| 2415781 | ecrin-mdr-crc
Project description:Overexpression of a transcription factor OsEREBP1 results in attenuation of disease symptoms upon infection with bacterial pathogen Xanthomonas oryzae pv. oryzae and tolerance to drought stress in transgenic rice plants. Microarray analysis was performed to identify genes regulated by the rice transcription factor OsERBP1.
2013-11-15 | GSE46173 | GEO
Project description:Previously, we successfully introduce the bacterial blight resistance trait from Oryza meyeriana into O. sativa using asymmetric somatic hybridization with O. meyeriana as the donor species. After years of breeding, a progeny named Y73 was generated with recurrent parent O. sativa L. ssp. japonica cv. Dalixiang, and it shows high resistance to broad-spectrum of bacterial blight pathogens Xanthomonas oryzae pv. Oryzae (Xoo). However, the resistance mechanism of Y73 is remain undiscovered. To provide insights into the high resistance phenotype of these plants, we examined the transcriptome response in leaves of Y73 to the bacterial blight infection in this study. Xoo inoculated and mock inoculated rice plants were grown in growth room and the global analysis of gene expression events in rice leaves at 24 hours post inoculation (hpi) were analyzed using Affymetrix Rice GeneChip microarrays. We used microarrays to detail the global programme of gene expression underlying Xoo infection in rice Y73.
2012-02-27 | GSE36093 | GEO
Project description:The microbiota plays a crucial role in protecting plants from pests and pathogens. The protection provided by the microbiota constitutes not just the plant’s first line of defense, but possibly its most potent one, as experimental disruptions to the microbiota cause plants to succumb to otherwise asymptomatic infections. To understand how microbial plant defense is deployed, we applied a complex and tractable plant-soil-microbiome microcosm. This system, consisting of Arabidopsis plants and a 150-member bacterial synthetic community, provides a platform for the discovery of novel bacterial plant-beneficial traits, under a realistically complex microbial community context. To identify which components of the plant microbiota are critical for plant defense, we deconstructed this microcosm top-down, removing different microbial groups from the community to examine their protective effect on the plant when challenged with the leaf pathogen Pseudomonas syringae. This process of community deconstruction revealed a critical role for the genus Bacillus in protecting the plant from infection. Using plant RNA-seq and bacterial co-culturing experiments, we demonstrated that Bacillus-provided plant protection is independent of plant immune system activation. We also show that the level of plant protection is strongly dependent on the diversity of the protective inoculum. We show that deconstructing the microbiome top-down is a powerful tool for identifying and prioritizing microbial taxa with specific functions within it.
2025-01-01 | GSE285599 | GEO
Project description:RNASeq of roots from two genotypes of Arabidopsis thaliana plants, Col-0 and myb36-2 grown axenically or with a 41 member bacterial Synthetic Community (SynCom) to explore the interaction between the root diffusion barriers and the root microbiome.
2020-11-01 | GSE151376 | GEO
Project description:An indica rice cultivar IET8585 (Ajaya), resists diverse races of the Xanthomonas oryzae pv oryzae (Xoo) pathogen attack, and is often cultivated as bacterial leaf blight (blb) resistant check in India. Earlier we reported a recessive blb resistance gene mapped to the long arm of chromosome 5 in IET8585. To further understand the mechanism of recessive and durable resistance response, two indica rice genotypes namely, i) IET8585 (Ajaya), a disease resistant indica veriety from India and ii) IR24, a bacterial leaf blight disease susceptible genotype were selected for this study. We used the 22K rice Oligoarray from Agilent technologies to study the transcript profile in the leaves of the two contrasting rice genotypes under inoculated and un-inoculated conditions during seedling stage. Experiment Overall Design: We used Agilent rice gene chips (G4138A) to investigate the transcript level changes in rice leaf tissues during bacterial pathogen infection. We used two contrasting rice genotypes (IET8585 (Ajaya) blb resistant IR24 blb susceptible) differing in bacterial disease response. Plants were grown growth chambers and inoculated with bacterial pathogen on 18th DAS. Leaf sampling was done in both un-inoculated and inoculated plants at 3 time points. Two replications of microarray experiments were carried out by hybridizing the resistant samples against the susceptible samples.
2008-06-14 | E-GEOD-6244 | biostudies-arrayexpress
Project description:Over expression of a transcription factor OsEREBP1 results in attenuation of disease symptoms upon infection with bacterial pathogen Xanthomonas oryzae pv. oryzae and tolerance to drought stress in transgenic rice plants. Microarray analysis was performed to identify genes regulated by the rice transcription factor OsERBP1. Four independent replicates of the experimental OsEREBP1-ox transgenic plants and the control non-transgenic Kitaake plants were grown under normal conditions.
2013-11-15 | E-GEOD-46173 | biostudies-arrayexpress